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Stellaris DesignReady Professionaly Designed Probe Sets

DesignReady Stellaris™ RNA FISH Probe Sets take the guesswork out of designing your own custom assay. These professionally designed sets go through rigorous pre- and post-design bioinformatic analysis to maximize specificity and most are available in the following dyes: CAL Fluor™ Red 590, Quasar™ 570, CAL Fluor Red 610, Quasar 670, CAL Fluor Red 635, CAL Fluor Orange 560 and FAM.

Enter your RNA target into the search filter below to determine whether there is a DesignReady probe set for your target or whether you will need to design a new probe set using our Custom Stellaris probe design software.

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Product information: One set of Stellaris® FISH probes contain a blend of up to 48 oligos labeled with a fluorophore. Probes arrive lyophilized and ready to use.

Delivered Amount: 5 nmol of pooled oligos

Turnaround time: Stellaris DesignReady Probe Sets ship in 5 to 15 business days.  A more precise shipping estimate will be given upon quotation or order.

Dye Selection: Please visit our Stellaris Dyes and Modifications Page to learn about our dyes and modifications.  Due to the variable autofluorescence in the green channel inherent to some cells and tissues, it is not recommended to use FAM for some Stellaris RNA FISH applications. We recommend testing your sample for green channel autofluorescence before ordering FAM labeled sets or ordering an alternative dye that is compatible with your experiment.

Storage Guidelines: Stellaris RNA FISH Probes are shipped dry at ambient temperature and can be stored at +2 to +8 °C in this state. Dissolved probe mix should be subjected to a minimum number of freeze-thaw cycles.  For daily and short-term use of dissolved probe mix, storage at +2 to +8 °C in the dark for up to a month is recommended.  For storage lasting longer than a month, we recommend aliquoting and freezing probes in the dark at -15 to -30 °C.

Reconstituting the dried probe stock: A DesignReady Probe Set can provide up to 400 hybridizations.  Re-dissolve the dried oligonucleotide probe blend in 400 μL of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) to create a probe stock of 12.5 μM.  Mix well by pipetting up and down, and then vortex and centrifuge briefly.  

Note: When performing Stellaris RNA FISH, it is imperative to limit RNA degradation. Ensure that all consumables and reagents are RNase-free.  Recipe above is for set volumes. Please adjust accordingly.

Protocols: Please visit our Stellaris RNA FISH Protocols page.

Absorption and emission spectral charts: Please visit our Calibration dyes page. 

You can find the most up-to-date protocols for Stellaris® RNA FISH Probes by visiting the Stellaris RNA FISH Protocols page. For answers to specific questions please visit our Stellaris RNA FISH FAQ section. The protocols and FAQs apply to imaging on a widefield fluorescence microscope with at least a 60X-oil, 1.4 NA objective, mercury or metal halide lamps, and cooled CCD camera. We do not recommend confocal applications as an entry point, although we have many successful experienced confocal users.

See Stellaris RNA FISH Probes at work by viewing our Stellaris image gallery. Images are contributed by customers and by scientists from LGC Biosearch.

Comprehensive Stellaris Education and Links Page

Dyes and Modifications for Stellaris

Stellaris Citation Center

Stellaris Getting Started Guide

The following peer-reviewed customer publications cite Stellaris RNA FISH products and/or services. Over 33% of publications citing Stellaris RNA FISH publish in Cell, Nature, or Science speaking volumes about the quality of our product and the thought leadership of our customers.

424

Publications

148

Nature, Cell or Science

How to Cite Stellaris RNA FISH

The following Publications include citations of all Stellaris® RNA FISH product types.

Research Focus

Organism

Application

RNA Target Type

Multiplexing

Publications citing DesignReady Stellaris Probe Sets

Dyes

Stellaris CitationsPapers labeled as Nature, Science, or Cell include sub-groups of these publishing groups such as communications, letters, methods etc.
*Updated August 2016

Stellaris Scoop Research Highlights

Stellaris® RNA FISH DesignReady probe sets take the guesswork out of designing custom assays

Reference

Programmable RNA Tracking in Live Cells with CRISPR/Cas9
Nelles et al. Cell. 2016.

Reference

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells
Orjalo et al. Methods in Molecular Biology. 2016.

Reference

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris® RNA Fluorescence In Situ Hybridization in Adherent Cells
Coassin et al. Methods in Molecular Biology. 2014.

Custom

Published using professionally designed DesignReady probe sets.

Comprehensive Publication List

DesignReady Probe Sets

RNA FISH DesignReady Product Page

Browse All DesignReady Probe Sets
Catalog Number Gene Name and Organism Associated Publications
VSMF-1014-5 eGFP

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003
VSMF-2415-5 Human TFRC
High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054
VSMF-2003-5 Human ACTB
High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054
VSMF-2162-5 Human H19
High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10
VSMF-2161-5 Human H19

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.
VSMF-2230-5 Human MYC
High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10
VSMF-2307-5 Human PVT1
High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10
VSMF-2430-5 Human XIST
High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10
VSMF-2448-5 Human CCNA2
High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054
VSMF-1019-5 GFP

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115
VSMF-2250-5 Human NEAT1 middle segment

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117
VSMF-2054-5 Human CDKN1A
High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15
VSMF-2211-5 Human MALAT1
High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15
VSMF-2102-5 Human ERBB2
Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t
VSMF-1011-5 dsRED2

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses

Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100
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Research Focus

Development

High Impact

Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Akanumaet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11963

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016. url: http://dx.doi.org/10.1016/j.ydbio.2016.06.038

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016. url: https://dx.doi.org/

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

 High Impact

Single-cell differences in matrix gene expression do not predict matrix deposition

Coteet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10865

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

 High Impact

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

Newhartet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/10.1091/mbc.E15-02-0099

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005680

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.1992

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically-disordered proteins in C. elegans

Wang et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.04591

Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The American Society for Biochemistry and Molecular Biology. 2014. url: https://dx.doi.org/10.1074/jbc.M114.593541

 High Impact

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.10.017

 High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-ayala et al. The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.114843

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

 High Impact

Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Malone et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1101/gad.245829.114

 High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014. url: https://dx.doi.org/10.1038/ncb3000

 High Impact

The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014. url: https://dx.doi.org/10.1016/j.tig.2014.06.002

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

 High Impact

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.04.031

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yücel et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.108910

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Blood. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

Aberrant Patterns of X Chromosome Inactivation in a New Line of Human Embryonic Stem Cells Established in Physiological Oxygen Concentrations

Oliveira Georges et al. Stem Cell Rev and Rep. 2014. url: https://dx.doi.org/10.1007/s12015-014-9505-4

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014. url: https://dx.doi.org/10.1182/blood-2013-10-530683.

 High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

 High Impact

Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013. url: https://dx.doi.org/10.1038/ng.2763

 High Impact

Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001618

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Developmental Cell. 2013. url: https://dx.doi.org/10.1016/j.devcel.2013.05.007

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013. url: https://dx.doi.org/10.1083/jcb.201302049

Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells

Tan et al. Development and Stem Cells. 2013. url: https://dx.doi.org/10.1242/dev.087551

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification

Tan et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2012.64

 High Impact

Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans

Cochellaet al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.10.049

The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012. url: https://dx.doi.org/10.1371/journal.pgen.1003079

 High Impact

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

Patelet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.09.020

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

 High Impact

Lgr5+ve Stem/Progenitor Cells Contribute to Nephron Formation during Kidney Development

Barkeret al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.08.018

 High Impact

Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012. url: https://dx.doi.org/10.1016/j.devcel.2012.08.004

 High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2011.10.002

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

 High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665

Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1111684108

MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and the transition from larva to adult in C. elegans

Harriset al. Development. 2011. url: https://dx.doi.org/10.1242/dev.065417

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010. url: https://dx.doi.org/10.1038/nature08781

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781
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Cancer

High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

 High Impact

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

Newhartet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/10.1091/mbc.E15-02-0099

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

 High Impact

A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1503157112

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

 High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26255629

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.09214

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015. url: https://dx.doi.org/10.1021/acs.biochem.5b00259

 High Impact

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

Wang et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2015.03.003

 High Impact

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

L'eveill'e et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7520

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

Lee et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv156

Molekulárna cytogenetika v problematike familiárnych malignít

Konečný et al. Hlavná téma. 2015. url: http://www.solen.sk/index.php/index.php?page=magazine_detail&issue_id=664&article_id=10288

 High Impact

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6812

 High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

Benzyl butyl phthalate induces migration, invasion, and angiogenesis of Huh7 hepatocellular carcinoma cells through nongenomic AhR/G-protein signaling

Tsai et al. BMC Cancer. 2014. url: https://dx.doi.org/10.1186/1471-2407-14-556

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

Therapeutic implications of activation of the host gene (Dleu2) promoter for miR-15a/16-1 in chronic lymphocytic leukemia

Kasar et al. Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2013.291

 High Impact

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.04.025

The role of high cell density in the promotion of neuroendocrine transdifferentiation of prostate cancer cells

Pernicova et al. Molecular Cancer. 2014. url: https://dx.doi.org/10.1186/1476-4598-13-113

 High Impact

Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Weis et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2014.114

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature

Facciponte et al. Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Differential Expression of Galectin-1 and Galectin-3 in Canine Nonmalignant and Malignant Mammary Tissues, and in Progression to Metastases in Mammary Tumours

Oliveira JT et al. Anticancer Research. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/24778023

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/25344859

Receptor-interacting protein kinase 2 promotes triple-negative breast cancer cell migration and invasion via activation of nuclear factor-kappaB and c-Jun N-terminal kinase pathways

Singel et al. Breast Cancer Research. 2014. url: https://dx.doi.org/10.1186/bcr3629

KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014. url: https://dx.doi.org/10.1016/j.neo.2014.03.008

 High Impact

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013. url: https://dx.doi.org/10.1038/nmeth.2657

 High Impact

Tumour angiogenesis regulation by the miR-200 family

Peot et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3427

Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays

Rantala et al. Microarrays. 2013. url: https://dx.doi.org/10.3390/microarrays2020097

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses

Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013. url: https://dx.doi.org/10.5483/BMBRep.2013.46.2.016

 High Impact

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz et al. Nature Research Letter. 2013. url: https://dx.doi.org/10.1038/nature11661

 High Impact

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steineet al. Journal of Clinical Investigation. 2011. url: https://dx.doi.org/10.1172/JCI43169
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Neuroscience

High Impact

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

Engineering Duplex RNAs for Challenging Targets: Recognition of GGGGCC/CCCCGG Repeats at the ALS/FTD C9orf72 Locus

Hu et al. Cell Chemistry & Biology. 2015. url: https://dx.doi.org/10.1016/j.chembiol.2015.09.016

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

 High Impact

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa1934

Regulation of Mechanosensation in C. elegans through Ubiquitination of the MEC-4 Mechanotransduction Channel

Chen et al. The Journal of Neuroscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.4082-14.2015

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

 KO lncRNA

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Sauvageau et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.01749

 High Impact

Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

 High Impact

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak et al. Nature Article. 2013. url: https://dx.doi.org/10.1038/nature11928

 High Impact

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

Patelet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.09.020

 High Impact

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1111226109                     

Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues

Nedelecet al. Journal of Neuorscience. 2012. url: https://dx.doi.org/10.1523/JNEUROSCI.4176-11.2012

Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1111684108

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1101329108
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Immunology

High Impact

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Profiling T Cell Activation Using Hybridization and Flow Cytometry Single-Molecule Fluorescence In Situ

Bushkin et al. The Journal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

Meisel et al. Cell, Elsevier . 2014. url: https://dx.doi.org/10.1016/j.cell.2014.09.011

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014. url: https://dx.doi.org/10.1073/pnas.1410087111/-/DCSupplemental

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

Discovery of J Chain in African Lungfish (Protopterus dolloi, Sarcopterygii) Using High Throughput Transcriptome Sequencing: Implications in Mucosal Immunity

Tacchi et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0070650

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012. url: https://dx.doi.org/10.1128/JVI.00662-12

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38
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Virus, Bacteria, or Pathogen

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Beckeret al. bioRxiv. 2016. url: https://dx.doi.org/10.1101/057299

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

Nelsonet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00459-16

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

 High Impact

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

Identification of a novel multiple kinase inhibitor with potent antiviral activity against influenza virus by reducing viral polymerase activity

Sasaki et al. Biochemical and Biophysical Research Communications. 2014. url: https://dx.doi.org/10.1016/j.bbrc.2014.05.058

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Characterization of novel inhibitors of HIV-1 replication that function via alteration of viral RNA processing and rev function

Wong et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt727

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012. url: https://dx.doi.org/10.1128/JVI.00662-12

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38
Collapse Virus, Bacteria, or Pathogen Publications

Aging, Telomeres, or Senescence

Transcription

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw596

 High Impact

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

 High Impact

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis

Sallamet al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17674

 High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016. url: https://dx.doi.org/10.1016/j.molcel.2016.03.007

A continuum model of transcriptional bursting

Corriganet al. Genes and Chromosomes. 2016. url: https://dx.doi.org/10.7554/eLife.13051.001

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016. url: http://www.ncbi.nlm.nih.gov/pubmed/?term=RNase+P+Protein+Subunit%2C+Rpp29%2C+Represses+Histone+H3.3+Nucleosome+Deposition

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by PUM2 in human cells

Tichon et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/033423

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

 High Impact

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015. url: https://dx.doi.org/10.1101/027870

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

Application of an RNA amplification method for reliable single-cell transcriptome analysis

Suslov et al. BioTechniques. 2015. url: http://www.biotechniques.com/multimedia/archive/00251/BTN_A_000114331_O__251167a.pdf  

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv839

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

 High Throughput

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20145704

 High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa6090

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

 High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

 High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015. url: http://www.sciencemag.org/cgi/doi/10.1126/science.1258849

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells

Silva et al. Human Molecular Genetics, Oxford. 2015. url: https://dx.doi.org/10.1093/hmg/ddv096

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

 High Impact

Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

Transcriptional Expression of Myelin Basic Protein in Oligodendrocytes Depends on Functional Syntaxin 4: a Potential Correlation with Autocrine Signaling

Bijlardet al. Molecular Cell Biology. 2015. url: https://dx.doi.org/10.1128/MCB.01389-14

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.255810.114

 High Impact

Promoter architecture dictates cell-to-cell variability in gene expression

Jones et al. Science. 2014. url: https://dx.doi.org/10.1126/science.1255301

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

 High Impact

Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

Lin et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.06.022

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.05.005

 High Impact

The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014. url: https://dx.doi.org/10.1016/j.tig.2014.06.002

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

 High Impact

Validation of noise models for single-cell transcriptomics

Grün et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2930

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.108910

 High Impact

Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2910

 High Impact

Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014. url: https://dx.doi.org//10.1016/j.molcel.2014.01.026

Expression of the Developmental Transcription Factor Fezf2 Identifies a Distinct Subpopulation of Layer 5 Intratelencephalic-Projection Neurons in Mature Mouse Motor Cortex

Tantirigama et al. the Journal of Neuroscience. 2014. url: https://dx.doi.org/10.1523/JNEUROSCI.3111-13.2014

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

 High Impact

Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-a protein levels and activity

Bolt et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2013.550

 High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014. url: https://dx.doi.org/10.1016/j.celrep.2013.12.013

A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/sb4001867

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014. url: https://dx.doi.org/10.1083/jcb.201304152

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014. url: https://dx.doi.org/10.1073/pnas.1410087111/-/DCSupplemental

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

 High Impact

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.051

 High Impact

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Ball et al. Cell Cycle. 2013. url: https://dx.doi.org/10.4161/cc.26257

Barriers to transmission of transcriptional noise in a c-fos c-jun pathway

Shah et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2013.45

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1303400110

 High Impact

Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013. url: https://dx.doi.org/10.1016/j.molcel.2013.08.009

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001618

 High Impact

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013. url: https://dx.doi.org/10.1038/nsmb.2598

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Cell. 2013. url: http://dx.doi.org/10.1016/j.devcel.2013.05.007

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001591

Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

Graindorge et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.214999.113

 High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses

Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

 High Impact

Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013. url: https://dx.doi.org/10.1126/science.1231456

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013. url: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r104

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

Gene location and DNA density determine transcription factor distributions in Escherichia coli

Kuhlmanet al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.42

 High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665

 High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024

Cell-to-cell variability of alternative RNA splicing

Wakset al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.32
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Translation

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

Truttmannet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1006023

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

 High Impact

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.07957

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

 High Impact

Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7078

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004512

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

 High Impact

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.04.025

 High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014. url: https://dx.doi.org/10.1016/j.celrep.2013.12.013

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

 High Impact

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

Yoon et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3939

Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae

Kraut-Cohen et al. Molecular Biology Cell . 2013. url: https://dx.doi.org/10.1091/mbc.E13-01-0038

mRNA encoding WAVE–Arp2/3-associated proteins is co-localized with foci of active protein synthesis at the leading edge of MRC5 fibroblasts during cell migration

Willett et al. Biochem Journal. 2013. url: https://dx.doi.org/10.1042/BJ20121803

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1111226109                     

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

Shihet al. Nucleic Acids Research. 2011. url: https://dx.doi.org/10.1093/nar/gkr456
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Methods and Protocols

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

 High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016. url: https://dx.doi.org/10.1016/j.biomaterials.2016.05.022

Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.13065

RNA LOCALIZATION Finding FISH in a small pond

Janet al. eLIFE Insight. 2016. url: https://dx.doi.org/10.7554/eLife.16598

Microfluidic Approaches to Fluorescence In Situ Hybridization (FISH) for Detecting RNA Targets in Single Cells

Meagheret al. Microfluidic Methods for Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-3-319-30019-1_5

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Palangatet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.04.009

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription

Leeet al. Molecular and Cellular Endocrinology. 2016. url: https://dx.doi.org/10.1016/j.mce.2016.04.001

Methods for studying RNA localization in bacteria

Kannaiahet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.010

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

Simultaneous RNA–DNA FISH

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_11

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

Methods for studying RNA localization in bacteria

Kannaiah et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.010

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

 High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep17295

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip†

Shaffer et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5lc00459d

Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Hassanet al. Bone. 2015. url: https://dx.doi.org/10.1016/j.bone.2015.05.026

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

 High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa6090

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 Machine Learning

Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images

Wu et al. BMC Bioinformatics. 2015. url: https://dx.doi.org/10.1186/s12859-015-0534-z

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_20

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_1

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells

Thompson et al. Analytical Chemistry. 2014. url: https://dx.doi.org/10.1021/ac5035924

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

 PACT Clearing, High Impact

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

Yang et al. Cell Resource. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.07.017

 High Impact

The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014. url: https://dx.doi.org/10.1016/j.tig.2014.06.002

 High Impact

Labeling native bacterial RNA in live cells

Toran et al. Nature Cell Research. 2014. url: https://dx.doi.org/10.1038/cr.2014.47

Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ

Markey et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0093488

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

 High Impact

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013. url: https://dx.doi.org/10.1038/nmeth.2657

 Turbo FISH, SNP FISH

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

Shaffer et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0075120

 SNP-FISH, High Impact

Allele-specific detection of single mRNA molecules in situ

Hansen et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2601

 High Impact

Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001591

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013. url: https://dx.doi.org/10.1021/ac303792p

 High Impact

A versatile genome-scale PCR-based pipeline for high-definition DNA FIISH

Bienko et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/NMETH.2306

Using variability in gene expression as a tool for studying gene regulation

Padovan-Merhar et al. WIREs Syst Biol Med. 2013. url: https://dx.doi.org/10.1002/wsbm.1243

Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

Rahman et al. Methods of Molecular Biology. 2013. url: https://dx.doi.org/10.1007/978-1-62703-526-2_3

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

 High Impact

RNA imaging in situ

Bakeret al. Nature Methods. 2012. url: https://dx.doi.org/10.1038/nmeth.2108

 High Impact, super resolution

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Lubecket al. Nature Methods. 2012. url: https://dx.doi.org/10.1038/nmeth.2069

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Evaluating Individual mRNA Molecules Detection Techniques in Microscope Images

Khutlandet al. Conference Paper. 2012. url: https://www.researchgate.net/publication/233867090_Evaluating_Individual_mRNA_Molecules_Detection_Techniques_in_Microscope_Images

 High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024

 High Impact

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf

 High Impact

Validating transcripts with probes and imaging technology

Itzkovitzet al. Nature Methods. 2011. url: https://dx.doi.org/10.1038/NMETH.1573

Single Molecule Imaging of RNA In Situ

Batishet al. Methods Molecular Biology. 2011. url: https://dx.doi.org/10.1007/978-1-61779-005-8_1

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010. url: https://dx.doi.org/10.1016/j.tcb.2010.03.006

Single-Molecule Approaches to Stochastic Gene Expression

Rajet al. Annual Review of Biophysics. 2009. url: https://dx.doi.org/10.1146/annurev.biophys.37.032807.125928

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse Methods and Protocols Publications

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Application

Adherent Cells

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Beckeret al. bioRxiv. 2016. url: https://dx.doi.org/10.1101/057299

 High Impact

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

 High Impact

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis

Sallamet al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17674

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

Nelsonet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00459-16

 High Impact

lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal

Zhuet al. Nature structural & molecular biology. 2016. url: https://dx.doi.org/10.1038/nsmb.3235

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016. url: https://dx.doi.org/10.1016/j.biomaterials.2016.05.022

Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.13065

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016. url: https://dx.doi.org/

 High Impact

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldneret al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17939

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

Pribadiet al. Cold Spring Harbor Laboratory Press. 2016. url: https://dx.doi.org/10.1101/051193

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

 High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016. url: https://dx.doi.org/10.1016/j.molcel.2016.03.007

 High Impact

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Palangatet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.04.009

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription

Leeet al. Molecular and Cellular Endocrinology. 2016. url: https://dx.doi.org/10.1016/j.mce.2016.04.001

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

 High Impact

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Xuet al. Nature. 2016. url: https://dx.doi.org/10.1038/cddis.2016.57

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

 High Impact

Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11099

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

 High Impact

Single-cell differences in matrix gene expression do not predict matrix deposition

Coteet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10865

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

 High Impact

Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.01.045

A continuum model of transcriptional bursting

Corriganet al. Genes and Chromosomes. 2016. url: https://dx.doi.org/10.7554/eLife.13051.001

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016. url: http://www.ncbi.nlm.nih.gov/pubmed/?term=RNase+P+Protein+Subunit%2C+Rpp29%2C+Represses+Histone+H3.3+Nucleosome+Deposition

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

 High Impact

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

Newhartet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/10.1091/mbc.E15-02-0099

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1131.abstract

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

 High Impact

A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005680

A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by PUM2 in human cells

Tichon et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/033423

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

 High Impact

Gene essentially and synthetic lethality in haploid human cells

Blomen et al. Science. 2015. url: http://www.sciencemag.org/content/350/6264/1092

 High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep17295

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

Engineering Duplex RNAs for Challenging Targets: Recognition of GGGGCC/CCCCGG Repeats at the ALS/FTD C9orf72 Locus

Hu et al. Cell Chemistry & Biology. 2015. url: https://dx.doi.org/10.1016/j.chembiol.2015.09.016

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

 High Impact

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015. url: https://dx.doi.org/10.1101/027870

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1503157112

Application of an RNA amplification method for reliable single-cell transcriptome analysis

Suslov et al. BioTechniques. 2015. url: http://www.biotechniques.com/multimedia/archive/00251/BTN_A_000114331_O__251167a.pdf  

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.07957

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv839

 High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep13339

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.09214

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005121

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

 High Throughput

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20145704

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

 High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa6090

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

 High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.03.025

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015. url: https://dx.doi.org/10.1021/acs.biochem.5b00259

 High Impact

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

Wang et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2015.03.003

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 High Impact

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

L'eveill'e et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7520

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

 High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015. url: http://www.sciencemag.org/cgi/doi/10.1126/science.1258849

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells

Silva et al. Human Molecular Genetics, Oxford. 2015. url: https://dx.doi.org/10.1093/hmg/ddv096

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

Lee et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv156

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.1992

PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201407105

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

Regulation of Mechanosensation in C. elegans through Ubiquitination of the MEC-4 Mechanotransduction Channel

Chen et al. The Journal of Neuroscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.4082-14.2015

Transcriptional Expression of Myelin Basic Protein in Oligodendrocytes Depends on Functional Syntaxin 4: a Potential Correlation with Autocrine Signaling

Bijlardet al. Molecular Cell Biology. 2015. url: https://dx.doi.org/10.1128/MCB.01389-14

 High Impact

Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7078

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

 High Impact

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6812

Profiling T Cell Activation Using Hybridization and Flow Cytometry Single-Molecule Fluorescence In Situ

Bushkin et al. The Journal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

Profiling T Cell Activation Using Single-Molecule Fluorescence In Situ Hybridization and Flow Cytometry

Bushkin et al. The Jornal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

 High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

 High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/ac5035924

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

Benzyl butyl phthalate induces migration, invasion, and angiogenesis of Huh7 hepatocellular carcinoma cells through nongenomic AhR/G-protein signaling

Tsai et al. BMC Cancer. 2014. url: https://dx.doi.org/10.1186/1471-2407-14-556

 High Impact

Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans

Garcia et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2858

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.05.005

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

 High Impact

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.04.025

The role of high cell density in the promotion of neuroendocrine transdifferentiation of prostate cancer cells

Pernicova et al. Molecular Cancer. 2014. url: https://dx.doi.org/10.1186/1476-4598-13-113

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.108910

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

 High Impact

Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2910

 High Impact

Labeling native bacterial RNA in live cells

Toran et al. Nature Cell Research. 2014. url: https://dx.doi.org/10.1038/cr.2014.47

 High Impact

Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2892

Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ

Markey et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0093488

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/25344859

 High Impact

Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014. url: https://dx.doi.org//10.1016/j.molcel.2014.01.026

Aberrant Patterns of X Chromosome Inactivation in a New Line of Human Embryonic Stem Cells Established in Physiological Oxygen Concentrations

Oliveira Georges et al. Stem Cell Rev and Rep. 2014. url: https://dx.doi.org/10.1007/s12015-014-9505-4

KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014. url: https://dx.doi.org/10.1016/j.neo.2014.03.008

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation

O'Grady et al. JVI, Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

 High Impact

Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-a protein levels and activity

Bolt et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2013.550

 High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014. url: https://dx.doi.org/10.1016/j.celrep.2013.12.013

A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/sb4001867

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014. url: https://dx.doi.org/10.1083/jcb.201304152

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014. url: https://dx.doi.org/10.1073/pnas.1410087111/-/DCSupplemental

 KO lncRNA

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Sauvageau et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.01749

 High Impact

Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

 High Impact

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

Yoon et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3939

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

 High Impact

Determinants of robustness in spindle assembly checkpoint signalling

Heinrich et al. Nature Cell Biology. 2013. url: https://dx.doi.org/10.1038/ncb2864

 High Impact

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.051

Identifying Division Symmetry of Mouse Embryonic Stem Cells: Negative Impact of DNA Methyltransferases on Symmetric Self-Renewal

Jasnos et al. Stem Cell Reports. 2013. url: https://dx.doi.org/10.1016/j.stemcr.2013.08.005

 High Impact

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013. url: https://dx.doi.org/10.1038/nmeth.2657

 High Impact

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Ball et al. Cell Cycle. 2013. url: https://dx.doi.org/10.4161/cc.26257

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae

Kraut-Cohen et al. Molecular Biology Cell . 2013. url: https://dx.doi.org/10.1091/mbc.E13-01-0038

 Turbo FISH, SNP FISH

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

Shaffer et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0075120

Barriers to transmission of transcriptional noise in a c-fos c-jun pathway

Shah et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2013.45

 SNP-FISH, High Impact

Allele-specific detection of single mRNA molecules in situ

Hansen et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2601

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1303400110

 High Impact

Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013. url: https://dx.doi.org/10.1016/j.molcel.2013.08.009

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001618

 High Impact

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013. url: https://dx.doi.org/10.1038/nsmb.2598

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Cell. 2013. url: http://dx.doi.org/10.1016/j.devcel.2013.05.007

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Developmental Cell. 2013. url: https://dx.doi.org/10.1016/j.devcel.2013.05.007

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001591

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Maamar et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.217018.113

Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

Graindorge et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.214999.113

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

mRNA encoding WAVE–Arp2/3-associated proteins is co-localized with foci of active protein synthesis at the leading edge of MRC5 fibroblasts during cell migration

Willett et al. Biochem Journal. 2013. url: https://dx.doi.org/10.1042/BJ20121803

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013. url: https://dx.doi.org/10.1021/ac303792p

Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays

Rantala et al. Microarrays. 2013. url: https://dx.doi.org/10.3390/microarrays2020097

Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells

Tan et al. Development and Stem Cells. 2013. url: https://dx.doi.org/10.1242/dev.087551

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

 High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses

Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

 High Impact

A versatile genome-scale PCR-based pipeline for high-definition DNA FIISH

Bienko et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/NMETH.2306

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013. url: https://dx.doi.org/10.5483/BMBRep.2013.46.2.016

 High Impact

Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013. url: https://dx.doi.org/10.1126/science.1231456

 High Impact

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz et al. Nature Research Letter. 2013. url: https://dx.doi.org/10.1038/nature11661

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013. url: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r104

Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

Rahman et al. Methods of Molecular Biology. 2013. url: https://dx.doi.org/10.1007/978-1-62703-526-2_3

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

Belmontet al. PLOS ONE. 2012. url: https://dx.doi.org/10.1371/journal.pone.0046868

 High Impact

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

 High Impact

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

 High Impact, super resolution

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Lubecket al. Nature Methods. 2012. url: https://dx.doi.org/10.1038/nmeth.2069

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1111226109                     

 High Impact

Single-mRNA counting using fluorescent in situ hybridization in budding yeast

Trceket al. Nature Protocol. 2012. url: https://dx.doi.org/10.1038/nprot.2011.451

Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues

Nedelecet al. Journal of Neuorscience. 2012. url: https://dx.doi.org/10.1523/JNEUROSCI.4176-11.2012

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

Gene location and DNA density determine transcription factor distributions in Escherichia coli

Kuhlmanet al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.42

 High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024

 High Impact

ncRNA- and Pc2 Methylation-Dependent GeneRelocationbetween NuclearStructures Mediates Gene Activation Programs

Yang et al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.08.054

 High Impact

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf

Cell-to-cell variability of alternative RNA splicing

Wakset al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.32

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

Hebenstreit et al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.28

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

Shihet al. Nucleic Acids Research. 2011. url: https://dx.doi.org/10.1093/nar/gkr456

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1101329108

Single Molecule Imaging of RNA In Situ

Batishet al. Methods Molecular Biology. 2011. url: https://dx.doi.org/10.1007/978-1-61779-005-8_1

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

Imaging single mRNA molecules in yeast

Youket al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)70017-3

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalilet al. PNAS. 2009. url: https://dx.doi.org/10.1073/pnas.0904715106

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse Adherent Cell Publications

Tissue

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

 High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016. url: http://dx.doi.org/10.1016/j.ydbio.2016.06.038

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

Thiruketheeswaranet al. Histochemistry and Cell Biology. 2016. url: https://dx.doi.org/10.1007/s00418-016-1463-2

 High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

 High Impact

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

 High Impact

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Quinn et al. Genes & Development. 2016. url: https://dx.doi.org/10.1101/gad.272187

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 High Impact

Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Han et al. Nature materials. 2016. url: https://dx.doi.org/10.1038/NMAT4520

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

 High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26255629

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

 High Impact

Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3143

 High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

 High Impact

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa1934

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

 High Impact

Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

 High Impact

A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015. url: https://dx.doi.org/10.1016/j.celrep.2014.12.029

The Novel Small Leucine-rich Protein Chondroadherin-like (CHADL) Is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The Journal of Biological Chemistry. 2015. url: https://dx.doi.org/10.1074/jbc.M114.593541

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.255810.114

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The American Society for Biochemistry and Molecular Biology. 2014. url: https://dx.doi.org/10.1074/jbc.M114.593541

 High Impact

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.10.017

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-ayala et al. The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.114843

 High Impact

Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

 High Impact

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

Meisel et al. Cell, Elsevier . 2014. url: https://dx.doi.org/10.1016/j.cell.2014.09.011

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014. url: https://dx.doi.org/10.1534/genetics.114.168823

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

 High Impact

Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

Lin et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.06.022

The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004512

 High Impact

Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans

Garcia et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2858

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Malone et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1101/gad.245829.114

 High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014. url: https://dx.doi.org/10.1038/ncb3000

 High Impact

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.04.031

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yücel et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

 High Impact

Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Weis et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2014.114

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Differential Expression of Galectin-1 and Galectin-3 in Canine Nonmalignant and Malignant Mammary Tissues, and in Progression to Metastases in Mammary Tumours

Oliveira JT et al. Anticancer Research. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/24778023

Receptor-interacting protein kinase 2 promotes triple-negative breast cancer cell migration and invasion via activation of nuclear factor-kappaB and c-Jun N-terminal kinase pathways

Singel et al. Breast Cancer Research. 2014. url: https://dx.doi.org/10.1186/bcr3629

Expression of the Developmental Transcription Factor Fezf2 Identifies a Distinct Subpopulation of Layer 5 Intratelencephalic-Projection Neurons in Mature Mouse Motor Cortex

Tantirigama et al. the Journal of Neuroscience. 2014. url: https://dx.doi.org/10.1523/JNEUROSCI.3111-13.2014

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014. url: https://dx.doi.org/10.1182/blood-2013-10-530683.

 High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013. url: https://dx.doi.org/10.1038/ng.2763

A dynamic population of stromal cells contributes to the follicle stem cell niche in the Drosophila ovary

Sahai-Hernandez et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.098558

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

 High Impact

Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

 High Impact

Tumour angiogenesis regulation by the miR-200 family

Peot et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3427

 High Impact

Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

Discovery of J Chain in African Lungfish (Protopterus dolloi, Sarcopterygii) Using High Throughput Transcriptome Sequencing: Implications in Mucosal Immunity

Tacchi et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0070650

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013. url: https://dx.doi.org/10.1083/jcb.201302049

Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

Graindorge et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.214999.113

 High Impact

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak et al. Nature Article. 2013. url: https://dx.doi.org/10.1038/nature11928

Both the Caspase CSP-1 and a Caspase-Independent Pathway Promote Programmed Cell Death in Parallel to the Canonical Pathway for Apoptosis in Caenorhabditis elegans

Denning et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1003341

Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction

Whitehead et al. JCEM Online. 2013. url: https://dx.doi.org/10.1210/jc.2012-2468

 High Impact

A versatile genome-scale PCR-based pipeline for high-definition DNA FIISH

Bienko et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/NMETH.2306

 High Impact

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz et al. Nature Research Letter. 2013. url: https://dx.doi.org/10.1038/nature11661

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013. url: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r104

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification

Tan et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2012.64

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012. url: https://dx.doi.org/10.1371/journal.pgen.1003079

 High Impact

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

Patelet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.09.020

 High Impact

Lgr5+ve Stem/Progenitor Cells Contribute to Nephron Formation during Kidney Development

Barkeret al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.08.018

 High Impact

Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012. url: https://dx.doi.org/10.1016/j.devcel.2012.08.004

 High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2011.10.002

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

Microglial Stimulation of Glioblastoma Invasion Involves Epidermal Growth Factor Receptor (EGFR) and Colony Stimulating Factor 1 Receptor (CSF-1R) Signaling

Coniglioet al. Molecular Medicine. 2012. url: https://dx.doi.org/10.2119/molmed.2011.00217

 High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665

Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1111684108

MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and the transition from larva to adult in C. elegans

Harriset al. Development. 2011. url: https://dx.doi.org/10.1242/dev.065417

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steineet al. Journal of Clinical Investigation. 2011. url: https://dx.doi.org/10.1172/JCI43169

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1101329108

 High Impact

EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011. url: https://dx.doi.org/10.1016/j.stem.2010.11.026

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010. url: https://dx.doi.org/10.1038/nature08781

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010. url: https://dx.doi.org/10.1016/j.tcb.2010.03.006

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse Tissue Publications

Whole Mount

High Impact

Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Akanumaet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11963

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

 High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

Truttmannet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1006023

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Malone et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1101/gad.245829.114

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yücel et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

 High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013. url: https://dx.doi.org/10.1038/ng.2763

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

 High Impact

Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

Both the Caspase CSP-1 and a Caspase-Independent Pathway Promote Programmed Cell Death in Parallel to the Canonical Pathway for Apoptosis in Caenorhabditis elegans

Denning et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1003341

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification

Tan et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2012.64

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

 High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2011.10.002

 High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665

MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and the transition from larva to adult in C. elegans

Harriset al. Development. 2011. url: https://dx.doi.org/10.1242/dev.065417

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010. url: https://dx.doi.org/10.1016/j.tcb.2010.03.006

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
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FFPE

Super Resolution

Microbe Screen

CLARITY

ChIRP

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Organism

Human

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

 High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Beckeret al. bioRxiv. 2016. url: https://dx.doi.org/10.1101/057299

 High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

 High Impact

lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal

Zhuet al. Nature structural & molecular biology. 2016. url: https://dx.doi.org/10.1038/nsmb.3235

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016. url: https://dx.doi.org/10.1016/j.biomaterials.2016.05.022

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

 High Impact

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldneret al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17939

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

Pribadiet al. Cold Spring Harbor Laboratory Press. 2016. url: https://dx.doi.org/10.1101/051193

 High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016. url: https://dx.doi.org/10.1016/j.molcel.2016.03.007

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Palangatet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.04.009

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

 High Impact

Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.01.045

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016. url: http://www.ncbi.nlm.nih.gov/pubmed/?term=RNase+P+Protein+Subunit%2C+Rpp29%2C+Represses+Histone+H3.3+Nucleosome+Deposition

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

 High Impact

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

Newhartet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/10.1091/mbc.E15-02-0099

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

 High Impact

A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by PUM2 in human cells

Tichon et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/033423

 High Impact

Gene essentially and synthetic lethality in haploid human cells

Blomen et al. Science. 2015. url: http://www.sciencemag.org/content/350/6264/1092

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

 High Impact

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015. url: https://dx.doi.org/10.1101/027870

A BRCA1-interacting lncRNA regulates homologous recombination

Sharma et al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540437

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.07957

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.09214

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005121

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

 High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa6090

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis

Kukharsky et al. Molecular Neurodegeneration. 2015. url: https://dx.doi.org/10.1186/s13024-015-0014-y

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015. url: https://dx.doi.org/10.1021/acs.biochem.5b00259

 High Impact

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

Wang et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2015.03.003

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 High Impact

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

L'eveill'e et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7520

Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells

Silva et al. Human Molecular Genetics, Oxford. 2015. url: https://dx.doi.org/10.1093/hmg/ddv096

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

Lee et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv156

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.1992

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_20

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

 High Impact

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6812

Profiling T Cell Activation Using Single-Molecule Fluorescence In Situ Hybridization and Flow Cytometry

Bushkin et al. The Jornal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

 High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/ac5035924

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

Benzyl butyl phthalate induces migration, invasion, and angiogenesis of Huh7 hepatocellular carcinoma cells through nongenomic AhR/G-protein signaling

Tsai et al. BMC Cancer. 2014. url: https://dx.doi.org/10.1186/1471-2407-14-556

 High Impact

Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans

Garcia et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2858

 High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014. url: https://dx.doi.org/10.1038/ncb3000

 High Impact

Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.05.005

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

The role of high cell density in the promotion of neuroendocrine transdifferentiation of prostate cancer cells

Pernicova et al. Molecular Cancer. 2014. url: https://dx.doi.org/10.1186/1476-4598-13-113

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/25344859

 High Impact

Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014. url: https://dx.doi.org//10.1016/j.molcel.2014.01.026

Receptor-interacting protein kinase 2 promotes triple-negative breast cancer cell migration and invasion via activation of nuclear factor-kappaB and c-Jun N-terminal kinase pathways

Singel et al. Breast Cancer Research. 2014. url: https://dx.doi.org/10.1186/bcr3629

Aberrant Patterns of X Chromosome Inactivation in a New Line of Human Embryonic Stem Cells Established in Physiological Oxygen Concentrations

Oliveira Georges et al. Stem Cell Rev and Rep. 2014. url: https://dx.doi.org/10.1007/s12015-014-9505-4

KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014. url: https://dx.doi.org/10.1016/j.neo.2014.03.008

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

 High Impact

Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-a protein levels and activity

Bolt et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2013.550

 High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014. url: https://dx.doi.org/10.1016/j.celrep.2013.12.013

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

 High Impact

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.051

 High Impact

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013. url: https://dx.doi.org/10.1038/nmeth.2657

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

 Turbo FISH, SNP FISH

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

Shaffer et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0075120

Barriers to transmission of transcriptional noise in a c-fos c-jun pathway

Shah et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2013.45

mRNA encoding WAVE–Arp2/3-associated proteins is co-localized with foci of active protein synthesis at the leading edge of MRC5 fibroblasts during cell migration

Willett et al. Biochem Journal. 2013. url: https://dx.doi.org/10.1042/BJ20121803

Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells

Tan et al. Development and Stem Cells. 2013. url: https://dx.doi.org/10.1242/dev.087551

 High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372

Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction

Whitehead et al. JCEM Online. 2013. url: https://dx.doi.org/10.1210/jc.2012-2468

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses

Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

 High Impact

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz et al. Nature Research Letter. 2013. url: https://dx.doi.org/10.1038/nature11661

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013. url: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r104

Using variability in gene expression as a tool for studying gene regulation

Padovan-Merhar et al. WIREs Syst Biol Med. 2013. url: https://dx.doi.org/10.1002/wsbm.1243

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38

 High Impact

ncRNA- and Pc2 Methylation-Dependent GeneRelocationbetween NuclearStructures Mediates Gene Activation Programs

Yang et al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.08.054

 High Impact

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf

Cell-to-cell variability of alternative RNA splicing

Wakset al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.32

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

Shihet al. Nucleic Acids Research. 2011. url: https://dx.doi.org/10.1093/nar/gkr456

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalilet al. PNAS. 2009. url: https://dx.doi.org/10.1073/pnas.0904715106

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse Human Publications

Mouse

High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

 High Impact

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis

Sallamet al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17674

 High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription

Leeet al. Molecular and Cellular Endocrinology. 2016. url: https://dx.doi.org/10.1016/j.mce.2016.04.001

 High Impact

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Xuet al. Nature. 2016. url: https://dx.doi.org/10.1038/cddis.2016.57

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

 High Impact

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005680

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

Application of an RNA amplification method for reliable single-cell transcriptome analysis

Suslov et al. BioTechniques. 2015. url: http://www.biotechniques.com/multimedia/archive/00251/BTN_A_000114331_O__251167a.pdf  

 High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep13339

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26255629

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

 High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

 High Impact

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa1934

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

 High Impact

Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

 High Impact

Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7078

The Novel Small Leucine-rich Protein Chondroadherin-like (CHADL) Is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The Journal of Biological Chemistry. 2015. url: https://dx.doi.org/10.1074/jbc.M114.593541

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The American Society for Biochemistry and Molecular Biology. 2014. url: https://dx.doi.org/10.1074/jbc.M114.593541

 High Impact

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.10.017

 High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-ayala et al. The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.114843

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

 PACT Clearing, High Impact

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

Yang et al. Cell Resource. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.07.017

 High Impact

Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

Lin et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.06.022

 High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014. url: https://dx.doi.org/10.1038/ncb3000

 High Impact

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.04.025

 High Impact

Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Weis et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2014.114

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.108910

 High Impact

Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2910

 High Impact

Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2892

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014. url: https://dx.doi.org/10.1182/blood-2013-10-530683.

A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/sb4001867

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014. url: https://dx.doi.org/10.1083/jcb.201304152

 KO lncRNA

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Sauvageau et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.01749

Identifying Division Symmetry of Mouse Embryonic Stem Cells: Negative Impact of DNA Methyltransferases on Symmetric Self-Renewal

Jasnos et al. Stem Cell Reports. 2013. url: https://dx.doi.org/10.1016/j.stemcr.2013.08.005

 High Impact

Tumour angiogenesis regulation by the miR-200 family

Peot et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3427

 SNP-FISH, High Impact

Allele-specific detection of single mRNA molecules in situ

Hansen et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2601

 High Impact

Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001618

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Maamar et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.217018.113

 High Impact

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak et al. Nature Article. 2013. url: https://dx.doi.org/10.1038/nature11928

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013. url: http://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-9-r104

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

 High Impact

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

 High Impact

Lgr5+ve Stem/Progenitor Cells Contribute to Nephron Formation during Kidney Development

Barkeret al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.08.018

Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues

Nedelecet al. Journal of Neuorscience. 2012. url: https://dx.doi.org/10.1523/JNEUROSCI.4176-11.2012

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

Microglial Stimulation of Glioblastoma Invasion Involves Epidermal Growth Factor Receptor (EGFR) and Colony Stimulating Factor 1 Receptor (CSF-1R) Signaling

Coniglioet al. Molecular Medicine. 2012. url: https://dx.doi.org/10.2119/molmed.2011.00217

 High Impact

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steineet al. Journal of Clinical Investigation. 2011. url: https://dx.doi.org/10.1172/JCI43169
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Drosophila

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016. url: http://dx.doi.org/10.1016/j.ydbio.2016.06.038

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

 High Impact

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Quinn et al. Genes & Development. 2016. url: https://dx.doi.org/10.1101/gad.272187

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

 High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

 High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.03.025

 High Impact

Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3143

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201407105

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Malone et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1101/gad.245829.114

 High Impact

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.04.031

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014. url: https://dx.doi.org/10.1073/pnas.1410087111/-/DCSupplemental

A dynamic population of stromal cells contributes to the follicle stem cell niche in the Drosophila ovary

Sahai-Hernandez et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.098558

 High Impact

Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

 High Impact

Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013. url: https://dx.doi.org/10.1016/j.molcel.2013.08.009

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Cell. 2013. url: http://dx.doi.org/10.1016/j.devcel.2013.05.007

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Developmental Cell. 2013. url: https://dx.doi.org/10.1016/j.devcel.2013.05.007

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013. url: https://dx.doi.org/10.1083/jcb.201302049

Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

Graindorge et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.214999.113

The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012. url: https://dx.doi.org/10.1371/journal.pgen.1003079

 High Impact

Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012. url: https://dx.doi.org/10.1016/j.devcel.2012.08.004

 High Impact

EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011. url: https://dx.doi.org/10.1016/j.stem.2010.11.026

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
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C. elegans

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

Truttmannet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1006023

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

Regulation of Mechanosensation in C. elegans through Ubiquitination of the MEC-4 Mechanotransduction Channel

Chen et al. The Journal of Neuroscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.4082-14.2015

 High Impact

A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015. url: https://dx.doi.org/10.1016/j.celrep.2014.12.029

The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.255810.114

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically-disordered proteins in C. elegans

Wang et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.04591

 High Impact

Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

 High Impact

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

Meisel et al. Cell, Elsevier . 2014. url: https://dx.doi.org/10.1016/j.cell.2014.09.011

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014. url: https://dx.doi.org/10.1534/genetics.114.168823

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004512

 High Impact

Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans

Garcia et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2858

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yücel et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013. url: https://dx.doi.org/10.1038/ng.2763

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

 High Impact

Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

Both the Caspase CSP-1 and a Caspase-Independent Pathway Promote Programmed Cell Death in Parallel to the Canonical Pathway for Apoptosis in Caenorhabditis elegans

Denning et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1003341

Using variability in gene expression as a tool for studying gene regulation

Padovan-Merhar et al. WIREs Syst Biol Med. 2013. url: https://dx.doi.org/10.1002/wsbm.1243

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification

Tan et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2012.64

 High Impact

Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans

Cochellaet al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.10.049

 High Impact

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

Patelet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.09.020

 High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2011.10.002

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

 High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665

Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1111684108

MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and the transition from larva to adult in C. elegans

Harriset al. Development. 2011. url: https://dx.doi.org/10.1242/dev.065417

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1101329108

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010. url: https://dx.doi.org/10.1038/nature08781

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010. url: https://dx.doi.org/10.1016/j.tcb.2010.03.006

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
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Yeast

High Impact

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

 High Impact

Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11099

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1131.abstract

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1503157112

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2892

 High Impact

Determinants of robustness in spindle assembly checkpoint signalling

Heinrich et al. Nature Cell Biology. 2013. url: https://dx.doi.org/10.1038/ncb2864

 High Impact

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Ball et al. Cell Cycle. 2013. url: https://dx.doi.org/10.4161/cc.26257

Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae

Kraut-Cohen et al. Molecular Biology Cell . 2013. url: https://dx.doi.org/10.1091/mbc.E13-01-0038

 High Impact

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013. url: https://dx.doi.org/10.1038/nsmb.2598

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

Rahman et al. Methods of Molecular Biology. 2013. url: https://dx.doi.org/10.1007/978-1-62703-526-2_3

Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

Belmontet al. PLOS ONE. 2012. url: https://dx.doi.org/10.1371/journal.pone.0046868

 High Impact, super resolution

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Lubecket al. Nature Methods. 2012. url: https://dx.doi.org/10.1038/nmeth.2069

 High Impact

Single-mRNA counting using fluorescent in situ hybridization in budding yeast

Trceket al. Nature Protocol. 2012. url: https://dx.doi.org/10.1038/nprot.2011.451

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

Imaging single mRNA molecules in yeast

Youket al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)70017-3

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
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Zebrafish

Bacteria or Parasite

Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.13065

 High Impact

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. Nature Microbiology. 2016. url: https://dx.doi.org/10.1038/NMICROBIOL.2016.55

Methods for studying RNA localization in bacteria

Kannaiahet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.010

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

 High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep17295

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv839

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

 High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015. url: http://www.sciencemag.org/cgi/doi/10.1126/science.1258849

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

 High Impact

Labeling native bacterial RNA in live cells

Toran et al. Nature Cell Research. 2014. url: https://dx.doi.org/10.1038/cr.2014.47

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1303400110

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001591

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013. url: https://dx.doi.org/10.1021/ac303792p

Gene location and DNA density determine transcription factor distributions in Escherichia coli

Kuhlmanet al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.42
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Virus

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip†

Shaffer et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5lc00459d

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

 High Throughput

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20145704

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

Identification of a novel multiple kinase inhibitor with potent antiviral activity against influenza virus by reducing viral polymerase activity

Sasaki et al. Biochemical and Biophysical Research Communications. 2014. url: https://dx.doi.org/10.1016/j.bbrc.2014.05.058

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Characterization of novel inhibitors of HIV-1 replication that function via alteration of viral RNA processing and rev function

Wong et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt727

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012. url: https://dx.doi.org/10.1128/JVI.00662-12

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38
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Other

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw596

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

Thiruketheeswaranet al. Histochemistry and Cell Biology. 2016. url: https://dx.doi.org/10.1007/s00418-016-1463-2

 High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

 High Impact

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

Differential Expression of Galectin-1 and Galectin-3 in Canine Nonmalignant and Malignant Mammary Tissues, and in Progression to Metastases in Mammary Tumours

Oliveira JT et al. Anticancer Research. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/24778023

 High Impact

Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

Discovery of J Chain in African Lungfish (Protopterus dolloi, Sarcopterygii) Using High Throughput Transcriptome Sequencing: Implications in Mucosal Immunity

Tacchi et al. PLOS ONE. 2013. url: https://dx.doi.org/10.1371/journal.pone.0070650

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

 High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024
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Messenger RNA

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw596

 High Impact

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

 High Impact

Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Akanumaet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11963

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016. url: http://dx.doi.org/10.1016/j.ydbio.2016.06.038

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

Thiruketheeswaranet al. Histochemistry and Cell Biology. 2016. url: https://dx.doi.org/10.1007/s00418-016-1463-2

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Beckeret al. bioRxiv. 2016. url: https://dx.doi.org/10.1101/057299

 High Impact

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

Nelsonet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00459-16

 High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016. url: https://dx.doi.org/10.1016/j.biomaterials.2016.05.022

Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.13065

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016. url: https://dx.doi.org/

 High Impact

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. Nature Microbiology. 2016. url: https://dx.doi.org/10.1038/NMICROBIOL.2016.55

 High Impact

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldneret al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17939

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

Truttmannet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1006023

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

Pribadiet al. Cold Spring Harbor Laboratory Press. 2016. url: https://dx.doi.org/10.1101/051193

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

 High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016. url: https://dx.doi.org/10.1016/j.molcel.2016.03.007

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription

Leeet al. Molecular and Cellular Endocrinology. 2016. url: https://dx.doi.org/10.1016/j.mce.2016.04.001

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

 High Impact

Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11099

 High Impact

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

 High Impact

Single-cell differences in matrix gene expression do not predict matrix deposition

Coteet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10865

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

 High Impact

Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.01.045

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

 High Impact

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 High Impact

Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Han et al. Nature materials. 2016. url: https://dx.doi.org/10.1038/NMAT4520

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1131.abstract

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

 High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep17295

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015. url: https://dx.doi.org/10.1101/027870

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.07957

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv839

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

 High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26255629

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

 High Throughput

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20145704

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

 High Impact

Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3143

 High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

 High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015. url: http://www.sciencemag.org/cgi/doi/10.1126/science.1258849

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201407105

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

 High Impact

Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

 High Impact

Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7078

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically-disordered proteins in C. elegans

Wang et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.04591

Profiling T Cell Activation Using Hybridization and Flow Cytometry Single-Molecule Fluorescence In Situ

Bushkin et al. The Journal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

Profiling T Cell Activation Using Single-Molecule Fluorescence In Situ Hybridization and Flow Cytometry

Bushkin et al. The Jornal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

 High Impact

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.10.017

Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/ac5035924

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014. url: https://dx.doi.org/10.1534/genetics.114.168823

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004512

Benzyl butyl phthalate induces migration, invasion, and angiogenesis of Huh7 hepatocellular carcinoma cells through nongenomic AhR/G-protein signaling

Tsai et al. BMC Cancer. 2014. url: https://dx.doi.org/10.1186/1471-2407-14-556

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Malone et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1101/gad.245829.114

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

The role of high cell density in the promotion of neuroendocrine transdifferentiation of prostate cancer cells

Pernicova et al. Molecular Cancer. 2014. url: https://dx.doi.org/10.1186/1476-4598-13-113

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.108910

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

 High Impact

Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2910

 High Impact

Labeling native bacterial RNA in live cells

Toran et al. Nature Cell Research. 2014. url: https://dx.doi.org/10.1038/cr.2014.47

 High Impact

Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014. url: https://dx.doi.org/10.1038/nmeth.2892

Differential Expression of Galectin-1 and Galectin-3 in Canine Nonmalignant and Malignant Mammary Tissues, and in Progression to Metastases in Mammary Tumours

Oliveira JT et al. Anticancer Research. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/24778023

Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ

Markey et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0093488

 High Impact

Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014. url: https://dx.doi.org//10.1016/j.molcel.2014.01.026

Receptor-interacting protein kinase 2 promotes triple-negative breast cancer cell migration and invasion via activation of nuclear factor-kappaB and c-Jun N-terminal kinase pathways

Singel et al. Breast Cancer Research. 2014. url: https://dx.doi.org/10.1186/bcr3629

Expression of the Developmental Transcription Factor Fezf2 Identifies a Distinct Subpopulation of Layer 5 Intratelencephalic-Projection Neurons in Mature Mouse Motor Cortex

Tantirigama et al. the Journal of Neuroscience. 2014. url: https://dx.doi.org/10.1523/JNEUROSCI.3111-13.2014

KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014. url: https://dx.doi.org/10.1016/j.neo.2014.03.008

 High Impact

Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014. url: https://dx.doi.org/10.1038/mi.2013.127

 High Impact

Systems level-based RNAi screening by high content analysis identifies UBR5 as a regulator of estrogen receptor-a protein levels and activity

Bolt et al. Nature Oncogene. 2014. url: https://dx.doi.org/10.1038/onc.2013.550

A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/sb4001867

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

 High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014. url: https://dx.doi.org/10.1073/pnas.1410087111/-/DCSupplemental

 High Impact

Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013. url: https://dx.doi.org/10.1371/journal.pgen.1004017

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013. url: https://dx.doi.org/10.1038/ng.2763

 High Impact

Determinants of robustness in spindle assembly checkpoint signalling

Heinrich et al. Nature Cell Biology. 2013. url: https://dx.doi.org/10.1038/ncb2864

 High Impact

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Ball et al. Cell Cycle. 2013. url: https://dx.doi.org/10.4161/cc.26257

Translation- and SRP-independent mRNA targeting to the endoplasmic reticulum in the yeast Saccharomyces cerevisiae

Kraut-Cohen et al. Molecular Biology Cell . 2013. url: https://dx.doi.org/10.1091/mbc.E13-01-0038

 High Impact

Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

Barriers to transmission of transcriptional noise in a c-fos c-jun pathway

Shah et al. Molecular Systems Biology. 2013. url: https://dx.doi.org/10.1038/msb.2013.45

 High Impact

Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1303400110

 High Impact

Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013. url: https://dx.doi.org/10.1016/j.molcel.2013.08.009

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Cell. 2013. url: http://dx.doi.org/10.1016/j.devcel.2013.05.007

 High Impact

Protein Aggregation Behavior Regulates Cyclin Transcript Localization and Cell-Cycle Control

Lee et al. Developmental Cell. 2013. url: https://dx.doi.org/10.1016/j.devcel.2013.05.007

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001591

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013. url: https://dx.doi.org/10.1083/jcb.201302049

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

mRNA encoding WAVE–Arp2/3-associated proteins is co-localized with foci of active protein synthesis at the leading edge of MRC5 fibroblasts during cell migration

Willett et al. Biochem Journal. 2013. url: https://dx.doi.org/10.1042/BJ20121803

Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays

Rantala et al. Microarrays. 2013. url: https://dx.doi.org/10.3390/microarrays2020097

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

 High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372

Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction

Whitehead et al. JCEM Online. 2013. url: https://dx.doi.org/10.1210/jc.2012-2468

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013. url: https://dx.doi.org/10.5483/BMBRep.2013.46.2.016

 High Impact

Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013. url: https://dx.doi.org/10.1126/science.1231456

Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae

Rahman et al. Methods of Molecular Biology. 2013. url: https://dx.doi.org/10.1007/978-1-62703-526-2_3

The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012. url: https://dx.doi.org/10.1371/journal.pgen.1003079

 High Impact

Removal of Polycomb Repressive Complex 2 Makes C. elegans Germ Cells Susceptible to Direct Conversion into Specific Somatic Cell Types

Patelet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2012.09.020

 High Impact

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

 High Impact

Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012. url: https://dx.doi.org/10.1016/j.devcel.2012.08.004

 High Impact, super resolution

Single-cell systems biology by super-resolution imaging and combinatorial labeling

Lubecket al. Nature Methods. 2012. url: https://dx.doi.org/10.1038/nmeth.2069

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1111226109                     

 High Impact

Single-mRNA counting using fluorescent in situ hybridization in budding yeast

Trceket al. Nature Protocol. 2012. url: https://dx.doi.org/10.1038/nprot.2011.451

 High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012. url: https://dx.doi.org/10.1016/j.celrep.2011.10.002

Concentration-Dependent Requirement for Local Protein Synthesis in Motor Neuron Subtype-Specific Response to Axon Guidance Cues

Nedelecet al. Journal of Neuorscience. 2012. url: https://dx.doi.org/10.1523/JNEUROSCI.4176-11.2012

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.38

Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012. url: https://dx.doi.org/10.1242/dev.074005

Gene location and DNA density determine transcription factor distributions in Escherichia coli

Kuhlmanet al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.42

Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1111684108

 High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024

Cell-to-cell variability of alternative RNA splicing

Wakset al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.32

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

Hebenstreit et al. Molecular Systems Biology. 2011. url: https://dx.doi.org/10.1038/msb.2011.28

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

Shihet al. Nucleic Acids Research. 2011. url: https://dx.doi.org/10.1093/nar/gkr456

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steineet al. Journal of Clinical Investigation. 2011. url: https://dx.doi.org/10.1172/JCI43169

Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression

Topalidou et al. PNAS. 2011. url: https://dx.doi.org/10.1073/pnas.1101329108

 High Impact

EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011. url: https://dx.doi.org/10.1016/j.stem.2010.11.026

Single Molecule Imaging of RNA In Situ

Batishet al. Methods Molecular Biology. 2011. url: https://dx.doi.org/10.1007/978-1-61779-005-8_1

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010. url: https://dx.doi.org/10.1016/j.tcb.2010.03.006

Imaging single mRNA molecules in yeast

Youket al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)70017-3

Single-Molecule Approaches to Stochastic Gene Expression

Rajet al. Annual Review of Biophysics. 2009. url: https://dx.doi.org/10.1146/annurev.biophys.37.032807.125928

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse mRNA Publications

Long Non-Coding RNA

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

 High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

 High Impact

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis

Sallamet al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17674

 High Impact

lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal

Zhuet al. Nature structural & molecular biology. 2016. url: https://dx.doi.org/10.1038/nsmb.3235

 High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

 High Impact

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Xuet al. Nature. 2016. url: https://dx.doi.org/10.1038/cddis.2016.57

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005680

A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by PUM2 in human cells

Tichon et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/033423

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

A BRCA1-interacting lncRNA regulates homologous recombination

Sharma et al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540437

 High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep13339

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Hassanet al. Bone. 2015. url: https://dx.doi.org/10.1016/j.bone.2015.05.026

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

 High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.03.025

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015. url: https://dx.doi.org/10.1021/acs.biochem.5b00259

 High Impact

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

Wang et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2015.03.003

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.1992

 High Impact

A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015. url: https://dx.doi.org/10.1016/j.celrep.2014.12.029

Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_20

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Hassan et al. Elsevier, Bone. 2015. url: https://dx.doi.org/10.1016/j.bone.2015.05.026

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_1

 High Impact

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6812

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

 High Impact

Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.05.005

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/25344859

Aberrant Patterns of X Chromosome Inactivation in a New Line of Human Embryonic Stem Cells Established in Physiological Oxygen Concentrations

Oliveira Georges et al. Stem Cell Rev and Rep. 2014. url: https://dx.doi.org/10.1007/s12015-014-9505-4

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014. url: https://dx.doi.org/10.1182/blood-2013-10-530683.

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014. url: https://dx.doi.org/10.1083/jcb.201304152

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

 High Impact

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

Yoon et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3939

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Maamar et al. Genes & Development. 2013. url: https://dx.doi.org/10.1101/gad.217018.113

 High Impact

Control of somatic tissue differentiation by the long non-coding RNA TINCR

Kretz et al. Nature Research Letter. 2013. url: https://dx.doi.org/10.1038/nature11661

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalilet al. PNAS. 2009. url: https://dx.doi.org/10.1073/pnas.0904715106
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Viral RNA

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

Identification of a novel multiple kinase inhibitor with potent antiviral activity against influenza virus by reducing viral polymerase activity

Sasaki et al. Biochemical and Biophysical Research Communications. 2014. url: https://dx.doi.org/10.1016/j.bbrc.2014.05.058

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Characterization of novel inhibitors of HIV-1 replication that function via alteration of viral RNA processing and rev function

Wong et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt727

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.00994

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012. url: https://dx.doi.org/10.1128/JVI.00662-12

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109
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Ribosomal RNA

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

 High Impact

Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

Lin et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.06.022

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12
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Precursor mRNA

Non-Coding RNA

Intronic RNA

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

 High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

 High Impact

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.051

 High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372
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Exonic RNA

Back to Top

Multiplexing

RNA FISH/RNA FISH

High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw596

 High Impact

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Palangatet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.04.009

 High Impact

Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11099

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

 High Impact

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

Application of an RNA amplification method for reliable single-cell transcriptome analysis

Suslov et al. BioTechniques. 2015. url: http://www.biotechniques.com/multimedia/archive/00251/BTN_A_000114331_O__251167a.pdf  

 High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep13339

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201407105

 High Impact

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa1934

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.255810.114

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014. url: https://dx.doi.org/10.1038/ncb3000

 High Impact

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

Dimitrova et al. Molecular Cell. 2014. url: https://dx.doi.org/10.1016/j.molcel.2014.04.025

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

 High Impact

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.060

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

 High Impact

Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013. url: https://dx.doi.org/10.1038/nsmb.2598

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

 High Impact

Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.066

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013. url: https://dx.doi.org/10.5483/BMBRep.2013.46.2.016

 High Impact

Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans

Cochellaet al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.10.049

 Quadraplex Multiplex

A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012. url: https://dx.doi.org/10.1242/dev.086975

 High Impact

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012. url: https://dx.doi.org/10.1128/JVI.00662-12

One influenza virus particle packages eight unique viral RNAs as shown by FISH analysis

Chouet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1206069109

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012. url: https://dx.doi.org/10.1073/pnas.1111226109                     

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Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011. url: https://dx.doi.org/10.1016/j.cell.2011.10.024

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Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf

Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer

Steineet al. Journal of Clinical Investigation. 2011. url: https://dx.doi.org/10.1172/JCI43169

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010. url: https://dx.doi.org/10.1038/nature08781

 High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010. url: https://dx.doi.org/10.1038/nature08781

Detection of Individual Endogenous RNA Transcripts In Situ Using Multiple Singly Labeled Probes

Rajet al. Methods in Enzymology. 2010. url: https://dx.doi.org/10.1016/S0076-6879(10)72004-8

 High Impact

Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008. url: https://dx.doi.org/10.1038/NMETH.1253
Collapse RNA/RNA Publications

RNA FISH/Protein IF

High Impact

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

Nelsonet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00459-16

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016. url: https://dx.doi.org/

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

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Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

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A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

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Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

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Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005121

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

 High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.03.025

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Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

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An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

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Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

Transcriptional Expression of Myelin Basic Protein in Oligodendrocytes Depends on Functional Syntaxin 4: a Potential Correlation with Autocrine Signaling

Bijlardet al. Molecular Cell Biology. 2015. url: https://dx.doi.org/10.1128/MCB.01389-14

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

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Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

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Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0099346

Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004380

MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014. url: https://dx.doi.org/10.1073/pnas.1408037111

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014. url: https://dx.doi.org/10.1172/JCI67382

Expression of the Developmental Transcription Factor Fezf2 Identifies a Distinct Subpopulation of Layer 5 Intratelencephalic-Projection Neurons in Mature Mouse Motor Cortex

Tantirigama et al. the Journal of Neuroscience. 2014. url: https://dx.doi.org/10.1523/JNEUROSCI.3111-13.2014

Aberrant Patterns of X Chromosome Inactivation in a New Line of Human Embryonic Stem Cells Established in Physiological Oxygen Concentrations

Oliveira Georges et al. Stem Cell Rev and Rep. 2014. url: https://dx.doi.org/10.1007/s12015-014-9505-4

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

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Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.11.022

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Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

Yoon et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3939

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

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Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013. url: https://dx.doi.org/10.1016/j.cell.2013.09.051

IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1311669110

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Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013. url: https://dx.doi.org/10.1038/nprot.2013.109

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Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013. url: https://dx.doi.org/10.1016/j.molcel.2013.08.009

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013. url: https://dx.doi.org/10.1371/journal.pbio.1001618

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays

Rantala et al. Microarrays. 2013. url: https://dx.doi.org/10.3390/microarrays2020097

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013. url: https://dx.doi.org/10.1128/MCB.01020-12

Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013. url: https://dx.doi.org/10.5483/BMBRep.2013.46.2.016

Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

Belmontet al. PLOS ONE. 2012. url: https://dx.doi.org/10.1371/journal.pone.0046868

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TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA

Shihet al. Nucleic Acids Research. 2011. url: https://dx.doi.org/10.1093/nar/gkr456
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RNA FISH/DNA FISH

High Impact

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

Simultaneous RNA–DNA FISH

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_11

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

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The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.04.031

Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014. url: https://dx.doi.org/10.1083/jcb.201304152

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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/nmeth.2372

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A versatile genome-scale PCR-based pipeline for high-definition DNA FIISH

Bienko et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/NMETH.2306

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TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012
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RNA FISH/IHC

RNA FISH/ICC

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High Impact

Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

 High Impact

p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

 High Impact

Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016. url: http://dx.doi.org/10.1016/j.ydbio.2016.06.038

 High Impact

Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

 High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

Pribadiet al. Cold Spring Harbor Laboratory Press. 2016. url: https://dx.doi.org/10.1101/051193

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

 High Impact

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Xuet al. Nature. 2016. url: https://dx.doi.org/10.1038/cddis.2016.57

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

A continuum model of transcriptional bursting

Corriganet al. Genes and Chromosomes. 2016. url: https://dx.doi.org/10.7554/eLife.13051.001

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016. url: http://www.ncbi.nlm.nih.gov/pubmed/?term=RNase+P+Protein+Subunit%2C+Rpp29%2C+Represses+Histone+H3.3+Nucleosome+Deposition

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Quinn et al. Genes & Development. 2016. url: https://dx.doi.org/10.1101/gad.272187

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

 High Impact

A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.09214

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis

Kukharsky et al. Molecular Neurodegeneration. 2015. url: https://dx.doi.org/10.1186/s13024-015-0014-y

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 High Impact

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

L'eveill'e et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7520

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

Lee et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv156

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically-disordered proteins in C. elegans

Wang et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.04591

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

 High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/ac5035924

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014. url: https://dx.doi.org/10.1534/genetics.114.168823

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014. url: https://dx.doi.org/10.1534/g3.114.010892

 High Impact

Defining Estrogenic Mechanisms of Bisphenol A Analogs through High Throughput Microscopy-Based Contextual Assays

Stossi et al. Cell Chemistry & Biology. 2014. url: https://dx.doi.org/10.1016/j.chembiol.2014.03.013

The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/25344859

Expression of the Developmental Transcription Factor Fezf2 Identifies a Distinct Subpopulation of Layer 5 Intratelencephalic-Projection Neurons in Mature Mouse Motor Cortex

Tantirigama et al. the Journal of Neuroscience. 2014. url: https://dx.doi.org/10.1523/JNEUROSCI.3111-13.2014

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014. url: https://dx.doi.org/10.1182/blood-2013-12-544494

 High Impact

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2764

 High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014. url: https://dx.doi.org/10.1016/j.celrep.2013.12.013

 High Impact

N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014. url: https://dx.doi.org/10.1038/nature12730

De novo translation initiation on membrane-bound ribosomes as a mechanism for localization of cytosolic protein mRNAs to the endoplasmic reticulum

Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.045526.114

 High Impact

Simultaneous Detection of Nuclear and Cytoplasmic RNA Variants Utilizing Stellaris ® RNA Fluorescence In Situ Hybridization in Adherent Cells

Coassin et al. Methods in Molecular Biology. 2014. url: https://dx.doi.org/10.1007/978-1-4939-1459-3_15

 KO lncRNA

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

Sauvageau et al. eLIFE. 2013. url: https://dx.doi.org/10.7554/eLife.01749

Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013. url: https://dx.doi.org/10.1002/stem.1622

Characterization of novel inhibitors of HIV-1 replication that function via alteration of viral RNA processing and rev function

Wong et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt727

 High Impact

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013. url: https://dx.doi.org/10.1038/nmeth.2657

 High Impact

Tumour angiogenesis regulation by the miR-200 family

Peot et al. Nature Communications. 2013. url: https://dx.doi.org/10.1038/ncomms3427

Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013. url: https://dx.doi.org/10.3791/50382

Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis

Chou et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003358

Single-cell gene expression profiling reveals functional heterogeneity of undifferentiated human epidermal cells

Tan et al. Development and Stem Cells. 2013. url: https://dx.doi.org/10.1242/dev.087551

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013. url: https://dx.doi.org/10.1371/journal.ppat.1003241

Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1219002110/-/DCSupplemental

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012. url: https://dx.doi.org/10.1128/EC.00228-12

 High Impact

TPP1 OB-Fold Domain Controls Telomere Maintenance by Recruiting Telomerase to Chromosome Ends

Zhonget al. Cell. 2012. url: https://dx.doi.org/10.1016/j.cell.2012.07.012

The P granule component PGL-1 promotes the localization and silencing activity of the PUF protein FBF-2 in germline stem cells

Voronina et al. Development and Stem Cells. 2012. url: https://dx.doi.org/10.1242/dev.083980

 High Impact

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

Orjalo et al. Nature Methods. 2011. url: http://www.nature.com/nmeth/journal/v8/n10/pdf/nmeth.f.349.pdf
Collapse Quasar 570 Publications

Quasar 670

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

 High Impact

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. Nature Microbiology. 2016. url: https://dx.doi.org/10.1038/NMICROBIOL.2016.55

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

 High Impact

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1503157112

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

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MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

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Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013. url: https://dx.doi.org/10.1021/ac303792p

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Memczak et al. Nature Article. 2013. url: https://dx.doi.org/10.1038/nature11928

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Bolt et al. Nucleic Acids Research. 2013. url: https://dx.doi.org/10.1093/nar/gkt100

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Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans

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Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

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Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

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Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

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The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

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Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

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Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

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New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

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Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

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CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

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A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

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Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

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Differential Expression of Galectin-1 and Galectin-3 in Canine Nonmalignant and Malignant Mammary Tissues, and in Progression to Metastases in Mammary Tumours

Oliveira JT et al. Anticancer Research. 2014. url: http://www.ncbi.nlm.nih.gov/pubmed/24778023

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Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014. url: https://dx.doi.org//10.1016/j.molcel.2014.01.026

Receptor-interacting protein kinase 2 promotes triple-negative breast cancer cell migration and invasion via activation of nuclear factor-kappaB and c-Jun N-terminal kinase pathways

Singel et al. Breast Cancer Research. 2014. url: https://dx.doi.org/10.1186/bcr3629

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

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Singel et al. Neoplasia. 2014. url: https://dx.doi.org/10.1016/j.neo.2014.03.008

Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation

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O’Grady et al. Journal of Virology. 2014. url: https://dx.doi.org/10.1128/JVI.02989-13

Orsay,Santeuil and LeBlancviruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

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Burdick et al. PNAS PLUS. 2013. url: https://dx.doi.org/10.1073/pnas.1315996110

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Determinants of robustness in spindle assembly checkpoint signalling

Heinrich et al. Nature Cell Biology. 2013. url: https://dx.doi.org/10.1038/ncb2864

Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013. url: https://dx.doi.org/10.1016/j.virol.2013.09.024

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

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Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans

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Schreiberet al. Nature Microbiology. 2016. url: https://dx.doi.org/10.1038/NMICROBIOL.2016.55

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Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

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Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

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Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

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Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

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Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

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Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

The Novel Small Leucine-rich Protein Chondroadherin-like (CHADL) Is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The Journal of Biological Chemistry. 2015. url: https://dx.doi.org/10.1074/jbc.M114.593541

Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The American Society for Biochemistry and Molecular Biology. 2014. url: https://dx.doi.org/10.1074/jbc.M114.593541

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Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

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Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans

Garcia et al. Nature structural & molecular biology. 2014. url: https://dx.doi.org/10.1038/nsmb.2858

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.02.020

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Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014. url: https://dx.doi.org/10.1038/nature13852

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013. url: https://dx.doi.org/10.1242/dev.096313

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Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013. url: https://dx.doi.org/10.1016/j.celrep.2013.07.045

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013. url: https://dx.doi.org/10.1073/pnas.1303400110

Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013. url: https://dx.doi.org/10.1021/ac303792p

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Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

Kuseket al. Cell Stem Cell. 2012. url: https://dx.doi.org/10.1016/j.stem.2012.06.006

Gene location and DNA density determine transcription factor distributions in Escherichia coli

Kuhlmanet al. Molecular Systems Biology. 2012. url: https://dx.doi.org/10.1038/msb.2012.42

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Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011. url: https://dx.doi.org/10.1038/nature10665
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Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016. url: https://dx.doi.org/10.1038/nmeth.3899

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p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016. url: https://dx.doi.org/10.1038/nm.4135

Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw596

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Altered RNA processing and export leads to retention of mRNAs near transcription sites, nuclear pore complexes, or within the nucleolus

Paulet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/

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Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Akanumaet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11963

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.11642

An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription

Djavadianet al. PLOS Pathogens. 2016. url: https://dx.doi.org/10.1371/journal.ppat.1005718

The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

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Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.138560

Soluble calcium-binding proteins (SCBPs) of the earthworm Lumbricus terrestris: molecular characterization and localization by FISH in muscle and neuronal tissue

Thiruketheeswaranet al. Histochemistry and Cell Biology. 2016. url: https://dx.doi.org/10.1007/s00418-016-1463-2

Perturbing HIV-1 genomic RNA subcellular location inhibits virus particle production

Beckeret al. bioRxiv. 2016. url: https://dx.doi.org/10.1101/057299

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Transcriptional enhancement of Smn levels in motoneurons is crucial for proper axon morphology in zebrafish

Spiroet al. Nature Scientific Reports. 2016. url: https://dx.doi.org/10.1038/srep27470

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Sallamet al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17674

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A small molecule improves Cas9 specificity

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Ebola virus does not induce stress granule formation during infection and sequesters stress granule proteins within viral inclusions

Nelsonet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00459-16

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Stahlet al. Science. 2016. url: https://dx.doi.org/10.1126/science.aaf2403

 High Impact

lnc-β-Catm elicits EZH2-dependent β-catenin stabilization and sustains liver CSC self-renewal

Zhuet al. Nature structural & molecular biology. 2016. url: https://dx.doi.org/10.1038/nsmb.3235

Nuclear speckles are detention centers for transcripts containing expanded CAG repeats

Urbaneket al. BBA Molecular Basis of Disease. 2016. url: https://dx.doi.org/10.1016/j.bbadis.2016.05.015

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016. url: https://dx.doi.org/10.1242/dev.130278

 High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.04.054

Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016. url: https://dx.doi.org/10.1016/j.biomaterials.2016.05.022

Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016. url: https://dx.doi.org/10.7554/eLife.13065

RNA LOCALIZATION Finding FISH in a small pond

Janet al. eLIFE Insight. 2016. url: https://dx.doi.org/10.7554/eLife.16598

Microfluidic Approaches to Fluorescence In Situ Hybridization (FISH) for Detecting RNA Targets in Single Cells

Meagheret al. Microfluidic Methods for Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-3-319-30019-1_5

Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016. url: https://dx.doi.org/10.1038/bjc.2016.123

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016. url: https://dx.doi.org/

 High Impact

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. Nature Microbiology. 2016. url: https://dx.doi.org/10.1038/NMICROBIOL.2016.55

 High Impact

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldneret al. Nature Letter. 2016. url: https://dx.doi.org/10.1038/nature17939

IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

Kochanet al. Biology Open. 2016. url: https://dx.doi.org/10.1242/bio.018010

 High Impact, Triplex

Wnt Ligands Secreted by Subepithelial Mesenchymal Cells Are Essential for the Survival of Intestinal Stem Cells and Gut Homeostasis

Valentaet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.03.088

The Caenorhabditis elegans Protein FIC-1 Is an AMPylase That Covalently Modifies Heat-Shock 70 Family Proteins, Translation Elongation Factors and Histones

Truttmannet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1006023

CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

Pribadiet al. Cold Spring Harbor Laboratory Press. 2016. url: https://dx.doi.org/10.1101/051193

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Suk-Yoonet al. MethodsX. 2016. url: https://dx.doi.org/10.1016/j.mex.2016.05.001

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies

Ramananet al. Virology. 2016. url: https://dx.doi.org/10.1016/j.virol.2016.04.020

Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/7651_2016_356

 High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016. url: https://dx.doi.org/10.1016/j.molcel.2016.03.007

 High Impact

Th17 Cells Are Preferentially Infected Very Early after Vaginal Transmission of SIV in Macaques

Stiehet al. Cell Host & Microbe. 2016. url: https://dx.doi.org/10.1016/j.chom.2016.03.005

Single-Gene Dual-Color Reporter Cell Line to Analyze RNA Synthesis in vivo

Palangatet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.04.009

 High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016. url: https://dx.doi.org/10.1016/j.cell.2016.02.054

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016. url: https://dx.doi.org/10.1128/mBio.00431-16

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription

Leeet al. Molecular and Cellular Endocrinology. 2016. url: https://dx.doi.org/10.1016/j.mce.2016.04.001

DDX3 Interacts with Influenza A Virus NS1 and NP Proteins and Exerts Antiviral Function through Regulation of Stress Granule Formation

Thulasi-Ramanet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Methods for studying RNA localization in bacteria

Kannaiahet al. Methods. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.010

 High Impact

Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

Xuet al. Nature. 2016. url: https://dx.doi.org/10.1038/cddis.2016.57

Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

Falliniet al. The Journal of Neuroscience. 2016. url: https://dx.doi.org/10.1523/JNEUROSCI.2396-15.2016

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016. url: https://dx.doi.org/10.1371/journal.pgen.1005918

 High Impact

Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms11099

Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

Guoet al. Journal of Virology. 2016. url: https://dx.doi.org/10.1128/JVI.00036-16

 High Impact

Localized Translation of gurken/TGF-a mRNA during Axis Specification Is Controlled by Access to Orb/ CPEB on Processing Bodies

Davidsonet al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.02.038

CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016. url: https://dx.doi.org/10.1016/j.scr.2016.03.003

cAMP/CREB-regulated LINC00473 marks LKB1- inactivated lung cancer and mediates tumor growth

Chenet al. The Journal of Clinical Investigation. 2016. url: https://dx.doi.org/10.1172/JCI85250

Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016. url: https://dx.doi.org/10.1073/pnas.1521826113

 High Impact

Single-cell differences in matrix gene expression do not predict matrix deposition

Coteet al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10865

Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016. url: https://dx.doi.org/10.1002/cne.23875

Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016. url: https://dx.doi.org/10.1101/gad.275958.115.

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Carlevaro-Fitaet al. Cold Spring Harbor Laboratory Press for the RNA Society. 2016. url: https://dx.doi.org/10.1261/rna.053561.115

Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016. url: https://dx.doi.org/10.1186/s12864-016-2482-z

 High Impact

Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016. url: https://dx.doi.org/10.1016/j.celrep.2016.01.045

A continuum model of transcriptional bursting

Corriganet al. Genes and Chromosomes. 2016. url: https://dx.doi.org/10.7554/eLife.13051.001

Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016. url: https://dx.doi.org/10.1016/j.ydbio.2016.02.013

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016. url: https://dx.doi.org/10.1016/bs.ctdb.2015.11.024

 CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016. url: https://dx.doi.org/10.1016/j.cell.2016.01.038

 High Impact

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016. url: https://dx.doi.org/10.1016/j.stem.2016.01.001

RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016. url: http://www.ncbi.nlm.nih.gov/pubmed/?term=RNase+P+Protein+Subunit%2C+Rpp29%2C+Represses+Histone+H3.3+Nucleosome+Deposition

 High Impact

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

Stojic et al. Nature Communications. 2016. url: https://dx.doi.org/10.1038/ncomms10406

Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016. url: https://dx.doi.org/10.1093/nar/gkw047

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016. url: https://dx.doi.org/10.1016/j.ymeth.2016.01.018

 High Impact

RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition

Newhartet al. Molecular Biology Cell . 2016. url: https://dx.doi.org/10.1091/mbc.E15-02-0099

DDX3 interacts with influenza A NS1 and NP proteins and exerts antiviral function through regulation of stress granule formation

Thulasi Raman et al. JVI. 2016. url: https://dx.doi.org/10.1128/JVI.03010-15

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Quinn et al. Genes & Development. 2016. url: https://dx.doi.org/10.1101/gad.272187

Brain regions and molecular pathways responding to food reward type and value in honey bees

Matthew S McNeill et al. Genes, Brain, and Behavior. 2016. url: https://dx.doi.org/10.1111/gbb.12275

 High Impact

Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Han et al. Nature materials. 2016. url: https://dx.doi.org/10.1038/NMAT4520

 Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5

Simultaneous RNA–DNA FISH

Lai et al. Methods in Molecular Biology. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_11

 High Impact

Stellaris® RNA Fluorescence In Situ Hybridization for the Simultaneous Detection of Immature and Mature Long Noncoding RNAs in Adherent Cells

Orjalo et al. Methods in Molecular Biology 1402 Springer Protocols. 2016. url: https://dx.doi.org/10.1007/978-1-4939-3378-5_10

Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016. url: https://dx.doi.org/10.1158/1078-0432.CCR-14-2796

Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016. url: https://dx.doi.org/10.1530/REP-15-0301

Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016. url: https://dx.doi.org/10.1016/bs.mie.2016.01.010

 High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015. url: https://dx.doi.org/

Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015. url: https://dx.doi.org/10.1242/dev.128918

In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p

Smith et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1121.abstract

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015. url: http://jcb.rupress.org/content/211/6/1131.abstract

Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv1368

Methods for studying RNA localization in bacteria

Kannaiah et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.010

 High Impact

A Polyadenylation-Dependent 3' End Maturation Pathway Is Required for the Synthesis of the Human Telomerase RNA

Nguyen et al. Cell . 2015. url: https://dx.doi.org/10.1016/j.celrep.2015.11.003

X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015. url: http://www.spandidos-publications.com/10.3892/ijmm.2014.2044

 FLOW-FISH

Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status

Vir et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0144904

Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.12.007

Studying epigenomics in single cells: what is feasible and what can we learn?

Wills et al. Epigenetics. 2015. url: https://dx.doi.org/10.2217/epi.15.93

Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015. url: https://dx.doi.org/10.1210/me.2015-1144

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005680

A conserved abundant cytoplasmic long noncoding RNA modulates repression of mRNAs by PUM2 in human cells

Tichon et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/033423

Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015. url: https://dx.doi.org/10.1042/BST20150169

 High Impact

Gene essentially and synthetic lethality in haploid human cells

Blomen et al. Science. 2015. url: http://www.sciencemag.org/content/350/6264/1092

 High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep17295

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.017

 High Impact

The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015. url: http://www.nature.com/doifinder/10.1038/ng.3449

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005692

Engineering Duplex RNAs for Challenging Targets: Recognition of GGGGCC/CCCCGG Repeats at the ALS/FTD C9orf72 Locus

Hu et al. Cell Chemistry & Biology. 2015. url: https://dx.doi.org/10.1016/j.chembiol.2015.09.016

Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015. url: http://linkinghub.elsevier.com/retrieve/pii/S1046202315301559

 High Impact

Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.028

Can we observe changes in mRNA “state”? Overview of methods to study mRNA interactions with regulatory proteins relevant in cancer related

Zurla et al. Analyst. 2015. url: https://dx.doi.org/10.1039/C5AN01959A

Nonspreading Rift Valley Fever Virus Infection of Human Dendritic Cells Results in Downregulation of CD83 and Full Maturation of Bystander Cells

Oreshkova et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0142670

Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.ymeth.2015.11.008

 High Impact

Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis

Liang et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.09.021

Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015. url: https://dx.doi.org/10.1002/dneu.22360

Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I

Xu et al. The American Society for Molecular Biology. 2015. url: https://dx.doi.org/10.1128/mBio.01265-15

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015. url: http://www.biotechniques.com/BiotechniquesJournal/2015/October/Simultaneous-detection-of-mRNA-and-protein-in-single-cells-using----immunofluorescence-combined-single-molecule-RNA-FISH/biotechniques-360938.html

Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015. url: https://dx.doi.org/10.1101/027870

A BRCA1-interacting lncRNA regulates homologous recombination

Sharma et al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540437

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1509317112

 High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14966

Female bias in systemic lupus erythematosus is associated with the differential expression of X-linked toll-like receptor 8

McDonald et al. frontiers in Immunology. 2015. url: https://dx.doi.org/10.3389/fimmu.2015.00457

Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1503157112

Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015. url: https://dx.doi.org/10.18632/oncotarget.5129

Application of an RNA amplification method for reliable single-cell transcriptome analysis

Suslov et al. BioTechniques. 2015. url: http://www.biotechniques.com/multimedia/archive/00251/BTN_A_000114331_O__251167a.pdf  

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.07957

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv839

 High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep13339

 High Impact

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis et al. Neuron Cell. 2015. url: https://dx.doi.org/10.1016/j.neuron.2015.07.031

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201504117

Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome

Deuve et al. Epigenetics. 2015. url: https://dx.doi.org/10.1080/15592294.2015.1081327

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mod.2015.08.004

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Kumar et al. Genome Research. 2015. url: https://dx.doi.org/10.1101/gr.184978.114

 High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.06.016

 Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015. url: http://www.nature.com/doifinder/10.1038/ncomms8962

mRNA encoding Sec61β, a tail-anchored protein, is localized on the endoplasmic reticulum

Cui et al. The Company of Biologists Ltd., Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.168583

 High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3214

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

Senti et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.267252.115

MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015. url: https://dx.doi.org/10.1016/j.ydbio.2015.04.025

A Novel Antiviral Target Structure Involved in the RNA Binding, Dimerization, and Nuclear Export Functions of the Influenza A Virus Nucleoprotein

Kakisaka et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1005062

Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0134458

Propionibacterium acnes Recovered from Atherosclerotic Human Carotid Arteries Undergoes Biofilm Dispersion and Releases Lipolytic and Proteolytic Enzymes in Response to Norepinephrine Challenge In Vitro

Lanter et al. Infection and Immunity. 2015. url: https://dx.doi.org/10.1128/IAI.00510-15

Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26255629

Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv731

Single Cell Analysis Reveals Concomitant Transcription of Pluripotent and Lineage Markers During the Early Steps of Differentiation of Embryonic Stem Cells

Lanctôt et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.2108

 High Impact

G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.06.013

Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015. url: https://dx.doi.org/10.1016/j.nbd.2015.07.006

Identification of Barramundi (Lates calcarifer) DC-SCRIPT, a Specific Molecular Marker for Dendritic Cells in Fish

Zoccola et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0132687

Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015. url: https://dx.doi.org/10.1242/jcs.158436

MERFISHing for spatial context

Shalek et al. Trends in Immunology. 2015. url: https://dx.doi.org/

New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription

Cao et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.00608-15

 High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/nmeth.3446

 High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015. url: https://dx.doi.org/10.1038/nature14321

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.09214

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015. url: https://dx.doi.org/10.15252/embr.201540538

Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20156198

Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip†

Shaffer et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5lc00459d

Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Hassanet al. Bone. 2015. url: https://dx.doi.org/10.1016/j.bone.2015.05.026

 High Impact

Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep09934

 High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015. url: https://dx.doi.org/10.1038/nature14413

 High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015. url: https://dx.doi.org/10.1016/j.cub.2015.03.028

Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0125315

 High Impact

Putting transcriptomics in its place

Burgess et al. Nature Research Highlights. 2015. url: https://dx.doi.org/10.1038/nrg3951

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005121

Single-Molecule Imaging of PSD-95 mRNA Translation in Dendrites and Its Dysregulation in a Mouse Model of Fragile X Syndrome

Ifrim et al. The Journal of Neuorscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.2802-14.2015

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1421197112

 High Throughput

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015. url: https://dx.doi.org/10.15252/msb.20145704

CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015. url: http://www.ncbi.nlm.nih.gov/pubmed/26124921

Tuning noise in gene expression

Tyagi et al. Molecular Systems Biology. 2015. url: https://dx.doi.org/10.15252/msb.20156210

The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015. url: https://dx.doi.org/10.1371/journal.pone.0124792

Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015. url: https://dx.doi.org/10.1039/c5ay00500k

Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015. url: https://dx.doi.org/10.1039/c5ib00057b

 High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa6090

 High Impact

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

Padovan-Merhar et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.03.005

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis

Osborne Nishimura et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005117

Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis

Kukharsky et al. Molecular Neurodegeneration. 2015. url: https://dx.doi.org/10.1186/s13024-015-0014-y

 High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.cell.2015.03.025

Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015. url: https://dx.doi.org/10.1021/acs.biochem.5b00259

 High Impact

A Noisy Tug of War: The Battle between Transcript Production and Degradation in the Liver

Lam et al. Cell. 2015. url: https://dx.doi.org/10.1016/j.devcel.2015.03.019

 High Impact

Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015. url: https://dx.doi.org/10.1038/ncb3143

 High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015. url: https://dx.doi.org/10.1016/j.molcel.2015.01.027

 High Impact

The Long Noncoding RNA lncTCF7 Promotes Self-Renewal of Human Liver Cancer Stem Cells through Activation of Wnt Signaling

Wang et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2015.03.003

Mining the Human Complexome Database Identifies RBM14 as an XPO1-Associated Protein Involved in HIV-1 Rev Function

Budhiraja et al. Journal of Virology. 2015. url: https://dx.doi.org/10.1128/JVI.03232-14

Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015. url: https://dx.doi.org/10.1101/gad.259358.115

 Machine Learning

Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images

Wu et al. BMC Bioinformatics. 2015. url: https://dx.doi.org/10.1186/s12859-015-0534-z

 High Impact

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

L'eveill'e et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7520

 High Impact

An RNA biosensor for imaging the first round of translation from single cells to living animals

Halstead et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa3380

 High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015. url: http://www.sciencemag.org/cgi/doi/10.1126/science.1258849

CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015. url: https://dx.doi.org/10.1242/dev.121434

Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus

McNeill et al. Insect Molecular Biology. 2015. url: https://dx.doi.org/10.1111/imb.12165

Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015. url: https://dx.doi.org/10.1073/pnas.1502461112

Expanded GAA repeats impair FXN gene expression and reposition the FXN locus to the nuclear lamina in single cells

Silva et al. Human Molecular Genetics, Oxford. 2015. url: https://dx.doi.org/10.1093/hmg/ddv096

The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation

Lee et al. Nucleic Acids Research. 2015. url: https://dx.doi.org/10.1093/nar/gkv156

Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015. url: https://dx.doi.org/10.1002/stem.1992

Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005019

The Bicoid Class Homeodomain Factors ceh-36/OTX and unc-30/PITX Cooperate in C. elegans Embryonic Progenitor Cells to Regulate Robust Development

Walton et al. PLOS Genetics. 2015. url: https://dx.doi.org/10.1371/journal.pgen.1005003

 High Impact

Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015. url: https://dx.doi.org/10.1038/srep08571

PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015. url: https://dx.doi.org/10.1083/jcb.201407105

 High Impact

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015. url: https://dx.doi.org/10.1126/science.aaa1934

Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015. url: https://dx.doi.org/10.1242/dev.123273

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015. url: https://dx.doi.org/10.1091/mbc.E14-08-1296

A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015. url: https://dx.doi.org/10.1371/journal.ppat.1004583

 High Impact

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

Patil et al. Science Signaling. 2015. url: https://dx.doi.org/10.1126/scisignal.2005728

Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

Lee et al. Molecular and Cellular Endocrinology, Elsevier. 2015. url: https://dx.doi.org/10.1016/j.mce.2015.01.022

 High Impact

Ascl2 Acts as an R-spondin/Wnt-Responsive Switch to Control Stemness in Intestinal Crypts

Schuijers et al. Cell Stem Cell. 2015. url: https://dx.doi.org/10.1016/j.stem.2014.12.006

Regulation of Mechanosensation in C. elegans through Ubiquitination of the MEC-4 Mechanotransduction Channel

Chen et al. The Journal of Neuroscience. 2015. url: https://dx.doi.org/10.1523/JNEUROSCI.4082-14.2015

Transcriptional Expression of Myelin Basic Protein in Oligodendrocytes Depends on Functional Syntaxin 4: a Potential Correlation with Autocrine Signaling

Bijlardet al. Molecular Cell Biology. 2015. url: https://dx.doi.org/10.1128/MCB.01389-14

 High Impact

Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015. url: https://dx.doi.org/10.1038/ncomms7078

 High Impact

A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015. url: https://dx.doi.org/10.1016/j.celrep.2014.12.029

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015. url: https://dx.doi.org/10.7554/eLife.05007.001

The Novel Small Leucine-rich Protein Chondroadherin-like (CHADL) Is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The Journal of Biological Chemistry. 2015. url: https://dx.doi.org/10.1074/jbc.M114.593541

Genome-Wide Analysis of Protein and mRNA Copy Numbers in Single Escherichia coli Cells with Single- Molecule Sensitivity

Taniguchi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2987-0_5

Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_20

 lncRNA probe set validation

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

Cabili et al. GenomeBiology. 2015. url: https://dx.doi.org/10.1186/s13059-015-0586-4

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015. url: https://dx.doi.org/10.1530/REP-14-0394

Molekulárna cytogenetika v problematike familiárnych malignít

Konečný et al. Hlavná téma. 2015. url: http://www.solen.sk/index.php/index.php?page=magazine_detail&issue_id=664&article_id=10288

Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Hassan et al. Elsevier, Bone. 2015. url: https://dx.doi.org/10.1016/j.bone.2015.05.026

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015. url: https://dx.doi.org/10.1007/978-1-4939-1369-5_11

Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2851-4_9

The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015. url: https://dx.doi.org/10.1101/gad.255810.114

Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015. url: https://dx.doi.org/10.1007/978-1-4939-2253-6_1

 Microbe Screen

A metagenomic approach from aphid’s hemolymph sheds light on the potential roles of co-existing endosymbionts

De Clerck et al. Microbiome. 2015. url: https://dx.doi.org/10.1186/s40168-015-0130-5

Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0116037

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically-disordered proteins in C. elegans

Wang et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.04591

 High Impact

Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6812

 High Impact

Promoter architecture dictates cell-to-cell variability in gene expression

Jones et al. Science. 2014. url: https://dx.doi.org/10.1126/science.1255301

Self-digitization microfluidic chip for absolute quantification of mRNA in single cells

Thompson et al. Analytical Chemistry. 2014. url: https://dx.doi.org/10.1021/ac5035924

Profiling T Cell Activation Using Hybridization and Flow Cytometry Single-Molecule Fluorescence In Situ

Bushkin et al. The Journal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

Profiling T Cell Activation Using Single-Molecule Fluorescence In Situ Hybridization and Flow Cytometry

Bushkin et al. The Jornal of Immunology. 2014. url: https://dx.doi.org/10.4049/jimmunol.1401515

 Super-resolution

Second Harmonic Super-resolution Microscopy for Quantification of mRNA at Single Copy Sensitivity

Liu et al. ACS Nano. 2014. url: https://dx.doi.org/10.1021/nn505096t

Jayaraman et al. eLife 2014;3:e04120. DOI: 10.7554/eLife.04120 1 of 17 RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev–Rev response element complex

Jayaraman et al. eLife, Biochemistry, Microbiology and infectious disease. 2014. url: https://dx.doi.org/10.7554/eLife.04120.001

 High Impact

Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014. url: https://dx.doi.org/10.1016/j.cell.2014.10.059

Novel Small Leucine-Rich Protein Chondroadherin-like (CHADL) is Expressed in Cartilage and Modulates Chondrocyte Differentiation*

Tillgren et al. The American Society for Biochemistry and Molecular Biology. 2014. url: https://dx.doi.org/10.1074/jbc.M114.593541

 Plant

Lignin and lignans in plant defence: Insight from expression profiling of cinnamyl alcohol dehydrogenase genes during development and following fungal infection in Populus

Bagniewska-Zadworna et al. Plant Science. 2014. url: https://dx.doi.org/10.1016/j.plantsci.2014.08.015

Inside single cells: quantitative analysis with advanced optics and nanomaterials

Cui et al. WIREs Nanomedicine and Nanobiotechnology. 2014. url: https://dx.doi.org/10.1002/wnan.1321

 High Impact

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.10.017

 High Impact

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014. url: https://dx.doi.org/10.1038/srep07125

Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014. url: https://dx.doi.org/10.1021/ac5035924

Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014. url: https://dx.doi.org/10.1007/s10126-014-9605-9

Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014. url: http://jvi.asm.org/lookup/doi/10.1128/JVI.02671-14

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

 High Impact

Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms6276

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-ayala et al. The Company of Biologists. 2014. url: https://dx.doi.org/10.1242/dev.114843

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku1014

 High Impact

Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.08.008

The role of antisense long noncoding RNA in small RNA-triggered gene activation

Zhang et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.043968.113

The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014. url: https://dx.doi.org/10.1261/rna.047332.114

 High Impact

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014. url: https://dx.doi.org/10.1038/bcj.2014.67

 High Impact

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

Meisel et al. Cell, Elsevier . 2014. url: https://dx.doi.org/10.1016/j.cell.2014.09.011

Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014. url: https://dx.doi.org/10.1093/nar/gku912

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014. url: https://dx.doi.org/10.7554/eLife.03939

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014. url: https://dx.doi.org/10.1534/genetics.114.168823

Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014. url: https://dx.doi.org/10.1371/journal.pone.0107425

The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014. url: https://dx.doi.org/10.7554/eLife.03164.001

Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014. url: https://dx.doi.org/10.1074/jbc.M114.580688

Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014. url: https://dx.doi.org/10.1371/journal.pgen.1004607

 High Impact

A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014. url: https://dx.doi.org/10.1016/j.devcel.2014.07.018

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

 High Impact

Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014. url: https://dx.doi.org/10.1038/ncomms5798

Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014. url: https://dx.doi.org/10.1002/cne.23666

SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014. url: https://dx.doi.org/10.1016/j.ydbio.2014.05.018

 PACT Clearing, High Impact

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing