Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation

(2014) Marcus J. Tindall et al.   PLoS Computational Biology

Probing the phenomics of noncoding RNA

(2014) John S Mattick   eLife

4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

(2014) Gilad Fuchs et al.   GENOME BIOLOGY

Hypoxia-regulated microRNAs in human cancer

(2013) Guomin Shen et al.   ACTA PHARMACOLOGICA SINICA

Microarray and deep sequencing cross-platform analysis of the mirRNome and isomiR variation in response to epidermal growth factor

(2013) Franc Llorens et al.   BMC GENOMICS

Nested sampling for parameter inference in systems biology: application to an exemplar circadian model

(2013) Stuart Aitken et al.   BMC Systems Biology

Regulation of Primary Response Genes in B Cells

(2013) Trent Fowler et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

miR-139-5p is a regulator of metastatic pathways in breast cancer

(2013) K. Krishnan et al.   RNA

Long Noncoding RNAs Promote Transcriptional Poising of Inducible Genes

(2013) Sara C. Cloutier et al.   PLOS BIOLOGY

Immediate-early gene activation by the MAPK pathways: what do and don't we know?

(2012) Amanda O'Donnell et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Regulation of signalling by microRNAs

(2012) Roi Avraham et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

MAP kinase signalling cascades and transcriptional regulation

(2012) Shen-Hsi Yang et al.   GENE

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

A Crossroad of microRNAs and Immediate Early Genes (IEGs) Encoding Oncogenic Transcription Factors in Breast Cancer

(2012) Aldema Sas-Chen et al.   JOURNAL OF MAMMARY GLAND BIOLOGY AND NEOPLASIA

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Immediate early response genes and cell transformation

(2012) Shannon Healy et al.   PHARMACOLOGY & THERAPEUTICS

Regulation of Primary Response Genes

(2011) Trent Fowler et al.   MOLECULAR CELL

Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli

(2011) A. Zeisel et al.   Molecular Systems Biology

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics

(2010) Takashi Nakakuki et al.   CELL

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors

(2010) R. Avraham et al.   Science Signaling

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

Integrin signalling at a glance

(2009) D. S. Harburger et al.   JOURNAL OF CELL SCIENCE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS