Stellaris® RNA FISH Citation Center

Find peer reviewed publications citing Stellaris® RNA FISH probe sets sorted by product, application, model organism and more.

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.

577

Publications

196

Nature, Cell or Science

Stellaris CitationsPapers labeled as Nature, Science, or Cell include sub-groups of these publishing groups such as communications, letters, methods etc.
*Updated March 2017

Stellaris Scoop Research Highlights

Stellaris for study in human pathologies

Reference

Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication.
Kjersti Aagaard et al. Nature Scientific Reports. 2017.

Reference

Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy.
Caroline Woo et al. PNAS PLUS. 2017.

Reference

LncBRM initiates YAP1 signalling activation to drive self-renewal of liver cancer stem cells.
Pingping Zhu et al. Nature Communications. 2016.

Reference

ANRIL: A Regulator of VEGF in Diabetic Retinopathy.
Anu Thomas et al. Investigative Ophthalmology & Visual Science. 2017.

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See our professionally designed Stellaris RNA FISH probe sets by searching our DesignReady RNA FISH probe sets, including our Zika probe sets.

Comprehensive Publication List

Research Focus

miRNAs cooperate in apoptosis regulation during C. elegans development

Sherrardet al. Genes and Development. 2017.
Products: Custom Stellaris Probe Set(s)

Sexually dimorphic control of gene expression in sensory neurons regulates decision-making behavior in C. elegans

Hilbertet al. eLIFE. 2017.
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High Impact

Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD

Yuet al. Nature Communications. 2017

Homeodomain protein Otp affects developmental neuropeptide switching in oxytocin neurons associated with a long-term effect on social behavior

Wirceret al. eLIFE. 2017

sm“FISH”ing for Hedgehog

Drummondet al. Journal of Investigative Dermatology. 2017

High Impact

Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain

Pilazet al. Cell Current Biology. 2016.
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Cover Image

A novel isoform of Drosophila non-muscle Tropomyosin interacts with Kinesin-1 and functions in mRNA localization

Veeranan-Karmegamet al. Journal of Cell Science. 2016.
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The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum

Krasnecet al. BMC Immunology. 2016.
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Super-Resolution

bicoid mRNA localises to the Drosophila oocyte anterior by random Dyneinmediated transport and anchoring

Troviscoet al. eLIFE. 2016

C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool

Leeet al. eLIFE. 2016.
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High Impact

DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

Daneshvaret al. Cell Reports. 2016.
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High Impact

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Petropouloset al. Cell. 2016

Temporal regulation of epithelium formation

Von-Stetinaet al. BioRxiv. 2016.
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Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

Adolpheet al. Journal of Investigative Dermatology. 2016

Meis/UNC-62 isoform dependent regulation of CoupTF-II/UNC-55 and GABAergic motor neuron subtype differentiation

Campbellet al. Developmental Biology. 2016.
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Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

Barkoulaset al. PLOS Genetics. 2016.
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Drosophila Wnt and STAT Define Apoptosis- Resistant Epithelial Cells for Tissue Regeneration after Irradiation

Vergheseet al. PLOS Biology. 2016.
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Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation

Chenet al. Genome Research. 2016.
Products: SMF-3011-1

Dynamics of lineage commitment revealed by single-¬cell transcriptomics of differentiating embryonic stem cells

Semrauet al. bioRxiv. 2016

High Impact

An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

Frokjaer-Jensenet al. Cell. 2016.
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High Impact

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

Akanumaet al. Nature Communications. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016.
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Emerging roles for long noncoding RNAs in skeletal biology and disease

Huynhet al. Connective Tissue Research. 2016

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016.
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Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016.
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High Impact

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

Luoet al. Cell Stem Cell. 2016.
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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

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

Neemset al. PNAS PLUS. 2016.
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High Impact

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

Coteet al. Nature Communications. 2016

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

Ginartet al. Genes and Development. 2016.
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Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016

Structure–function analysis of myomaker domains\ required for myoblast fusion

Millayet al. PNAS. 2016.
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Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016

High Impact

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

Newhartet al. Molecular Biology Cell . 2016

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

Zheng et al. Reproduction. 2016.
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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.
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Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015.
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LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

Carlson et al. PLOS Genetics. 2015.
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High Impact

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

Durruthy-Durruthy et al. Nature Genetics. 2015.
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High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015

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

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

Kumar et al. Genome Research. 2015.
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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.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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.
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High Impact

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

Ruijtenberg et al. Cell. 2015.
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Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015

DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015

High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015.
Products: SMF-3011-1

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

Gibson et al. Royal Society of Chemistry. 2015

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

Campbell et al. The Company of Biologists. 2015.
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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.
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Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015.
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Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015

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

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

Gorman et al. PLOS ONE. 2014

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

Wang et al. eLIFE. 2014.
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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.
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High Impact

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

Junker et al. Cell, Developmental Cell. 2014

High Impact

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

Ochiai et al. Nature Scientific Reports. 2014.
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Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-ayala et al. The Company of Biologists. 2014

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014.
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High Impact

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

Mentink et al. Developmental Cell. 2014

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

Standaert et al. Cold Spring Harbor Laboratory Press. 2014.
Products: SMF-3010-1

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

Weng et al. PLOS Genetics. 2014.
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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.
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SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014

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.
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High Impact

Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014.
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High Impact

The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014

High Impact

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

Stossi et al. Cell Chemistry & Biology. 2014.
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High Impact

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

Mohn et al. Cell. 2014

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

Yücel et al. Developmental Biology, Elsevier. 2014.
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Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology. 2014

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

Xu et al. PLOS Genetics. 2014.
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Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014.
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Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Blood. 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.
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Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

Finn et al. Developmental Biology, Elsevier. 2014.
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Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014.
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High Impact

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

Hacisuleyman et al. Nature structural & molecular biology. 2014.
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Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014

High Impact

Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014.
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High Impact

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

Spillane et al. Cell. 2013.
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Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013.
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Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013.
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High Impact

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

Ji et al. Cell. 2013

High Impact

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

Jiet al. Cell. 2013

Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013.
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High Impact

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

Kimet al. Nature Genetics. 2013

High Impact

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

Kennedy et al. Cell Article. 2013.
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Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013

High Impact

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

Lee et al. Developmental Cell. 2013.
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Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013

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

Tan et al. Development and Stem Cells. 2013.
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Deconvolving the roles of Wnt ligands and receptors in sensing and amplification

Tan et al. Molecular Systems Biology. 2013

High Impact

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

Cochellaet al. Cell. 2012.
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The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012.
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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

Quadraplex Multiplex

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

Jakt et al. Development. 2012

High Impact

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

Barkeret al. Cell Reports. 2012

High Impact

Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012

High Impact

Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 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.
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Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012

High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011.
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Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011.
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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

High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010

High Impact

Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010

A single cell level measurement of StAR expression and activity in adrenal cells

Leeet al. Molecular and Cellular Endocrinology. 2017.
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sm“FISH”ing for Hedgehog

Drummondet al. Journal of Investigative Dermatology. 2017

Potential of long non-coding RNAs in cancer patients: From biomarkers to therapeutic targets

Guptaet al. IJC International Journal of Cancer. 2016

High Impact

LncBRM initiates YAP1 signalling activation to drive self-renewal of liver cancer stem cells

Zhuet al. Nature Communications. 2016

High Impact

Macrophage-dependent tumor cell transendothelial migration is mediated by Notch1/MenaINVinitiated invadopodium formation

Pignatelliet al. Nature Scientific Reports. 2016.
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Primate-specific oestrogen-responsive long non-coding RNAs regulate proliferation and viability of human breast cancer cells

Linet al. Open Biology. 2016.
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Epigenetic inactivation of the p53-induced long noncoding RNA TP53 target 1 in human cancer

Diaz-Lagareset al. PNAS PLUS. 2016.
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Long noncoding RNA ZEB1-AS1 acts as an oncogene in osteosarcoma by epigenetically activating ZEB1

Liuet al. American Journal of Translational Research. 2016.
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High Impact

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression

Niknafset al. Nature Communications. 2016

Long Noncoding RNA lncCAMTA1 Promotes Proliferation and Cancer Stem Cell-Like Properties of Liver Cancer by Inhibiting CAMTA1

Dinget al. International Journal of Molecular Sciences. 2016.
Products: ChIRP

Temporal regulation of epithelium formation

Von-Stetinaet al. BioRxiv. 2016.
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Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

Adolpheet al. Journal of Investigative Dermatology. 2016

The emerging role of long non-coding RNAs in cutaneous melanoma

Leucciet al. Pigment Cell Melanoma. 2016

High Impact

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

Haiyang Guo et al. Nature Genetcs. 2016

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells

Moenkeet al. bioRxiv. 2016.
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Regulation of star by the n-terminal Domain and coinduction of siK1 and Tis11b/Znf36l1 in single cells

Leeet al. Frontiers in Endocrinology. 2016.
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High Impact

LncSox4 promotes the self-renewal of liver tumour-initiating cells through Stat3-mediated Sox4 expression

Chenet al. Nature Communications. 2016

Global transcript structure resolution of high gene density genomes through multi-platform data integration

O’Gradyet al. Nucleic Acids Research. 2016.
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Long noncoding RNA GIHCG promotes hepatocellular carcinoma progression through epigenetically regulating miR-200b/a/429

Suiet al. Journal of Molecular Medicine. 2016.
Products: ChIRP

High Impact

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

Adriaenset al. Nature Medicine. 2016.
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Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer

Meseureet al. British Journal of Cancer. 2016.
Products: SMF-2035-1

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

Chenet al. The Journal of Clinical Investigation. 2016.
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High Impact

Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

Stojicet al. Nature Communications. 2016.
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High Impact

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

Newhartet al. Molecular Biology Cell . 2016

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

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016.
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High Impact

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

Nguyen et al. Cell . 2015.
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p53 genes function to restrain mobile elements

Wylieet al. Genes & Development. 2015.
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Telomerase RNA stem terminus element affects template boundary element function, telomere sequence, and shelterin binding

Webb et al. PNAS. 2015.
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Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015

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

Chandrakesanet al. Oncotarget. 2015

High Impact

Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015.
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Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015.
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Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015

High Impact

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

Ruijtenberg et al. Cell. 2015.
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Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015.
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CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015.
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Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015.
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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

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.
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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.
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Molekulárna cytogenetika v problematike familiárnych malignít

Konečný et al. Hlavná téma. 2015

High Impact

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

S'anchez et al. Nature Communications. 2014

High Impact

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

Freund et al. Cell. 2014.
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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

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

Gordon et al. Nucleic Acids Research. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014.
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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.
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High Impact

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

Stossi et al. Cell Chemistry & Biology. 2014.
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Therapeutic implications of activation of the host gene (Dleu2) promoter for miR-15a/16-1 in chronic lymphocytic leukemia

Kasar et al. Oncogene. 2014

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

Pernicova et al. Molecular Cancer. 2014.
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High Impact

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

Weis et al. Nature Oncogene. 2014

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014

Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature

Facciponte et al. Journal of Clinical Investigation. 2014

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Wooet al. PNAS PlUS. 2017

Neural Progenitor Cells Promote Axonal Growth and Alter Axonal mRNA Localization in Adult Neurons

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Age-Dependent Neuroendocrine Signaling from Sensory Neurons Modulates the Effect of Dietary Restriction on Longevity of Caenorhabditis elegans

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

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

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

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

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

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

Ji et al. Cell. 2013

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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

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Neuronal mRNAs travel singly into dendrites

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Shared gene expression in distinct neurons expressing common selector genes

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

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Nicoletet al. The Journal of Immunology. 2016

Intact NYN/PIN-Like Domain is Crucial for the Degradation of Inflammation-Related Transcripts by ZC3H12D

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The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

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The Mitochondria-Regulated Immune Pathway Activated in the C. elegans Intestine Is Neuroprotective

Chikkaet al. Cell Reports. 2016.
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Aire knockdown in medullary thymic epithelial cells affects Aire protein, deregulates cell adhesion genes and decreases thymocyte interaction

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An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

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Global transcript structure resolution of high gene density genomes through multi-platform data integration

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

Stiehet al. Cell Host & Microbe. 2016.
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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.
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Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

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

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FLOW-FISH

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

Vir et al. PLOS ONE. 2015

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

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

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

Balla et al. PLOS Pathogens. 2015.
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Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-b response to viral infection

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

Bushkin et al. The Journal of Immunology. 2014

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

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

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

Meisel et al. Cell, Elsevier . 2014

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014

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

O’Grady et al. Journal of Virology. 2014.
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Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

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

Panda et al. PNAS. 2014

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

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

Ashe et al. eLIFE. 2013.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013.
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IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013

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

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.
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Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013.
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Microsporidian Infection in a Free-Living Marine Nematode

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

Gaoet al. JVI . 2012

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

Chouet al. PNAS. 2012

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

Singh et al. Molecular Systems Biology. 2012

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Intercellular Transmission of Viral Populations with Vesicles

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Human metapneumovirus Induces Reorganization of the Actin Cytoskeleton for Direct Cell-to-Cell Spread

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A Multicomponent Animal Virus Isolated from Mosquitoes

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Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

Schreuret al. PLOS Pathogens. 2016

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Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia

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A systematic view on influenza induced host shutoff

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Wilburnet al. Retrovirology. 2016

New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes

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

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

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

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

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The lncRNA RZE1 Controls Cryptococcal Morphological Transition

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

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Powellet al. Journal of Cell Biology. 2015

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

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

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

Gibson et al. Royal Society of Chemistry. 2015

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

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

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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses

Chenet al. Cell. 2015

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

De Clerck et al. Microbiome. 2015.
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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.
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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014.
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MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014.
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Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014.
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Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014.
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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

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

Franz et al. Virology, Elsevier. 2013.
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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.
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Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013.
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A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013.
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IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013

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.
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Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013.
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Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012.
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The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012

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

Chouet al. PNAS. 2012

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

Singh et al. Molecular Systems Biology. 2012

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Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication

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Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

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Chromatin decondensation is accompanied by a transient increase in transcriptional output

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RNA decay systems enhance reciprocal switching of sense and antisense transcripts in response to glucose starvation

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Xuet al. Physical kinetics of Nascent RNA. 2016

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Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016

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

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Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip

Pradeppaet al. Cold Spring Harbor Laboratory. 2016

ChIRP

Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip

Pradeepaet al. BioRxiv. 2016

High Impact

Sallamet al. Nature Letter. 2016.
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High Impact

Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016

Lights, camera, action! Capturing the spliceosome and pre-mRNA splicing with single-molecule fluorescence microscopy

DeHavenet al. WIREs RNA. 2016

High Impact

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016

Transcriptional pulsing of a nucleolar transgene

Hausnerovaet al. Cold Spring Harbor Laboratory. 2016.
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A continuum model of transcriptional bursting

Corriganet al. Genes and Chromosomes. 2016.
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RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016.
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Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

Stojicet al. Nature Communications. 2016.
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High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015

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

Stapel et al. Development. 2015.
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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

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

Backlund et al. Nucleic Acids Research. 2015.
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Quantitative spatial analysis of transcripts in multinucleate cells using single-molecule FISH

Lee et al. Methods, Elsevier. 2015.
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Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015

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

The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015.
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Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues

Bahar Halpern et al. Elsevier. 2015.
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High Impact

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

Lenstra et al. Molecular Cell. 2015.
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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.
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Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015.
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RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

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

Suslov et al. BioTechniques. 2015

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015

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

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

Kumar et al. Genome Research. 2015.
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High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015.
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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.
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Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve

Fritz et al. Nucleic Acids Research. 2015.
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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.
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Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015

High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015.
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Single-cell polyadenylation site mapping reveals 3' isoform choice variability

Velten et al. Molecular systems biology. 2015.
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High Impact

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

Hocine et al. Nature Scientific Reports. 2015.
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Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015.
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Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015.
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High Throughput

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

Dey et al. Molecular Systems biology. 2015.
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Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015.
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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

High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015.
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High Impact

Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015

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

Zorca et al. PNAS. 2015

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.
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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

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

Newton et al. The Company of Biologists Ltd.. 2015.
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The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015.
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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.
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High Impact

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

Schuijers et al. Cell Stem Cell. 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

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015.
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The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015

High Impact

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

Jones et al. Science. 2014

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014.
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The long noncoding RNA Neat1 is required for mammary gland development and lactation

Standaert et al. Cold Spring Harbor Laboratory Press. 2014.
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Removal of 8-oxo-GTP by MutT hydrolase is not a major contributor to transcriptional fidelity

Gordon et al. Nucleic Acids Research. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014.
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The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014.
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High Impact

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

Schwabe et al. Nature Communications. 2014

High Impact

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

Schwabe et al. Nature Communications. 2014

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.
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Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014.
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High Impact

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

Liz et al. Molecular Cell. 2014.
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High Impact

The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014

High Impact

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

Stossi et al. Cell Chemistry & Biology. 2014.
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Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014

High Impact

Validation of noise models for single-cell transcriptomics

Grün et al. Nature Methods. 2014

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014.
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High Impact

Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014

High Impact

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

Lee et al. Molecular Cell. 2014.
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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.
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High Impact

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

Hacisuleyman et al. Nature structural & molecular biology. 2014.
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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

High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014.
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A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014.
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Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014

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

Panda et al. PNAS. 2014

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013.
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High Impact

Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013

High Impact

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

Ball et al. Cell Cycle. 2013

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

Shah et al. Molecular Systems Biology. 2013

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013.
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High Impact

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

Guglielmi et al. Molecular Cell. 2013

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013

High Impact

Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs

Faddahet al. Cell Stem Cell. 2013

High Impact

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

Castelnuovo et al. Nature structural & molecular biology. 2013

High Impact

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

Lee et al. Cell. 2013

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

Hensel et al. PLOS Biology. 2013.
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Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW

Graindorge et al. Genes & Development. 2013

High Impact

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013

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

Bolt et al. Nucleic Acids Research. 2013.
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Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013

High Impact

Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013

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

Marín-Béjar et al. Genome Biology. 2013

Quadraplex Multiplex

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

Jakt et al. Development. 2012

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

Yuet al. Development. 2012

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

Kuhlmanet al. Molecular Systems Biology. 2012.
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High Impact

Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011.
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High Impact

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

Vargaset al. Cell. 2011

Cell-to-cell variability of alternative RNA splicing

Wakset al. Molecular Systems Biology. 2011

ATPase activity of the DEAD-box protein Dhh1 controls processing body formation

Mugleret al. eLIFE. 2016.
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Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

Pichonet al. Journal of Cell Biology. 2016

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

High Impact

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016.
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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.
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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.
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High Impact

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015

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

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

Backlund et al. Nucleic Acids Research. 2015.
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Rate control in yeast protein synthesis at the population and single-cell levels

Dacheux et al. Biochemical Society Transactions. 2015.
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Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015

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

Fritz et al. Nucleic Acids Research. 2015.
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High Impact

Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015.
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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.
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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.
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Temporal and spatial regulation of translation in the mammalian oocyte via the mTOR–eIF4F pathway

Susor et al. Nature Communications. 2015.
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Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015.
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The translation elongation factor eEF1A1 couples transcription to translation during heat shock response

Vera et al. eLIFE. 2014.
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Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014.
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The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014.
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Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014

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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.
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High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014.
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N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014.
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High Impact

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

Yoon et al. Nature Communications. 2013

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

Kraut-Cohen et al. Molecular Biology Cell . 2013.
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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.
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Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013.
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Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

Mazumder et al. Molecular Cell Biology. 2013

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012

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

Shihet al. Nucleic Acids Research. 2011

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.
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Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook

Yaoet al. Journal of Molecular Biology. 2017

seqFISH, High Impact

Synthetic recording and in situ readout of lineage information in single cells

Friedaet al. Nature Letter. 2017

High Impact

Molecular memoirs of a cellular family

Becket al. Nature Commentary. 2017

Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights

Heinrichet al. Bioessays. 2017

Imaging mRNA and protein interactions within neurons

Eliscovichet al. PNAS PLUS. 2017.
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sm“FISH”ing for Hedgehog

Drummondet al. Journal of Investigative Dermatology. 2017

Quantitative approaches for investigating the spatial context of gene expression

Leeet al. WIREs Syst Biol Med. 2016

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Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

Hormozet al. Cell Systems. 2016

High Impact, Super-Resolution

Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing

Choet al. Nature Scientific Reports. 2016.
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ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

Chenet al. Nature Methods. 2016.
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Experimental Approaches to Study Genome Packaging of Influenza A Viruses

Iselet al. Viruses. 2016

Visualization of Enhancer-Derived Noncoding RNA

Shibayamaet al. Methods in Molecular Biology. 2016

Visualization of Enhancer-Derived Noncoding RNA

Shibayamaet al. Methods in Molecular Biology. 2016

Understanding RNA-Chromatin Interactions Using Ch romatin I solation by R NA P urifi cation (ChIRP)

Chuet al. Methods in Molecular Biology. 2016

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

Moffittet al. PNAS. 2016.
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Plant, Super Resolution

A method for detecting single mRNA molecules in Arabidopsis thaliana

Duncanet al. Plant Methods. 2016.
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Large-Scale Image-Based Screening and Profiling of Cellular Phenotypes

Bougen-Zhukovet al. Cytometry. 2016

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Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016.
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Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016

seqFISH, High Impact

Dense transcript profiling in single cells by image correlation decoding

Coskunet al. Nature Methods. 2016

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

Stahlet al. Science. 2016

A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016.
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Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016.
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Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016

RNA LOCALIZATION Finding FISH in a small pond

Janet al. eLIFE Insight. 2016

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

Meagheret al. Microfluidic Methods for Molecular Biology. 2016

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

Kochanet al. Biology Open. 2016.
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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

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

Guedeset al. Methods in Molecular Biology. 2016.
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Dissecting Transcriptional Heterogeneity in Pluripotency: Single Cell Analysis of Mouse Embryonic Stem Cells

Guedeset al. Methods in Molecular Biology. 2016

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

Palangatet al. Methods. 2016

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

Methods for studying RNA localization in bacteria

Kannaiahet al. Methods. 2016

CLARITY, High Impact

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016

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.
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Quadraplex multiplex

Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016.
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Simultaneous RNA–DNA FISH

Lai et al. Methods in Molecular Biology. 2016

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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.
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Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016.
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Methods for studying RNA localization in bacteria

Kannaiah et al. Methods. 2015

FLOW-FISH

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

Vir et al. PLOS ONE. 2015

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

Lee et al. Methods, Elsevier. 2015.
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High Impact

Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015

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

Bahar Halpern et al. Elsevier. 2015.
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Quantitative gene expression analysis in Caenorhabditis elegans using single molecule RNA FISH

Bolkov'a et al. Elsevier. 2015.
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Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

Treweeket al. Nature Protocol. 2015

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

Kochan et al. BioTechniques. 2015.
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High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015.
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Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip†

Shaffer et al. Royal Society of Chemistry. 2015

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

Hassanet al. Bone. 2015

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

Xiao et al. Analytical Methods. 2015.
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High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015.
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Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015.
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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

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.
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Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015.
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Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015.
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lncRNA probe set validation

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

Cabili et al. GenomeBiology. 2015

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015.
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Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015

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

Gorman et al. PLOS ONE. 2014

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

Thompson et al. Analytical Chemistry. 2014

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Yang et al. Cell Resource. 2014

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Gregor et al. Cell Trends in Genetics. 2014

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Toran et al. Nature Cell Research. 2014.
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Markey et al. PLOS ONE. 2014

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Coassin et al. Methods in Molecular Biology. 2014.
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Battich et al. Nature Methods. 2013

Turbo FISH, SNP FISH

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Shaffer et al. PLOS ONE. 2013

SNP-FISH, High Impact

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Hansen et al. Nature Communications. 2013

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Lyubimova et al. Nature Protocol. 2013

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Bienko et al. Nature Communications. 2013

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

Rahman et al. Methods of Molecular Biology. 2013

Quadraplex Multiplex

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

Jakt et al. Development. 2012

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RNA imaging in situ

Bakeret al. Nature Methods. 2012

High Impact, super resolution

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

Lubecket al. Nature Methods. 2012

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Chouet al. PNAS. 2012

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Trceket al. Nature Protocol. 2012

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Rajet al. Methods in Enzymology. 2010

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Rajet al. Annual Review of Biophysics. 2009

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Rajet al. Nature Brief Communications. 2008

Back to Top

Organism

Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy

Wooet al. PNAS PlUS. 2017

ANRIL: A Regulator of VEGF in Diabetic Retinopathy

Thomaset al. Investigative Ophthalmology & Visual Science. 2017

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Nicoletet al. The Journal of Immunology. 2016

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LncBRM initiates YAP1 signalling activation to drive self-renewal of liver cancer stem cells

Zhuet al. Nature Communications. 2016

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Melliset al. bioRxiv. 2016

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Niknafset al. Nature Communications. 2016

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Long Noncoding RNA lncCAMTA1 Promotes Proliferation and Cancer Stem Cell-Like Properties of Liver Cancer by Inhibiting CAMTA1

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Conservation of context-dependent splicing activity in distant Muscleblind homologs

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Bercovich-Kinoriet al. eLIFE. 2016

FLOW-FISH

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Wilburnet al. Retrovirology. 2016

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Long noncoding RNA GIHCG promotes hepatocellular carcinoma progression through epigenetically regulating miR-200b/a/429

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FRI0247 The Involvement of The Long Noncoding H19x in tGFβ Signaling and Its Profibrotic Effects in Systemic Sclerosis and Other Fibrotic Diseases

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

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Stahlet al. Science. 2016

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Zhuet al. Nature structural & molecular biology. 2016

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Soldneret al. Nature Letter. 2016

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

Kochanet al. Biology Open. 2016.
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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

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Bartmanet al. Molecular Cell. 2016

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Palangatet al. Methods. 2016

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Nelleset al. Cell. 2016.
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Topologically associated domains enriched for lineage specific genes reveal expression-dependent nuclear topologies during myogenesis

Neemset al. PNAS PLUS. 2016.
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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.
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Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016

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Hausnerovaet al. Cold Spring Harbor Laboratory. 2016.
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RNase P Protein Subunit, Rpp29, Represses Histone H3.3 Nucleosome Deposition

Newhart et al. Molecular Biology Cell . 2016.
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Stojicet al. Nature Communications. 2016.
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Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016

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

Newhartet al. Molecular Biology Cell . 2016

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Lai et al. Methods in Molecular Biology. 2016.
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Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016.
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Identifying Centromeric RNAs Involved in Histone Dynamics In Vivo

Quénetet al. Methods in Enzymology. 2016.
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Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism

Backlund et al. Nucleic Acids Research. 2015.
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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.
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X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015

FLOW-FISH

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

Vir et al. PLOS ONE. 2015

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

Trevino et al. Molecular Endocrinology. 2015

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

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Gene essentially and synthetic lethality in haploid human cells

Blomen et al. Science. 2015.
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RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015.
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The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015.
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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.
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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.
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Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015.
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Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015.
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A BRCA1-interacting lncRNA regulates homologous recombination

Sharma et al. EMBO reports. 2015

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015

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

Hennig et al. The Journal of Cell Biology. 2015.
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Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015.
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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.
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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.
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Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015

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.
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Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015.
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Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015.
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The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015.
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Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015.
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CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015.
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Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

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Chen et al. Science. 2015.
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Padovan-Merhar et al. Molecular Cell. 2015

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Kukharsky et al. Molecular Neurodegeneration. 2015.
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Functional Characterization of Long Noncoding RNA Lnc_bc060912 in Human Lung Carcinoma Cells

Luo et al. Biochemistry . 2015.
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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

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

Wu et al. Genes & Development. 2015.
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L'eveill'e et al. Nature Communications. 2015.
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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.
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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.
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Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015.
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The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015.
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Patil et al. Science Signaling. 2015.
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Knockdown of Nuclear-Retained Long Noncoding RNAs Using Modifi ed DNA Antisense Oligonucleotides

Zong et al. Methods in Molecular Biology. 2015.
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RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015.
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Multi-Scale Imaging and Informatics Pipeline for In Situ Pluripotent Stem Cell Analysis

Gorman et al. PLOS ONE. 2014

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

S'anchez et al. Nature Communications. 2014

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

Bushkin et al. The Jornal of Immunology. 2014

Super-resolution

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

Liu et al. ACS Nano. 2014.
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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.
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Freund et al. Cell. 2014.
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Thompson et al. American Chemical Society. 2014.
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Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014.
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Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014.
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Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014

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

Vera et al. eLIFE. 2014.
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Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014.
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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.
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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.
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Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014.
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Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014.
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Stossi et al. Cell Chemistry & Biology. 2014.
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The role of high cell density in the promotion of neuroendocrine transdifferentiation of prostate cancer cells

Pernicova et al. Molecular Cancer. 2014.
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MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014.
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The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

Mazar et al. Oncotarget. 2014.
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Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014.
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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.
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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.
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KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014.
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Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

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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

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RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014.
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Wang et al. Nature Research Letter. 2014.
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Coassin et al. Methods in Molecular Biology. 2014.
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Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013.
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Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013

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

Battich et al. Nature Methods. 2013

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

Jakobsen et al. PNAS PLUS. 2013

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Turbo FISH: A Method for Rapid Single Molecule RNA FISH

Shaffer et al. PLOS ONE. 2013

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

Shah et al. Molecular Systems Biology. 2013

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.
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Rajet al. Methods in Enzymology. 2010

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Bahar Halpern et al. Cell Reports. 2015

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Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

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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

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AM et al. Oncotarget. 2015

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

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

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

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

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Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014

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

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Yang et al. Cell Resource. 2014

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Klemm et al. Nature Methods. 2014

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Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013

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linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

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Jakt et al. Development. 2012

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Steineet al. Journal of Clinical Investigation. 2011

Cover Image

A novel isoform of Drosophila non-muscle Tropomyosin interacts with Kinesin-1 and functions in mRNA localization

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bicoid mRNA localises to the Drosophila oocyte anterior by random Dyneinmediated transport and anchoring

Troviscoet al. eLIFE. 2016

Stochastic Kinetics of Nascent RNA

Xuet al. Physical kinetics of Nascent RNA. 2016

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Drosophila Wnt and STAT Define Apoptosis- Resistant Epithelial Cells for Tissue Regeneration after Irradiation

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

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Vilmontet al. Development. 2016

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

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Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016

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Patel et al. Nature Cell Biology. 2015.
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Chu et al. Cell. 2015

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Little et al. Nature Cell Biology. 2015

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PolyQ-dependent RNA–protein assemblies control symmetry breaking

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

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

Mohn et al. Cell. 2014

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

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

Panda et al. PNAS. 2014

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Sahai-Hernandez et al. The Company of Biologists Ltd., Development. 2013

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Single-molecule mRNA detection and counting in mammalian tissue

Lyubimova et al. Nature Protocol. 2013

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

Guglielmi et al. Molecular Cell. 2013

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Lee et al. Cell. 2013

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Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

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

Graindorge et al. Genes & Development. 2013

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

Xu et al. PLOS Genetics. 2012.
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Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012

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EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011

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

Rajet al. Methods in Enzymology. 2010

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Rajet al. Nature Brief Communications. 2008

miRNAs cooperate in apoptosis regulation during C. elegans development

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Sexually dimorphic control of gene expression in sensory neurons regulates decision-making behavior in C. elegans

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Age-Dependent Neuroendocrine Signaling from Sensory Neurons Modulates the Effect of Dietary Restriction on Longevity of Caenorhabditis elegans

Fletcheret al. PLOS Genetics. 2017

Structural and Functional Recovery of Sensory Cilia in C. elegans IFT Mutants upon Aging

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A C. elegans Thermosensory Circuit Regulates Longevity through crh-1/CREB-Dependent flp-6 Neuropeptide Signaling

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C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool

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Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

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The Mitochondria-Regulated Immune Pathway Activated in the C. elegans Intestine Is Neuroprotective

Chikkaet al. Cell Reports. 2016.
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Inhibition of Lithium-Sensitive Phosphatase BPNT-1 Causes Selective Neuronal Dysfunction in C. elegans

Meiselet al. Curent Biology. 7-25

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Frokjaer-Jensenet al. Cell. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

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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

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

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

Burdiket al. BMC Genomics. 2016

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

Duet al. Developmental Biology. 2016

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

Bolkov'a et al. Elsevier. 2015.
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RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

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

Stefanakis et al. Neuron Cell. 2015.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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Ruijtenberg et al. Cell. 2015.
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Kratsios et al. Cell Current Biology. 2015.
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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.
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CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

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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

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

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

Chen et al. The Journal of Neuroscience. 2015

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A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015

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

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

Wang et al. eLIFE. 2014.
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Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014

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Meisel et al. Cell, Elsevier . 2014

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014.
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SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014

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

Hirose et al. PLOS Genetics. 2014

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

Yücel et al. Developmental Biology, Elsevier. 2014.
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Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013.
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Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji et al. Cell. 2013

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

Jiet al. Cell. 2013

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

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Regulation of maternal Wnt mRNA translation in C. elegans embryos

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

Kimet al. Nature Genetics. 2013

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

Ashe et al. eLIFE. 2013.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013.
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Kennedy et al. Cell Article. 2013.
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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

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Padovan-Merhar et al. WIREs Syst Biol Med. 2013

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

Tan et al. Molecular Systems Biology. 2013

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

Cochellaet al. Cell. 2012.
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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

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Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 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.
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Burgaet al. Nature Letter. 2011.
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Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011.
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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

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

Topalidou et al. PNAS. 2011

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Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010

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Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010

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

Rajet al. Methods in Enzymology. 2010

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Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010

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Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008

Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest

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Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis

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Babouret al. Cell. 2016.
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RNA decay systems enhance reciprocal switching of sense and antisense transcripts in response to glucose starvation

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Contribution of Bistability and Noise to Cell Fate Transitions Determined by Feedback Opening

Hsuet al. Journal of Molecular Biology. 2016

Size-Dependent Accumulation of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast

Keifenheimet al. BioRxiv. 2016.
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ATPase activity of the DEAD-box protein Dhh1 controls processing body formation

Mugleret al. eLIFE. 2016.
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Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms

Garvey-Brickneret al. Molecular Biology of the Cell. 2016.
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Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus

Paulet al. MBoC. 2016.
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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.
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Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016.
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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

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015

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

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The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015.
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The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chackoet al. PLOS Genetics. 2015.
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Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015.
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Webb et al. PNAS. 2015.
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Hocine et al. Nature Scientific Reports. 2015.
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Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

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Bonde et al. Nucleic Acids Research. 2014.
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Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014

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

Schwabe et al. Nature Communications. 2014

Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

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Lubeck et al. Nature Methods. 2014

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Heinrich et al. Nature Cell Biology. 2013.
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Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Ball et al. Cell Cycle. 2013

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

Kraut-Cohen et al. Molecular Biology Cell . 2013.
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Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013

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

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

Mazumder et al. Molecular Cell Biology. 2013

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

Rahman et al. Methods of Molecular Biology. 2013

Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

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

Lubecket al. Nature Methods. 2012

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Single-mRNA counting using fluorescent in situ hybridization in budding yeast

Trceket al. Nature Protocol. 2012

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

Rajet al. Methods in Enzymology. 2010

Imaging single mRNA molecules in yeast

Youket al. Methods in Enzymology. 2010

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Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008

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Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication

Aagaardet al. Nature Scientific Reports. 2017.
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NES masking regulates HIV-1 Rev trafficking and viral RNA nuclear export

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Altan-Bonnetet al. JVI. 2016

Human metapneumovirus Induces Reorganization of the Actin Cytoskeleton for Direct Cell-to-Cell Spread

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Schreuret al. PLOS Pathogens. 2016

A systematic view on influenza induced host shutoff

Bercovich-Kinoriet al. eLIFE. 2016

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Heterogeneous loss of HIV transcription and proviral DNA from 8E5/LAV lymphoblastic leukemia cells revealed by RNA FISH:FLOW analyses

Wilburnet al. Retrovirology. 2016

New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes

YoungKimet al. PLOS Pathogens. 2016.
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NXT1, a Novel Influenza A NP Binding Protein, Promotes the Nuclear Export of NP via a CRM1-Dependent Pathway

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Hepatitis B virus polymerase localizes to the mitochondria and its terminal protein domain contains the mitochondrial-targeting signal

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

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

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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.
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Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

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

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

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

Shaffer et al. Royal Society of Chemistry. 2015

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

Platt et al. PLOS ONE. 2015.
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The Ubiquitin Proteasome System Plays a Role in Venezuelan Equine Encephalitis Virus Infection

Amaya et al. PLOS ONE. 2015.
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Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015

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.
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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses

Chenet al. Cell. 2015

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.
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Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

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

Chen et al. PNAS PLUS. 2014.
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Global Bidirectional Transcription of the Epstein-Barr Virus Genome 1 During Reactivation

O’Grady et al. Journal of Virology. 2014.
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Sasaki et al. Biochemical and Biophysical Research Communications. 2014

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

Franz et al. Virology, Elsevier. 2013.
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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.
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Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013.
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A deletion polymorphism in the Caenorhabditis elegans RIG-I homolog disables viral RNA dicing and antiviral immunity

Ashe et al. eLIFE. 2013.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013.
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IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication

Jakobsen et al. PNAS PLUS. 2013

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.
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Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013.
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The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

Gaoet al. JVI . 2012

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

Chouet al. PNAS. 2012

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

Singh et al. Molecular Systems Biology. 2012

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Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaisset al. Cell. 2016

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Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia

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Bottset al. G3. 2016.
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Moffittet al. eLIFE. 2016

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Kannaiahet al. Methods. 2016

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

Vir et al. PLOS ONE. 2015

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Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015

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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Fei et al. Science. 2015

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

Gordon et al. Nucleic Acids Research. 2014

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Toran et al. Nature Cell Research. 2014.
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Transcription termination controls prophage maintenance in Escherichia coli genomes

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Skinner et al. Nature Protocol. 2013

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

Kuhlmanet al. Molecular Systems Biology. 2012.
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Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia

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Tajiket al. Nature Materials. 2016.
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New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes

YoungKimet al. PLOS Pathogens. 2016.
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Microsporidia intracellular development relies on Myc interaction network transcription factors in the host

Bottset al. G3. 2016.
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Iyeret al. Nucleic Acids Research. 2016

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

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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016.
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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016

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

Stiehet al. Cell Host & Microbe. 2016.
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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.
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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.
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Hypoxia Up-Regulates Galectin-3 in Mammary Tumor Progression and Metastasis

Oliveira et al. PLOS ONE. 2015.
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Fritz et al. Nucleic Acids Research. 2015.
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Zoccola et al. PLOS ONE. 2015.
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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.
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Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014.
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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014.
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Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014

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

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Application

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CRISPR-Cas9 targeted deletion of the C9orf72 repeat expansion mutation corrects cellular phenotypes in patient-derived iPS cells

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

Guedeset al. Methods in Molecular Biology. 2016

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Leeet al. Molecular and Cellular Endocrinology. 2016

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

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Long non-coding RNA C2dat1 regulates CaMKIIδ expression to promote neuronal survival through the NF-κB signaling pathway following cerebral ischemia

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

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The nuclear basket mediates perinuclear mRNA scanning in budding yeast

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

Trevino et al. Molecular Endocrinology. 2015

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Satory et al. Nucleic Acids Research. 2015

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Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015

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

Shah et al. Journal of Cell Science. 2015

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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Padovan-Merhar et al. Molecular Cell. 2015

High Impact

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Chu et al. Cell. 2015

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

Luo et al. Biochemistry . 2015.
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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

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

Wu et al. Genes & Development. 2015.
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L'eveill'e et al. Nature Communications. 2015.
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Fei et al. Science. 2015

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

Zorca et al. PNAS. 2015

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Silva et al. Human Molecular Genetics, Oxford. 2015.
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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.
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Single-Cell XIST Expression in Human Preimplantation Embryos and Newly Reprogrammed Female Induced Pluripotent Stem Cells

Briggs et al. Stem Cells. 2015.
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PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015

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

Kempe et al. Molecular Biology Cell . 2015.
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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses

Chenet al. Cell. 2015

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Patil et al. Science Signaling. 2015.
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Regulation of Mechanosensation in C. elegans through Ubiquitination of the MEC-4 Mechanotransduction Channel

Chen et al. The Journal of Neuroscience. 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

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Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015.
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lncRNA probe set validation

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Cabili et al. GenomeBiology. 2015

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

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Microbe Screen

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

Gorman et al. PLOS ONE. 2014

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S'anchez et al. Nature Communications. 2014

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

Bushkin et al. The Journal of Immunology. 2014

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

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Liu et al. ACS Nano. 2014.
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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

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Freund et al. Cell. 2014.
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Ochiai et al. Nature Scientific Reports. 2014.
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Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014.
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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014.
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Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014.
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Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014

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

Gordon et al. Nucleic Acids Research. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014.
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Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014

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

Vera et al. eLIFE. 2014.
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Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014.
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Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014.
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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.
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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.
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Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014.
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Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014.
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Stossi et al. Cell Chemistry & Biology. 2014.
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Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014

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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.
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Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

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

Chen et al. PNAS PLUS. 2014.
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Klemm et al. Nature Methods. 2014

High Impact

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Toran et al. Nature Cell Research. 2014.
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Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014

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

Markey et al. PLOS ONE. 2014

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

Mazar et al. Oncotarget. 2014.
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Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014.
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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.
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KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014.
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Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014.
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Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation

O'Grady et al. JVI, Journal of Virology. 2014

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

O’Grady et al. Journal of Virology. 2014.
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Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014.
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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014.
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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

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RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014.
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A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014.
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Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014

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N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014.
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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.
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Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila

Panda et al. PNAS. 2014

KO lncRNA

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

Sauvageau et al. eLIFE. 2013.
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Mitochondria Coordinate Sites of Axon Branching through Localized Intra-axonal Protein Synthesis

Spillane et al. Cell. 2013.
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Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

Lippmann et al. Stem Cells. 2013.
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Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination

Yoon et al. Nature Communications. 2013

High Impact

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

Ji et al. Cell. 2013

Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes

Burdick et al. PNAS PLUS. 2013.
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Determinants of robustness in spindle assembly checkpoint signalling

Heinrich et al. Nature Cell Biology. 2013.
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Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013

Identifying Division Symmetry of Mouse Embryonic Stem Cells: Negative Impact of DNA Methyltransferases on Symmetric Self-Renewal

Jasnos et al. Stem Cell Reports. 2013.
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Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Battich et al. Nature Methods. 2013

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

Ball et al. Cell Cycle. 2013

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

Jakobsen et al. PNAS PLUS. 2013

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

Kraut-Cohen et al. Molecular Biology Cell . 2013.
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Turbo FISH, SNP FISH

Turbo FISH: A Method for Rapid Single Molecule RNA FISH

Shaffer et al. PLOS ONE. 2013

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

Shah et al. Molecular Systems Biology. 2013

SNP-FISH, High Impact

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Hansen et al. Nature Communications. 2013

Transcription termination controls prophage maintenance in Escherichia coli genomes

Menouni et al. PNAS. 2013.
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Gene-Specific Transcriptional Mechanisms at the Histone Gene Cluster Revealed by Single-Cell Imaging

Guglielmi et al. Molecular Cell. 2013

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

Fang et al. PLOS Biology. 2013

High Impact

Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs

Faddahet al. Cell Stem Cell. 2013

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

Castelnuovo et al. Nature structural & molecular biology. 2013

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

Lee et al. Cell. 2013

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

Lee et al. Developmental Cell. 2013.
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Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

Hensel et al. PLOS Biology. 2013.
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Visualization and Analysis of mRNA Molecules Using Fluorescence In Situ Hybridization in Saccharomyces cerevisiae

McIsaac et al. Jove. 2013.
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linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

Maamar et al. Genes & Development. 2013

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

Graindorge et al. Genes & Development. 2013

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Skinner et al. Nature Protocol. 2013.
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Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization

Skinner et al. Nature Protocol. 2013

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.
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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.
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Counting Small RNA in Pathogenic Bacteria

Shepherd et al. Analytical Chemistry. 2013.
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Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays

Rantala et al. Microarrays. 2013

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

Tan et al. Development and Stem Cells. 2013.
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Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

Wong et al. PLOS Pathogens. 2013.
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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013

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

Bolt et al. Nucleic Acids Research. 2013.
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Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells

Mandal et al. PNAS. 2013.
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A versatile genome-scale PCR-based pipeline for high-definition DNA FIISH

Bienko et al. Nature Communications. 2013

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

Mazumder et al. Molecular Cell Biology. 2013

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

Kwon et al. BMBReports. 2013

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Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013

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

Kretz et al. Nature Research Letter. 2013.
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Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013

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

Rahman et al. Methods of Molecular Biology. 2013

Quadraplex Multiplex

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

Jakt et al. Development. 2012

Inducible Control of Subcellular RNA Localization Using a Synthetic Protein-RNA Aptamer Interaction

Belmontet al. PLOS ONE. 2012.
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Kuseket al. Cell Stem Cell. 2012.
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Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

Buganimet al. Cell. 2012

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Zhonget al. Cell. 2012.
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Lubecket al. Nature Methods. 2012

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

Chouet al. PNAS. 2012

Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012

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Single-mRNA counting using fluorescent in situ hybridization in budding yeast

Trceket al. Nature Protocol. 2012

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

Nedelecet al. Journal of Neuorscience. 2012.
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Dynamics of protein noise can distinguish between alternate sources of gene-expression variability

Singh et al. Molecular Systems Biology. 2012

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Yuet al. Development. 2012

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Kuhlmanet al. Molecular Systems Biology. 2012.
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Vargaset al. Cell. 2011

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ncRNA- and Pc2 Methylation-Dependent GeneRelocationbetween NuclearStructures Mediates Gene Activation Programs

Yang et al. Cell. 2011

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Wakset al. Molecular Systems Biology. 2011

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Hebenstreit et al. Molecular Systems Biology. 2011

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Shihet al. Nucleic Acids Research. 2011

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

Topalidou et al. PNAS. 2011

Single Molecule Imaging of RNA In Situ

Batishet al. Methods Molecular Biology. 2011

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

Rajet al. Methods in Enzymology. 2010

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Youket al. Methods in Enzymology. 2010

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalilet al. PNAS. 2009

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Rajet al. Nature Brief Communications. 2008

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Jagannathan et al. Cold Spring Harbor Laboratory Press. 2014.
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Cornilset al. PLOS Genetics. 2016.
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Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaisset al. Cell. 2016

Cover Image

A novel isoform of Drosophila non-muscle Tropomyosin interacts with Kinesin-1 and functions in mRNA localization

Veeranan-Karmegamet al. Journal of Cell Science. 2016.
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The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum

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Linet al. Nature Genetics. 2016.
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Super-Resolution

bicoid mRNA localises to the Drosophila oocyte anterior by random Dyneinmediated transport and anchoring

Troviscoet al. eLIFE. 2016

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A C. elegans Thermosensory Circuit Regulates Longevity through crh-1/CREB-Dependent flp-6 Neuropeptide Signaling

Chenet al. Developmental Cell. 2016.
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seqFISH, High Impact

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

Shahet al. Cell Neuron. 2016

High Impact, Plant

Mutually exclusive sense–antisense transcription at FLC facilitates environmentally induced gene repression

Rosaet al. Nature Communications. 2016.
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C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool

Leeet al. eLIFE. 2016.
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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Petropouloset al. Cell. 2016

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Von-Stetinaet al. BioRxiv. 2016.
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Stochastic Kinetics of Nascent RNA

Xuet al. Physical kinetics of Nascent RNA. 2016

Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

Adolpheet al. Journal of Investigative Dermatology. 2016

Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

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Drosophila Wnt and STAT Define Apoptosis- Resistant Epithelial Cells for Tissue Regeneration after Irradiation

Vergheseet al. PLOS Biology. 2016.
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The Mitochondria-Regulated Immune Pathway Activated in the C. elegans Intestine Is Neuroprotective

Chikkaet al. Cell Reports. 2016.
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Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia

Ballaet al. Nature Microbiology. 2016.
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Plant, Super Resolution

A method for detecting single mRNA molecules in Arabidopsis thaliana

Duncanet al. Plant Methods. 2016.
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Chromatin remodelling and antisense-mediated up-regulation of the developmental switch gene eud-1 control predatory feeding plasticity

Serobyanet al. Nature Communications. 2016.
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Inhibition of Lithium-Sensitive Phosphatase BPNT-1 Causes Selective Neuronal Dysfunction in C. elegans

Meiselet al. Curent Biology. 7-25

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An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

Frokjaer-Jensenet al. Cell. 2016.
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Chenet al. Nature Methods. 2016.
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p53 induces formation of NEAT1 lncRNA-containing paraspeckles that modulate replication stress response and chemosensitivity

Adriaenset al. Nature Medicine. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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ChIRP

Psip1/p52 regulates distal Hoxa genes through activation of lncRNA Hottip

Pradeepaet al. BioRxiv. 2016

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

Mottier-Pavieet al. Developmental Biology. 2016.
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Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016

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

FRI0247 The Involvement of The Long Noncoding H19x in tGFβ Signaling and Its Profibrotic Effects in Systemic Sclerosis and Other Fibrotic Diseases

Pacheraet al. Annals of the Rheumatic Diseases. 2016

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

Stahlet al. Science. 2016

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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016

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

Meseureet al. British Journal of Cancer. 2016.
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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

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

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

Bacharachet al. mBio. 2016.
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Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016.
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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.
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CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016.
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CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016.
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Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016.
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Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016

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

Duet al. Developmental Biology. 2016

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016

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Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016

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Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016

Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016

Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

Quinn et al. Genes & Development. 2016.
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Unequal distribution of 16S mtrRNA at the 2-cell stage regulates cell lineage allocations in mouse embryos

Zheng et al. Reproduction. 2016.
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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.
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Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Han et al. Nature materials. 2016

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Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015

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

Stapel et al. Development. 2015.
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X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015

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Durruthy-Durruthy et al. Nature Genetics. 2015.
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p53 genes function to restrain mobile elements

Wylieet al. Genes & Development. 2015.
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Bolkov'a et al. Elsevier. 2015.
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RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

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Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015

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

Chandrakesan et al. Oncotarget. 2015

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

Chandrakesanet al. Oncotarget. 2015

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

Stefanakis et al. Neuron Cell. 2015.
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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

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015

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Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015.
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Patel et al. Nature Cell Biology. 2015.
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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.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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

Oliveira et al. PLOS ONE. 2015.
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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.
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Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015

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

Ruijtenberg et al. Cell. 2015.
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Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015.
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Xu et al. Nature Communications. 2015.
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Kratsios et al. Cell Current Biology. 2015.
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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.
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Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015

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Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015.
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CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015.
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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.
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Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015

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

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Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015.
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Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

Budakian et al. Science. 2015

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

Newton et al. The Company of Biologists Ltd.. 2015.
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A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015.
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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

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A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015

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.
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Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015.
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Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015.
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The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015

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

De Clerck et al. Microbiome. 2015.
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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.
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A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

Junker et al. Cell, Developmental Cell. 2014

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

Guzman-ayala et al. The Company of Biologists. 2014

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

Mentink et al. Developmental Cell. 2014

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

Standaert et al. Cold Spring Harbor Laboratory Press. 2014.
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Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

Meisel et al. Cell, Elsevier . 2014

Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014.
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Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014.
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A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014.
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Cadherin-8 Expression, Synaptic Localization, and Molecular Control of Neuronal Form in Prefrontal Corticostriatal Circuits

Friedman et al. The Journal of Comparative Neurology. 2014.
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Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

Lin et al. Developmental Cell. 2014.
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The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014

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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.
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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.
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Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014.
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The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn et al. Cell. 2014

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

Yücel et al. Developmental Biology, Elsevier. 2014.
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Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a

Weis et al. Nature Oncogene. 2014

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

Xu et al. PLOS Genetics. 2014.
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Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014

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

Finn et al. Developmental Biology, Elsevier. 2014.
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Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014

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Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014.
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Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013.
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Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013

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

Franz et al. Virology, Elsevier. 2013.
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Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013.
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Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013

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

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

Ashe et al. eLIFE. 2013.
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Orsay, Santeuil and Le Blanc viruses primarily infect intestinal cells in Caenorhabditis nematodes

Franz et al. Virology, Elsevier. 2013.
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Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013.
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Tumour angiogenesis regulation by the miR-200 family

Peot et al. Nature Communications. 2013.
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Lyubimova et al. Nature Protocol. 2013

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

Injury-induced BMP signaling negatively regulates Drosophila midgut homeostasis

Guo et al. Journal of Cell Biology. 2013

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

Graindorge et al. Genes & Development. 2013

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

Memczak et al. Nature Article. 2013.
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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

Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction

Whitehead et al. JCEM Online. 2013

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

Bienko et al. Nature Communications. 2013

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

Kretz et al. Nature Research Letter. 2013.
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Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

Marín-Béjar et al. Genome Biology. 2013

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

Tan et al. Molecular Systems Biology. 2013

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012.
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Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012.
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The CPEB Protein Orb2 Has Multiple Functions during Spermatogenesis in Drosophila melanogaster

Xu et al. PLOS Genetics. 2012.
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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

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

Barkeret al. Cell Reports. 2012

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Extradenticle and Homothorax Control Adult Muscle Fiber Identity in Drosophila

Bryantsevet al. Developmental Cell. 2012

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Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 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.
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Identification of molecular compartments and genetic circuitry in the developing mammalian kidney

Yuet al. Development. 2012

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

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Burgaet al. Nature Letter. 2011.
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Shared gene expression in distinct neurons expressing common selector genes

Topalidou et al. PNAS. 2011.
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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

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

Steineet al. Journal of Clinical Investigation. 2011

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

Topalidou et al. PNAS. 2011

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EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011

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Variability in gene expression underlies incomplete penetrance

Rajet al. Nature Article. 2010

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Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010

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

Rajet al. Methods in Enzymology. 2010

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Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010

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Rajet al. Nature Brief Communications. 2008

Structural and Functional Recovery of Sensory Cilia in C. elegans IFT Mutants upon Aging

Cornilset al. PLOS Genetics. 2016.
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A novel isoform of Drosophila non-muscle Tropomyosin interacts with Kinesin-1 and functions in mRNA localization

Veeranan-Karmegamet al. Journal of Cell Science. 2016.
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Diaz-Lagareset al. PNAS PLUS. 2016.
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bicoid mRNA localises to the Drosophila oocyte anterior by random Dyneinmediated transport and anchoring

Troviscoet al. eLIFE. 2016

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A C. elegans Thermosensory Circuit Regulates Longevity through crh-1/CREB-Dependent flp-6 Neuropeptide Signaling

Chenet al. Developmental Cell. 2016.
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Temporal regulation of epithelium formation

Von-Stetinaet al. BioRxiv. 2016.
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Stochastic Kinetics of Nascent RNA

Xuet al. Physical kinetics of Nascent RNA. 2016

Meis/UNC-62 isoform dependent regulation of CoupTF-II/UNC-55 and GABAergic motor neuron subtype differentiation

Campbellet al. Developmental Biology. 2016.
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Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

Barkoulaset al. PLOS Genetics. 2016.
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Drosophila Wnt and STAT Define Apoptosis- Resistant Epithelial Cells for Tissue Regeneration after Irradiation

Vergheseet al. PLOS Biology. 2016.
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The Mitochondria-Regulated Immune Pathway Activated in the C. elegans Intestine Is Neuroprotective

Chikkaet al. Cell Reports. 2016.
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Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia

Ballaet al. Nature Microbiology. 2016.
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Chromatin remodelling and antisense-mediated up-regulation of the developmental switch gene eud-1 control predatory feeding plasticity

Serobyanet al. Nature Communications. 2016.
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Inhibition of Lithium-Sensitive Phosphatase BPNT-1 Causes Selective Neuronal Dysfunction in C. elegans

Meiselet al. Curent Biology. 7-25

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An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

Frokjaer-Jensenet al. Cell. 2016.
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Microsporidia intracellular development relies on Myc interaction network transcription factors in the host

Bottset al. G3. 2016.
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Memory of cell shape biases stochastic fate decision-making despite mitotic rounding

Akanumaet al. Nature Communications. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016

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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016.
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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

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

Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016.
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Fezf2 Expression in Layer 5 Projection Neurons of Mature Mouse Motor Cortex

Tantirigama et al. The Journal of Comparative Neurology. 2016.
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Overlapping cell population expression profiling and regulatory inference in C. elegans

Burdiket al. BMC Genomics. 2016

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

Duet al. Developmental Biology. 2016

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016

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Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016

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

Zheng et al. Reproduction. 2016.
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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.
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Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos

Stapel et al. Development. 2015.
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RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

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

Stefanakis et al. Neuron Cell. 2015.
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Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015

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Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015.
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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.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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

Ruijtenberg et al. Cell. 2015.
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Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015.
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Wu et al. Nature. 2015.
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Kratsios et al. Cell Current Biology. 2015.
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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.
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CSR-1 and P granules suppress sperm-specific transcription in the C. elegans germline

Campbell et al. The Company of Biologists. 2015.
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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.
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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

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Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015.
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Coordinate post-transcriptional repression of Dpp-dependent transcription factors attenuates signal range during development

Newton et al. The Company of Biologists Ltd.. 2015.
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A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015.
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Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015.
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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.
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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.
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SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yücel et al. Developmental Biology, Elsevier. 2014.
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Spermatid Cyst Polarization in Drosophila Depends upon apkc and the CPEB Family Translational Regulator orb2

Xu et al. PLOS Genetics. 2014.
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Luminal signalling links cell communication to tissue architecture during organogenesis

Durdu et al. Nature Letter. 2014.
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Histone Methylation Restrains the Expression of Subtype-Specific Genes during Terminal Neuronal Differentiation in Caenorhabditis elegans

Zheng et al. PLOS Genetics. 2013.
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Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Jiet al. Cell. 2013

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

Franz et al. Virology, Elsevier. 2013.
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Regulation of maternal Wnt mRNA translation in C. elegans embryos

Oldenbroek et al. The Company of Biologists Ltd., Development. 2013.
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Dampening of expression oscillations by synchronous regulation of a microRNA and its target

Kimet al. Nature Genetics. 2013

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

Franz et al. Virology, Elsevier. 2013.
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Nonautonomous Regulation of Neuronal Migration by Insulin Signaling, DAF-16/FOXO, and PAK-1

Kennedy et al. Cell Article. 2013.
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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

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

Tan et al. Molecular Systems Biology. 2013

Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garcia et al. Eukaryotic Cell. 2012.
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Microsporidian Infection in a Free-Living Marine Nematode

Ardila-Garciaet al. Eukaryotic Cell. 2012.
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Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012

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Predicting mutation outcome from early stochastic variation in genetic interaction partners

Burgaet al. Nature Letter. 2011.
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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

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Variability in gene expression underlies incomplete penetrance

Rajet al. Nature PMC. 2010

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

Rajet al. Methods in Enzymology. 2010

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Making the message clear: visualizing mRNA localization

Weilet al. Cell Review. 2010

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Imaging individual mRNA molecules using multiple singly labeled probes

Rajet al. Nature Brief Communications. 2008

Back to Top

RNA Target Type

miRNAs cooperate in apoptosis regulation during C. elegans development

Sherrardet al. Genes and Development. 2017.
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A single cell level measurement of StAR expression and activity in adrenal cells

Leeet al. Molecular and Cellular Endocrinology. 2017.
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Neural Progenitor Cells Promote Axonal Growth and Alter Axonal mRNA Localization in Adult Neurons

Meriandaet al. eNeuro. 2017

Sexually dimorphic control of gene expression in sensory neurons regulates decision-making behavior in C. elegans

Hilbertet al. eLIFE. 2017.
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Age-Dependent Neuroendocrine Signaling from Sensory Neurons Modulates the Effect of Dietary Restriction on Longevity of Caenorhabditis elegans

Fletcheret al. PLOS Genetics. 2017

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Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD

Yuet al. Nature Communications. 2017

Homeodomain protein Otp affects developmental neuropeptide switching in oxytocin neurons associated with a long-term effect on social behavior

Wirceret al. eLIFE. 2017

Imaging mRNA and protein interactions within neurons

Eliscovichet al. PNAS PLUS. 2017.
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Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest

Bisschopset al. BBA-Molecular Cell Research. 2017.
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Dynamic mRNA Transport and Local Translation in Radial Glial Progenitors of the Developing Brain

Pilazet al. Cell Current Biology. 2016.
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RNA Transport: From Head to Toe in Radial Glial Cells

Ehseset al. Cell Commentary. 2016

Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

Rahmanet al. Nucleic Acids Research. 2016

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Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis

Menget al. Nucleic Acids Research. 2016.
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Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaisset al. Cell. 2016

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Macrophage-dependent tumor cell transendothelial migration is mediated by Notch1/MenaINVinitiated invadopodium formation

Pignatelliet al. Nature Scientific Reports. 2016.
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Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

Hormozet al. Cell Systems. 2016

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The Chromatin Remodeler ISW1 Is a Quality Control Factor that Surveys Nuclear mRNP Biogenesis

Babouret al. Cell. 2016.
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Visualizing adenosine to inosine RNA editing in single mammalian cells

Melliset al. bioRxiv. 2016

Cover Image

A novel isoform of Drosophila non-muscle Tropomyosin interacts with Kinesin-1 and functions in mRNA localization

Veeranan-Karmegamet al. Journal of Cell Science. 2016.
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Intact NYN/PIN-Like Domain is Crucial for the Degradation of Inflammation-Related Transcripts by ZC3H12D

Wawroet al. Journal of Cellular Biochemistry. 2016.
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The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum

Krasnecet al. BMC Immunology. 2016.
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Stabilizing mutations of KLHL24 ubiquitin ligase cause loss of keratin 14 and human skin fragility

Linet al. Nature Genetics. 2016.
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bicoid mRNA localises to the Drosophila oocyte anterior by random Dyneinmediated transport and anchoring

Troviscoet al. eLIFE. 2016

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Super-resolution imaging of fluorescently labeled, endogenous RNA Polymerase II in living cells with CRISPR/Cas9-mediated gene editing

Choet al. Nature Scientific Reports. 2016.
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A C. elegans Thermosensory Circuit Regulates Longevity through crh-1/CREB-Dependent flp-6 Neuropeptide Signaling

Chenet al. Developmental Cell. 2016.
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Size-Dependent Accumulation of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast

Keifenheimet al. BioRxiv. 2016.
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C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool

Leeet al. eLIFE. 2016.
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DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

Daneshvaret al. Cell Reports. 2016.
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ATPase activity of the DEAD-box protein Dhh1 controls processing body formation

Mugleret al. eLIFE. 2016.
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Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient

Adolpheet al. Journal of Investigative Dermatology. 2016

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Moffittet al. PNAS. 2016.
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Meis/UNC-62 isoform dependent regulation of CoupTF-II/UNC-55 and GABAergic motor neuron subtype differentiation

Campbellet al. Developmental Biology. 2016.
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Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

Pichonet al. Journal of Cell Biology. 2016

Drosophila Wnt and STAT Define Apoptosis- Resistant Epithelial Cells for Tissue Regeneration after Irradiation

Vergheseet al. PLOS Biology. 2016.
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Profiling stem cell states in three-dimensional biomaterial niches using high content image informatics

Dhaliwalet al. Acta Biomaterialia. 2016.
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The Mitochondria-Regulated Immune Pathway Activated in the C. elegans Intestine Is Neuroprotective

Chikkaet al. Cell Reports. 2016.
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Conservation of context-dependent splicing activity in distant Muscleblind homologs

Oddoet al. Nucleic Acids Research. 2016.
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Transcription upregulation via force-induced direct stretching of chromatin

Tajiket al. Nature Materials. 2016.
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Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size

Perryet al. Cell Reports. 0216

Aire knockdown in medullary thymic epithelial cells affects Aire protein, deregulates cell adhesion genes and decreases thymocyte interaction

Pezziet al. Molecular Immunology. 2016.
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Dynamics of lineage commitment revealed by single-¬cell transcriptomics of differentiating embryonic stem cells

Semrauet al. bioRxiv. 2016

Plant, Super Resolution

A method for detecting single mRNA molecules in Arabidopsis thaliana

Duncanet al. Plant Methods. 2016.
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Regulation of star by the n-terminal Domain and coinduction of siK1 and Tis11b/Znf36l1 in single cells

Leeet al. Frontiers in Endocrinology. 2016.
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Inhibition of Lithium-Sensitive Phosphatase BPNT-1 Causes Selective Neuronal Dysfunction in C. elegans

Meiselet al. Curent Biology. 7-25

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An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

Frokjaer-Jensenet al. Cell. 2016.
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Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus

Paulet al. MBoC. 2016.
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Nanoscale imaging of RNA with expansion microscopy

Chenet al. Nature Methods. 2016.
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Absolute quantitative measurement of transcriptional kinetic parameters in vivo

Iyeret al. Nucleic Acids Research. 2016

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

Akanumaet al. Nature Communications. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways

Simset al. eLIFE. 2016.
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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.
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The Wnt pathway limits BMP signaling outside of the germline stem cell niche in Drosophila ovaries

Mottier-Pavieet al. Developmental Biology. 2016.
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Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing

Shahet al. Development. 2016

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

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

Beckeret al. bioRxiv. 2016.
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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.
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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.
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Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Stahlet al. Science. 2016

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Influenza virus mRNA trafficking through host nuclear speckles

Moret al. Nature Microbiology. 2016.
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A system to study mechanisms of neuromuscular junction development and maintenance

Vilmontet al. Development. 2016.
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Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons

Zhaoet al. Biomaterials. 2016.
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Spatial organization shapes the turnover of a bacterial transcriptome

Moffittet al. eLIFE. 2016

Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium

Dundonet al. MBoC. 2016.
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Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. . 2016.
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Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Schreiberet al. Nature Microbiology. 2016.
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Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression

Soldneret al. Nature Letter. 2016

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

Kochanet al. Biology Open. 2016.
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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

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

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

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

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

Guedeset al. Methods in Molecular Biology. 2016

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Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

Bartmanet al. Molecular Cell. 2016

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Programmable RNA Tracking in Live Cells with CRISPR/Cas9

Nelleset al. Cell. 2016.
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Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

Bacharachet al. mBio. 2016.
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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

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.
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Transposon Dysregulation Modulates dWnt4 Signaling to Control Germline Stem Cell Differentiation in Drosophila

Upadhyayet al. PLOS Genetics. 2016.
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Regulation of cell-to-cell variability in divergent gene expression

Yanet al. Nature Communications. 2016.
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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.
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CD133 does not enrich for the stem cell activity in vivo in adult mouse prostates

Weiet al. Stem Cell Research. 2016.
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Single-cell differences in matrix gene expression do not predict matrix deposition

Coteet al. Nature Communications. 2016

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

Tantirigama et al. The Journal of Comparative Neurology. 2016.
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Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant

Ginartet al. Genes and Development. 2016.
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Dynamics of CDKN1A in Single Cells Defined by an Endogenous Fluorescent Tagging Toolkit

Stewart-Ornstein et al. Cell Reports. 2016

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Hausnerovaet al. Cold Spring Harbor Laboratory. 2016.
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Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements

Duet al. Developmental Biology. 2016

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Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

Sylwestrak et al. Cell . 2016

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Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016

Single-cell analysis of transcription kinetics across the cell cycle

Skinneret al. eLIFE. 2016.
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Fixed and live visualization of RNAs in Drosophila oocytes and embryos

Abbaszadeh et al. Methods, Elsevier. 2016

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.
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Microstructural heterogeneity directs micromechanics and mechanobiology in native and engineered fibrocartilage

Han et al. Nature materials. 2016

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Long Non-Coding RNAs

Lai et al. Methods in Molecular Biology. 2016.
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Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma

Misiewicz-Krzeminska et al. Clinical Cancer Research. 2016.
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Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern et al. Cell Reports. 2015

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

Stapel et al. Development. 2015.
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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

The nuclear basket mediates perinuclear mRNA scanning in budding yeast

Saroufim et al. The Journal of Cell Biology. 2015

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

Backlund et al. Nucleic Acids Research. 2015.
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FLOW-FISH

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

Vir et al. PLOS ONE. 2015

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

Lee et al. Methods, Elsevier. 2015.
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Differential Regulation of Progesterone Receptor-Mediated Transcription by CDK2 and DNA-PK

Trevino et al. Molecular Endocrinology. 2015

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

Dacheux et al. Biochemical Society Transactions. 2015.
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Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015

p53 genes function to restrain mobile elements

Wylieet al. Genes & Development. 2015.
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Bahar Halpern et al. Elsevier. 2015.
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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.
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Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015

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Xu et al. The American Society for Molecular Biology. 2015.
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Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Kochan et al. BioTechniques. 2015.
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Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015.
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Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015

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

Chandrakesan et al. Oncotarget. 2015

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

Chandrakesanet al. Oncotarget. 2015

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015

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Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015.
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Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015.
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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.
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Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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

Oliveira et al. PLOS ONE. 2015.
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Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015

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

Fritz et al. Nucleic Acids Research. 2015.
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G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015.
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Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015.
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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.
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Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015

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Xu et al. Nature Communications. 2015.
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DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015

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

Velten et al. Molecular systems biology. 2015.
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Promoter-Autonomous Functioning in a Controlled Environment using Single Molecule FISH

Hocine et al. Nature Scientific Reports. 2015.
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Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015.
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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.
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Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

Dey et al. Molecular Systems biology. 2015.
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Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015

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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

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.
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Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015

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Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015.
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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.
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Synonymous modification results in highfidelity gene expression of repetitive protein and nucleotide sequences

Wu et al. Genes & Development. 2015.
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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.
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Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015

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

Campbell et al. The Company of Biologists. 2015.
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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.
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PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015

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

Newton et al. The Company of Biologists Ltd.. 2015.
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The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015.
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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.
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Stimulation of StAR expression by cAMP is controlled by inhibition of highly inducible SIK1 via CRTC2, a co-activator of CREB

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Cabili et al. GenomeBiology. 2015

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Gorman et al. PLOS ONE. 2014

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Mentink et al. Developmental Cell. 2014

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

Gordon et al. Nucleic Acids Research. 2014

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

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Hirose et al. PLOS Genetics. 2014

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

Xu et al. PLOS Genetics. 2014.
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Chen et al. PNAS PLUS. 2014.
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Lubeck et al. Nature Methods. 2014

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

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

Markey et al. PLOS ONE. 2014

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Tantirigama et al. the Journal of Neuroscience. 2014.
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KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

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Bolt et al. Nature Oncogene. 2014

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Wang et al. Nature Research Letter. 2014.
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Ji et al. Cell. 2013

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Kimet al. Nature Genetics. 2013

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Ball et al. Cell Cycle. 2013

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

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Guglielmi et al. Molecular Cell. 2013

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

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Guo et al. Journal of Cell Biology. 2013

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Rantala et al. Microarrays. 2013

Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

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Levesque et al. Nature Communications. 2013

Placental Specific mRNA in the Maternal Circulation Are Globally Dysregulated in Pregnancies Complicated by Fetal Growth Restriction

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Mazumder et al. Molecular Cell Biology. 2013

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Kwon et al. BMBReports. 2013

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Systematic Identification of Signal-Activated Stochastic Gene Regulation

Neuert et al. Science. 2013

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

Rahman et al. Methods of Molecular Biology. 2013

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

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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

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Bryantsevet al. Developmental Cell. 2012

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Neuronal mRNAs travel singly into dendrites

Batishet al. PNAS. 2012

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Trceket al. Nature Protocol. 2012

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Global Analysis of RNA Secondary Structure in Two Metazoans

Liet al. Cell Reports. 2012

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

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Singh et al. Molecular Systems Biology. 2012

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

Yuet al. Development. 2012

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Shihet al. Nucleic Acids Research. 2011

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

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

Topalidou et al. PNAS. 2011

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EGFR/Ras/MAPK Signaling Mediates Adult Midgut Epithelial Homeostasis and Regeneration in Drosophila

Jiang et al. Cell Stem Cell. 2011

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Batishet al. Methods Molecular Biology. 2011

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Rajet al. Nature PMC. 2010

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FRI0247 The Involvement of The Long Noncoding H19x in tGFβ Signaling and Its Profibrotic Effects in Systemic Sclerosis and Other Fibrotic Diseases

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meleet al. Molecular Cell. 2016

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X chromosome inactivation in human parthenogenetic embryonic stem cells following prolonged passaging

Qi et al. International Journal of Molecular Medicine. 2015

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Tichon et al. Cold Spring Harbor Laboratory Press. 2015

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Nair et al. Nature Scientific Reports. 2015

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

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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Wang et al. Cell Stem Cell. 2015

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Essers et al. Cell Reports. 2015

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Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015

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S'anchez et al. Nature Communications. 2014

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Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

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Liz et al. Molecular Cell. 2014.
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The functional characterization of long noncoding RNA SPRY4-IT1 in human melanoma cells

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

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Yoon et al. Nature Communications. 2013

linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis

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Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

Khalilet al. PNAS. 2009

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Intercellular Transmission of Viral Populations with Vesicles

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New World and Old World Alphaviruses Have Evolved to Exploit Different Components of Stress Granules, FXR and G3BP Proteins, for Assembly of Viral Replication Complexes

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

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Porcine reproductive and respiratory syndrome virus utilizes nanotubes for intercellular spread

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

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

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Chenet al. Cell. 2015

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

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

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

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

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

Jakobsen et al. PNAS PLUS. 2013

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.
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Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing

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Gaoet al. JVI . 2012

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

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Pathogen load

Microsporidia intracellular development relies on Myc interaction network transcription factors in the host

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RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

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

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

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Microbe Screen

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

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

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Microsporidian Infection in a Free-Living Marine Nematode

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

Neemset al. PNAS PLUS. 2016.
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Topologically associated domains enriched for lineagespecific genes reveal expression-dependent nuclear topologies during myogenesis

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Structure–function analysis of myomaker domains\ required for myoblast fusion

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Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

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

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Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015

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Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015.
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Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

Ochiai et al. Nature Scientific Reports. 2014.
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Most Human Proteins Made in Both Nucleus and Cytoplasm Turn Over within Minutes

Baboo et al. PLOS ONE. 2014

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Chromosomal Contact Permits Transcription between Coregulated Genes

Fanucchi et al. Cell. 2013

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Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

Levesque et al. Nature Communications. 2013

Back to Top

Multiplexing

Gene activation of SMN by selective disruption of lncRNA-mediated recruitment of PRC2 for the treatment of spinal muscular atrophy

Wooet al. PNAS PlUS. 2017

miRNAs cooperate in apoptosis regulation during C. elegans development

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Primary Human Placental Trophoblasts are Permissive for Zika Virus (ZIKV) Replication

Aagaardet al. Nature Scientific Reports. 2017.
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Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

Rahmanet al. Nucleic Acids Research. 2016

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Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

Hormozet al. Cell Systems. 2016

Visualizing adenosine to inosine RNA editing in single mammalian cells

Melliset al. bioRxiv. 2016

The UT family of MHC class I loci unique to non-eutherian mammals has limited polymorphism and tissue specific patterns of expression in the opossum

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A C. elegans Thermosensory Circuit Regulates Longevity through crh-1/CREB-Dependent flp-6 Neuropeptide Signaling

Chenet al. Developmental Cell. 2016.
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Size-Dependent Accumulation of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast

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DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

Daneshvaret al. Cell Reports. 2016.
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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Petropouloset al. Cell. 2016

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A Multicomponent Animal Virus Isolated from Mosquitoes

Ladneret al. Cell Host & Microbe. 2016.
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Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

Pichonet al. Journal of Cell Biology. 2016

A systematic view on influenza induced host shutoff

Bercovich-Kinoriet al. eLIFE. 2016

Dynamics of lineage commitment revealed by single-¬cell transcriptomics of differentiating embryonic stem cells

Semrauet al. bioRxiv. 2016

Plant, Super Resolution

A method for detecting single mRNA molecules in Arabidopsis thaliana

Duncanet al. Plant Methods. 2016.
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Chromatin remodelling and antisense-mediated up-regulation of the developmental switch gene eud-1 control predatory feeding plasticity

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

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Chenet al. Nature Methods. 2016.
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Iyeret al. Nucleic Acids Research. 2016

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

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Shahet al. Development. 2016

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Influenza virus mRNA trafficking through host nuclear speckles

Moret al. Nature Microbiology. 2016.
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Centromeric Transcription Regulates Aurora-B Localization and Activation

Bloweret al. Cell Reports. 2016

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

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

Ramananet al. Virology. 2016

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

Palangatet al. Methods. 2016

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Regulation of cell-to-cell variability in divergent gene expression

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

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

Duet al. Developmental Biology. 2016

Germ Plasm Biogenesis—An Oskar-Centric Perspective

Lehmannet al. Current Topics in Developmental Biology. 2016

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Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

Tettehet al. Cell Stem Cell. 2016

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Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions

Stojicet al. Nature Communications. 2016.
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Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA

Zong et al. Nucleic Acids Research. 2016

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Fixed and live visualization of RNAs in Drosophila oocytes and embryos

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

Zheng et al. Reproduction. 2016.
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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.
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Long Non-Coding RNAs

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

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Stapel et al. Development. 2015.
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FLOW-FISH

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

Vir et al. PLOS ONE. 2015

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

Jain et al. Developmental Neurobiology. 2015

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Xu et al. The American Society for Molecular Biology. 2015.
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Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015

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

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

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

Suslov et al. BioTechniques. 2015

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Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015

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Widespread Inducible Transcription Downstream of Human Genes

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

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

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DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015

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

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

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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

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

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PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015

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Budakian et al. Science. 2015

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Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

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lncRNA probe set validation

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

Cabili et al. GenomeBiology. 2015

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015.
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The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015

Microbe Screen

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

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Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014.
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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014.
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Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

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

Wang et al. Developmental Cell. 2014.
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Dimitrova et al. Molecular Cell. 2014.
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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014.
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Coassin et al. Methods in Molecular Biology. 2014.
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Defined Human Pluripotent Stem Cell Culture Enables Highly Efficient Neuroepithelium Derivation Without Small Molecule Inhibitors

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

Jiet al. Cell. 2013

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Oldenbroek et al. The Company of Biologists Ltd., Development. 2013.
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Bimodal expression of PHO84 is modulated by early termination of antisense transcription

Castelnuovo et al. Nature structural & molecular biology. 2013

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

McIsaac et al. Jove. 2013.
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Skinner et al. Nature Protocol. 2013.
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Skinner et al. Nature Protocol. 2013

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

Mandal et al. PNAS. 2013.
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Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules

Kwon et al. BMBReports. 2013

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

Cochellaet al. Cell. 2012.
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A continuum of transcriptional identities visualized by combinatorial fluorescent in situ hybridization

Jakt et al. Development. 2012

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Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

Buganimet al. Cell. 2012

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

Zhonget al. Cell. 2012.
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The Influenza A Virus PB2, PA, NP, and M Segments Play a Pivotal Role during Genome Packaging

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Cover Image

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Pradeepaet al. BioRxiv. 2016

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Huynhet al. Connective Tissue Research. 2016

FRI0247 The Involvement of The Long Noncoding H19x in tGFβ Signaling and Its Profibrotic Effects in Systemic Sclerosis and Other Fibrotic Diseases

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meleet al. Molecular Cell. 2016

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Stahlet al. Science. 2016

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RNA LOCALIZATION Finding FISH in a small pond

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

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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

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

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

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

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

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Kannaiahet al. Methods. 2016

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Deficiency of the Survival of Motor Neuron Protein Impairs mRNA Localization and Local Translation in the Growth Cone of Motor Neurons

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Abbaszadeh et al. Methods, Elsevier. 2016

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

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Tichon et al. Cold Spring Harbor Laboratory Press. 2015

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

Dacheux et al. Biochemical Society Transactions. 2015.
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Gene essentially and synthetic lethality in haploid human cells

Blomen et al. Science. 2015.
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Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

Zhang et al. Nature Scientific Reports. 2015

RNA FISH for detecting expanded repeats in human diseases

Urbanek et al. Methods. 2015.
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The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming

Durruthy-Durruthy et al. Nature Genetics. 2015.
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p53 genes function to restrain mobile elements

Wylieet al. Genes & Development. 2015.
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The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chacko et al. PLOS Genetics. 2015.
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The lncRNA RZE1 Controls Cryptococcal Morphological Transition

Chackoet al. PLOS Genetics. 2015.
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Engineering Duplex RNAs for Challenging Targets: Recognition of GGGGCC/CCCCGG Repeats at the ALS/FTD C9orf72 Locus

Hu et al. Cell Chemistry & Biology. 2015

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

Bahar Halpern et al. Elsevier. 2015.
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Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription

Lenstra et al. Molecular Cell. 2015.
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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

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

Bolkov'a et al. Elsevier. 2015.
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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.
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Netrin-1 Induces Local Translation of Down Syndrome Cell Adhesion Molecule in Axonal Growth Cones

Jain et al. Developmental Neurobiology. 2015

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Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

Treweeket al. Nature Protocol. 2015

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

Kochan et al. BioTechniques. 2015.
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Sphinx: modeling transcriptional heterogeneity in single-cell RNA-Seq

Gu et al. bioRxIV. 2015.
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Nihal Altan-Bonnet: Tracking viruses that hijack membranes

Powellet al. Journal of Cell Biology. 2015

A BRCA1-interacting lncRNA regulates homologous recombination

Sharma et al. EMBO reports. 2015

RNA transcription modulates phase transition-driven nuclear body assembly

Berry et al. PNAS. 2015

High Impact

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Lyubimova et al. Nature. 2015

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

Webb et al. PNAS. 2015.
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Dclk1+ small intestinal epithelial tuft cells display the hallmarks of quiescence and self-renewal

Chandrakesan et al. Oncotarget. 2015

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

Chandrakesanet al. Oncotarget. 2015

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

Suslov et al. BioTechniques. 2015

Regulation of mRNA translation during mitosis

Tanenbaum et al. eLife. 2015

DksA involvement in transcription fidelity buffers stochastic epigenetic change

Satory et al. Nucleic Acids Research. 2015

High Impact

Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation

Nair et al. Nature Scientific Reports. 2015

High Impact

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

Stefanakis et al. Neuron Cell. 2015.
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Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

Hennig et al. The Journal of Cell Biology. 2015.
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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

Following the intracellular localization of the iab-8ncRNA of the bithorax complex using the MS2-MCP-GFP system

Arib et al. Elsevier. 2015

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

Kumar et al. Genome Research. 2015.
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High Impact

Widespread Inducible Transcription Downstream of Human Genes

Vilborg et al. Molecular Cell. 2015.
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Super Resolution, High Impact

Drosophila germ granules are structured and contain homotypic mRNA clusters

Trcek et al. Nature Communications. 2015.
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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.
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Niche appropriation by Drosophila intestinal stem cell tumours

Patel et al. Nature Cell Biology. 2015.
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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.
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MED GATA factors promote robust development of the C. elegans endoderm

Maduroet al. Developmental Biology. 2015

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

Oliveira et al. PLOS ONE. 2015.
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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.
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Mutant p53 accumulates in cycling and proliferating cells in the normal tissues of p53 R172H mutant mice

AM et al. Oncotarget. 2015

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

Fritz et al. Nucleic Acids Research. 2015.
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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.
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G1/S Inhibitors and the SWI/SNF Complex Control Cell-Cycle Exit during Muscle Differentiation

Ruijtenberg et al. Cell. 2015.
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Paclitaxel inhibits mRNA transport in axons☆

Bobylev et al. Elsevier. 2015.
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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.
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Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue

Shah et al. Journal of Cell Science. 2015

MERFISHing for spatial context

Shalek et al. Trends in Immunology. 2015

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.
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High Impact

Combining protein and mRNA quantification to decipher transcriptional regulation

Xu et al. Nature Communications. 2015.
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Alternative 39UTRs act as scaffolds to regulate membrane protein localization

Berkovits et al. Nature Research Letter. 2015.
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Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma

Grosso et al. eLife. 2015.
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DAZL regulates Tet1 translation in murine embryonic stem cells

Wellinget al. EMBO reports. 2015

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

Velten et al. Molecular systems biology. 2015.
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Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip†

Shaffer et al. Royal Society of Chemistry. 2015

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

Hassanet al. Bone. 2015

High Impact

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

Hocine et al. Nature Scientific Reports. 2015.
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High Impact

An alternative pluripotent state confers interspecies chimaeric competency

Wu et al. Nature. 2015.
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High Impact

Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling

Kratsios et al. Cell Current Biology. 2015.
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Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression

Platt et al. PLOS ONE. 2015.
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High Impact

Putting transcriptomics in its place

Burgess et al. Nature Research Highlights. 2015

The Zinc-Finger Antiviral Protein ZAP Inhibits LINE and Alu Retrotransposition

Moldovan et al. PLOS Genetics. 2015.
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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.
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Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

Boque-Sastre et al. PNAS. 2015.
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High Throughput

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

Dey et al. Molecular Systems biology. 2015.
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CArG-driven GADD45α activated by resveratrol inhibits lung cancer cells

Shi et al. Genes & Cancer. 2015.
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Tuning noise in gene expression

Tyagi et al. Molecular Systems Biology. 2015

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

Amaya et al. PLOS ONE. 2015.
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Multiplexed single-cell in situ RNA analysis by reiterative hybridization†

Xiao et al. Analytical Methods. 2015.
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Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment†

Gibson et al. Royal Society of Chemistry. 2015

High Impact

Spatially resolved, highly multiplexed RNA profiling in single cells

Chen et al. Science. 2015.
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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

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.
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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.
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High Impact

Systematic Discovery of Xist RNA Binding Proteins

Chu et al. Cell. 2015

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

Luo et al. Biochemistry . 2015.
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High Impact

A Noisy Tug of War: The Battle between Transcript Production and Degradation in the Liver

Lam et al. Cell. 2015

High Impact

Independent and coordinate trafficking of single Drosophila germ plasm mRNAs

Little et al. Nature Cell Biology. 2015

High Impact

Bursty Gene Expression in the Intact Mammalian Liver

Bahar Halpern et al. Molecular Cell. 2015.
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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

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

Wu et al. Genes & Development. 2015.
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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

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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.
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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.
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Determination of in vivo target search kinetics of regulatory noncoding RNA

Fei et al. Science. 2015

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

Campbell et al. The Company of Biologists. 2015.
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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.
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Myosin VI regulates gene pairing and transcriptional pause release in T cells

Zorca et al. PNAS. 2015

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

Briggs et al. Stem Cells. 2015.
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Licensing of Primordial Germ Cells for Gametogenesis Depends on Genital Ridge Signaling

Hu et al. PLOS Genetics. 2015

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

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Whole-mount single molecule FISH method for zebrafish embryo

Oka et al. Nature Scientific Reports. 2015.
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PolyQ-dependent RNA–protein assemblies control symmetry breaking

Lee et al. The Journal of Cell Biology. 2015

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

Budakian et al. Science. 2015

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

Newton et al. The Company of Biologists Ltd.. 2015.
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The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

Kempe et al. Molecular Biology Cell . 2015.
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A Wild C. Elegans Strain Has Enhanced Epithelial Immunity to a Natural Microsporidian Parasite

Balla et al. PLOS Pathogens. 2015.
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Phosphatidylserine Vesicles Enable Efficient En Bloc Transmission of Enteroviruses

Chenet al. Cell. 2015

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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.
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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.
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High Impact

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

Schuijers et al. Cell Stem Cell. 2015

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

Chen et al. The Journal of Neuroscience. 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

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

Susor et al. Nature Communications. 2015.
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A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension

Essers et al. Cell Reports. 2015

Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae

Dodson et al. eLife. 2015.
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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.
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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

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

Zong et al. Methods in Molecular Biology. 2015.
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lncRNA probe set validation

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

Cabili et al. GenomeBiology. 2015

Mechanisms of translational repression of the Smcp mRNA in round spermatids

Cullinane et al. Reproduction Reserach. 2015.
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Molekulárna cytogenetika v problematike familiárnych malignít

Konečný et al. Hlavná téma. 2015

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

Hassan et al. Elsevier, Bone. 2015

RNA Fluorescence In Situ Hybridization in Cultured Mammalian Cells

Tripathi et al. Methods in Molecular Biology. 2015.
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Single-Molecule RNA In Situ Hybridization (smFISH) and Immunofl uorescence (IF) in the Drosophila Egg Chamber

Bayer et al. Protocol Drosophila Oogenesis. 2015.
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The DREAM complex promotes gene body H2A.Z for target repression

Latorre et al. Cold Spring Harbor Laboratory Press. 2015

Visualization of lncRNA by Single-Molecule Fluorescence In Situ Hybridization

Dunagin et al. Methods in Molecular Biology Springer Protocols. 2015

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.
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Labelling and imaging of single endogenous messenger RNA particles in vivo

Spilleet al. Journal of Cell Science. 2015

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

Gorman et al. PLOS ONE. 2014

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

Wang et al. eLIFE. 2014.
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Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature

S'anchez et al. Nature Communications. 2014

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

Jones et al. Science. 2014

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

Thompson et al. Analytical Chemistry. 2014

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

Bushkin et al. The Journal of Immunology. 2014

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

Bushkin et al. The Jornal of Immunology. 2014

Super-resolution

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

Liu et al. ACS Nano. 2014.
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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.
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Proteostatic Control of Telomerase Function through TRiC-Mediated Folding of TCAB1

Freund et al. Cell. 2014.
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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.
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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

Inside single cells: quantitative analysis with advanced optics and nanomaterials

Cui et al. WIREs Nanomedicine and Nanobiotechnology. 2014

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

Junker et al. Cell, Developmental Cell. 2014

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

Ochiai et al. Nature Scientific Reports. 2014.
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Self-Digitization Microfluidic Chip for Absolute Quantification of mRNA in Single Cells

Thompson et al. American Chemical Society. 2014.
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Distribution and Characterization of Rhogocyte Cell Types in the Mantle Tissue of Haliotis laevigata

Sairi et al. Marine Biotechnoloy. 2014.
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Activation of the Chicken Type I Interferon Response by Infectious Bronchitis Coronavirus

Kint et al. Journal of Virology. 2014.
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Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014.
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Autophagy supports genomic stability by degrading retrotransposon RNA

Guo et al. Nature Communications. 2014

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

Guzman-ayala et al. The Company of Biologists. 2014

Quantification of pre-mRNA escape rate and synergy in splicing

Bonde et al. Nucleic Acids Research. 2014.
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Cell Intrinsic Modulation of Wnt Signaling Controls Neuroblast Migration in C. elegans

Mentink et al. Developmental Cell. 2014

The role of antisense long noncoding RNA in small RNA-triggered gene activation

Zhang et al. Cold Spring Harbor Laboratory Press. 2014

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

Standaert et al. Cold Spring Harbor Laboratory Press. 2014.
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Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma

Barreca et al. Nature Blood Cancer Journal. 2014

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

Meisel et al. Cell, Elsevier . 2014

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

Gordon et al. Nucleic Acids Research. 2014

Kinetic competition during the transcription cycle results in stochastic RNA processing

Coulon et al. eLIFE, Biophysics and structural biology. 2014.
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Translational Control of the Oogenic Program by Components of OMA Ribonucleoprotein Particles in Caenorhabditis elegans

Spike et al. Genetics. 2014.
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Using Amino-Labeled Nucleotide Probes for Simultaneous Single Molecule RNA-DNA FISH

Basu et al. PLOS ONE. 2014

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

Vera et al. eLIFE. 2014.
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Multifunctional Roles for the Protein Translocation Machinery in RNA Anchoring to the Endoplasmic Reticulum*

Jagannathan et al. The Journal of Biological Chemistry. 2014.
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Rejuvenation of Meiotic Cohesion in Oocytes during Prophase I Is Required for Chiasma Maintenance and Accurate Chromosome Segregation

Weng et al. PLOS Genetics. 2014.
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A Gene Regulatory Network Controls the Binary Fate Decision of Rod and Bipolar Cells in the Vertebrate Retina

Wang et al. Developmental Cell. 2014.
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Single yeast cells vary in transcription activity not in delay time after a metabolic shift

Schwabe et al. Nature Communications. 2014

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

Schwabe et al. Nature Communications. 2014

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

Friedman et al. The Journal of Comparative Neurology. 2014.
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SUMV-1 antagonizes the activity of synthetic multivulva genes in Caenorhabditis elegans

Yucel et al. Developmental Biology. 2014

PACT Clearing, High Impact

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

Yang et al. Cell Resource. 2014

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

Lin et al. Developmental Cell. 2014.
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The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in C. elegans

Hirose et al. PLOS Genetics. 2014

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.
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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.
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Cells in Suspension, High Impact

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

Singer et al. Molecular Cell. 2014

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.
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Genetic basis for Saccharomyces cerevisiae biofilm in liquid medium

Andersen et al. G3: Genes, Genomes, Genetics. 2014.
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Lgr5 marks stem/progenitor cells in ovary and tubal epithelia

Ng et al. Nature Cell Biology. 2014.
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Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region

Liz et al. Molecular Cell. 2014.
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The embryo as a laboratory: Quantifying transcription in Drosophila

Gregor et al. Cell Trends in Genetics. 2014

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

Stossi et al. Cell Chemistry & Biology. 2014.
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Therapeutic implications of activation of the host gene (Dleu2) promoter for miR-15a/16-1 in chronic lymphocytic leukemia

Kasar et al. Oncogene. 2014

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

Baboo et al. PLOS ONE. 2014

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

Mohn et al. Cell. 2014

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

Yücel et al. Developmental Biology, Elsevier. 2014.
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RNA sequencing in situ

Ginart et al. Nature Biotechnology. 2014

High Impact

Validation of noise models for single-cell transcriptomics

Grün et al. Nature Methods. 2014

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

Finn et al. Developmental Biology. 2014

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

Pernicova et al. Molecular Cancer. 2014.
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High Impact

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

Weis et al. Nature Oncogene. 2014

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

Xu et al. PLOS Genetics. 2014.
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Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

Abranches et al. Development, The Company of Biologists. 2014.
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MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production

Chen et al. PNAS PLUS. 2014.
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Transcriptional profiling of cells sorted by RNA abundance

Klemm et al. Nature Methods. 2014

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Labeling native bacterial RNA in live cells

Toran et al. Nature Cell Research. 2014.
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Single-cell in situ RNA profiling by sequential hybridization

Lubeck et al. Nature Methods. 2014

Tumor endothelial marker 1–specific DNA vaccination targets tumor vasculature

Facciponte et al. The Journal of Clinical Investigation. 2014

Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature

Facciponte et al. Journal of Clinical Investigation. 2014

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

Markey et al. PLOS ONE. 2014

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Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

Junkeret al. Cell Minireview. 2014

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

Mazar et al. Oncotarget. 2014.
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Fold Change of Nuclear NF-kB Determines TNF-Induced Transcription in Single Cells

Lee et al. Molecular Cell. 2014.
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Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Blood. 2014

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.
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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.
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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.
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Influenza A Virus Assembly Intermediates Fuse in the Cytoplasm

of star by the n-terminal Domain and coinduction of siK1 and Tis11b/Znf36l1 in single cells et al. PLOS Pathogens. 2014

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

Finn et al. Developmental Biology, Elsevier. 2014.
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KIF14 Promotes AKT Phosphorylation and Contributes to Chemoresistance in Triple-Negative Breast Cancer

Singel et al. Neoplasia. 2014.
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Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

Paralkar et al. Red Cells, Iron, and Erythropoiesis. 2014.
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Global Bidirectional Transcription of the Epstein-Barr Virus Genome during Reactivation

O'Grady et al. JVI, Journal of Virology. 2014

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

O’Grady et al. Journal of Virology. 2014.
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Small alveolar macrophages are infected preferentially by HIV and exhibit impaired phagocytic function

Jambo et al. Nature Mucosal Immunology. 2014.
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Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre

Hacisuleyman et al. Nature structural & molecular biology. 2014.
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Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation

Alvarez-Dominguezet al. Blood Journal. 2014

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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

High Impact

RNAi Factors Are Present and Active in Human Cell Nuclei

Gagnon et al. Cell Reports. 2014.
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A microRNA-based single-gene circuit buffers protein synthesis rates against perturbations

Strovas et al. American Chemical Society. 2014.
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Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus

Zhang et al. Journal of Cell Biology. 2014

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N6-methyladenosine-dependent regulation of messenger RNA stability

Wang et al. Nature Research Letter. 2014.
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