ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

(2012) Xin Lai et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNAs and cancer: a new frontier of translational research?

(2012) R Spizzo et al.   ONCOGENE

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

(2011) Li Chen et al.   BIOINFORMATICS

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

(2011) Oli MV Grober et al.   BMC GENOMICS

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network

(2011) Yen-Sin Ang et al.   CELL

Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs

(2011) Si Wan Kim et al.   DEVELOPMENTAL BIOLOGY

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells

(2011) Hong-Bing Yu et al.   GENOME RESEARCH

The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle

(2011) Hans-Jörg Warnatz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes

(2011) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

GATA4 Regulates Estrogen Receptor-α-Mediated Osteoblast Transcription

(2011) Gustavo A. Miranda-Carboni et al.   MOLECULAR ENDOCRINOLOGY

Species-Specific Strategies Underlying Conserved Functions of Metabolic Transcription Factors

(2011) Raymond E. Soccio et al.   MOLECULAR ENDOCRINOLOGY

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Erratum: Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

(2011) Bum-Kyu Lee et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb

(2011) Liang Zhao et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes

(2011) Kinyui Alice Lo et al.   PLoS One

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

(2011) Anja Nitzsche et al.   PLoS One

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

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

(2011)   PLOS BIOLOGY

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

(2011) Jenny Schlesinger et al.   PLoS Genetics

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Estrogen Receptor α Controls a Gene Network in Luminal-Like Breast Cancer Cells Comprising Multiple Transcription Factors and MicroRNAs

(2010) Luigi Cicatiello et al.   AMERICAN JOURNAL OF PATHOLOGY

CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse

(2010) Olivier Friard et al.   BMC BIOINFORMATICS

An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression

(2010) Jindan Yu et al.   CANCER CELL

Polycomb-like 2 Associates with PRC2 and Regulates Transcriptional Networks during Mouse Embryonic Stem Cell Self-Renewal and Differentiation

(2010) Emily Walker et al.   Cell Stem Cell

The Nuclear Receptor Nr5a2 Can Replace Oct4 in the Reprogramming of Murine Somatic Cells to Pluripotent Cells

(2010) Jian-Chien Dominic Heng et al.   Cell Stem Cell

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Cooperative interaction between retinoic acid receptor-  and estrogen receptor in breast cancer

(2010) C. S. Ross-Innes et al.   GENES & DEVELOPMENT

Propagation of adipogenic signals through an epigenomic transition state

(2010) D. J. Steger et al.   GENES & DEVELOPMENT

Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA

(2010) H. Yao et al.   GENES & DEVELOPMENT

Liver-enriched transcription factors regulate MicroRNA-122 that targets CUTL1 during liver development

(2010) Hui Xu et al.   HEPATOLOGY

Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin

(2010) Thomas Treiber et al.   IMMUNITY

Estrogen Receptor β Binds to and Regulates Three Distinct Classes of Target Genes

(2010) Omar I. Vivar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-Wide Analysis of Estrogen Receptor   DNA Binding and Tethering Mechanisms Identifies Runx1 as a Novel Tethering Factor in Receptor-Mediated Transcriptional Activation

(2010) J. D. Stender et al.   MOLECULAR AND CELLULAR BIOLOGY

Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor   Function in Adipocytes and Macrophages

(2010) M. I. Lefterova et al.   MOLECULAR AND CELLULAR BIOLOGY

A Functional Link between the Histone Demethylase PHF8 and the Transcription Factor ZNF711 in X-Linked Mental Retardation

(2010) Daniela Kleine-Kohlbrecher et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells

(2010) Diego Pasini et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

MicroRNA control of signal transduction

(2010) Masafumi Inui et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions

(2010) K. Robasky et al.   NUCLEIC ACIDS RESEARCH

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

Identification of β-catenin binding regions in colon cancer cells using ChIP-Seq

(2010) Daniel Bottomly et al.   NUCLEIC ACIDS RESEARCH

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

(2010) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

(2010) Kenzie D. MacIsaac et al.   PLoS Computational Biology

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

(2010) Mei Zhong et al.   PLoS Genetics

Genome-Wide Profiling of p63 DNA–Binding Sites Identifies an Element that Regulates Gene Expression during Limb Development in the 7q21 SHFM1 Locus

(2010) Evelyn N. Kouwenhoven et al.   PLoS Genetics

Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

(2009) Jamy C. Peng 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

A general mechanism for transcription regulation by Oct1 and Oct4 in response to genotoxic and oxidative stress

(2009) J. Kang et al.   GENES & DEVELOPMENT

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

(2009) Y. Cheng et al.   GENOME RESEARCH

Genomic Targets of the KRAB and SCAN Domain-containing Zinc Finger Protein 263

(2009) Seth Frietze et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy

(2009) Tohru Fujiwara et al.   MOLECULAR CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

deepBase: a database for deeply annotating and mining deep sequencing data

(2009) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

(2009) Peter C. Hollenhorst et al.   PLoS Genetics

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA