iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

Male-Specific Fruitless Isoforms Target Neurodevelopmental Genes to Specify a Sexually Dimorphic Nervous System

(2014) Megan C. Neville et al.   CURRENT BIOLOGY

cisExpress: motif detection in DNA sequences

(2013) Martin Triska et al.   BIOINFORMATICS

Identifying targets of the Sox domain protein Dichaete in the Drosophila CNS via targeted expression of dominant negative proteins

(2013) Shih Pei Shen et al.   BMC DEVELOPMENTAL BIOLOGY

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

(2013) M. S. Enuameh et al.   GENOME RESEARCH

Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells

(2013) Daniel Menendez et al.   NUCLEIC ACIDS RESEARCH

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

TDP-43 Loss-of-Function Causes Neuronal Loss Due to Defective Steroid Receptor-Mediated Gene Program Switching in Drosophila

(2013) Lies Vanden Broeck et al.   Cell Reports

oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets

(2013) Andrew T. Kwon et al.   G3-Genes Genomes Genetics

Characterization of the p53 Cistrome – DNA Binding Cooperativity Dissects p53's Tumor Suppressor Functions

(2013) Katharina Schlereth et al.   PLoS Genetics

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

(2013) Delphine Menoret et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis

(2012) F Nikulenkov et al.   CELL DEATH AND DIFFERENTIATION

Transcription factories: genetic programming in three dimensions

(2012) Lucas Brandon Edelman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

(2012) M. Naval-Sanchez et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

dJun and Vri/dNFIL3 Are Major Regulators of Cardiac Aging in Drosophila

(2012) Véronique Monnier et al.   PLoS Genetics

InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

(2012) Alain Coletta et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Linking specification to differentiation: from proneural genes to the regulation of ciliogenesis

(2011) Petra I. zur Lage et al.   FLY

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

(2011) A. C. Culhane et al.   NUCLEIC ACIDS RESEARCH

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

(2011) C. G. de Boer et al.   NUCLEIC ACIDS RESEARCH

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

NF-Y joins E2Fs, p53 and other stress transcription factors at the apoptosis table

(2011) R Gatta et al.   Cell Death & Disease

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs

(2010) Srinivas Veerla et al.   BMC GENOMICS

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

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

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

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction

(2010) Amaya Ortiz-Barahona et al.   NUCLEIC ACIDS RESEARCH

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification

(2010) Stein Aerts et al.   PLOS BIOLOGY

Assessing Computational Methods of Cis-Regulatory Module Prediction

(2010) Jing Su et al.   PLoS Computational Biology

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Module networks revisited: computational assessment and prioritization of model predictions

(2009) A. Joshi et al.   BIOINFORMATICS

hPDI: a database of experimental human protein-DNA interactions

(2009) Z. Xie et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Blinded by the Light: The Growing Complexity of p53

(2009) Karen H. Vousden et al.   CELL

The Notch signaling pathway: Transcriptional regulation at Notch target genes

(2009) T. Borggrefe et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Regulation of the p53 transcriptional response by structurally diverse core promoters

(2009) J. M. Morachis et al.   GENES & DEVELOPMENT

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Allegro: Analyzing expression and sequence in concert to discover regulatory programs

(2009) Yonit Halperin 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

Genome-Wide Discovery of cis-Elements in Promoter Sequences Using Gene Expression

(2009) Maxim Troukhan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

(2008) Rekin's Janky et al.   BMC BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Identification of Regulatory Factor X as a Novel Mismatch Repair Stimulatory Factor

(2008) Yanbin Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transcriptional control of human p53-regulated genes

(2008) Todd Riley et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response

(2008) Paolo Benatti et al.   NUCLEIC ACIDS RESEARCH

DiRE: identifying distant regulatory elements of co-expressed genes

(2008) V. Gotea et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

(2008) Peter Van Loo et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY