Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms

(2014) Melina Claussnitzer et al.   CELL

Integrating Diverse Datasets Improves Developmental Enhancer Prediction

(2014) Genevieve D. Erwin et al.   PLoS Computational Biology

A CpG Mutational Hotspot in a ONECUT Binding Site Accounts for the Prevalent Variant of Hemophilia B Leyden

(2013) Alister P.W. Funnell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals

(2013) Klara Stefflova et al.   CELL

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

(2013) J. Ernst et al.   GENOME RESEARCH

Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Profiling of Parkin-Binding Partners Using Tandem Affinity Purification

(2013) Alessandra Zanon et al.   PLoS One

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle 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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Interpreting noncoding genetic variation in complex traits and human disease

(2012) Lucas D Ward et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Mutation in the factor VII hepatocyte nuclear factor 4α-binding site contributes to factor VII deficiency

(2011) Xing-Wu Zheng et al.   BLOOD COAGULATION & FIBRINOLYSIS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Functional Characterization of Liver Enhancers That Regulate Drug-Associated Transporters

(2011) M J Kim et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes

(2011) Claudia Kutter et al.   NATURE GENETICS

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Theoretical and empirical quality assessment of transcription factor-binding motifs

(2011) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

RSAT 2011: regulatory sequence analysis tools

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

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

A database and API for variation, dense genotyping and resequencing data

(2010) Daniel Rios et al.   BMC BIOINFORMATICS

A High-Frequency Regulatory Polymorphism in the p53 Pathway Accelerates Tumor Development

(2010) Sean M. Post et al.   CANCER CELL

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

(2010) D. L. Goode et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean 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

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Finding regulatory DNA motifs using alignment-free evolutionary conservation information

(2010) Raluca Gordân 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

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

(2010) D. Schmidt et al.   SCIENCE

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Ensembl's 10th year

(2009) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

(2009) Mehdi Motallebipour et al.   GENOME BIOLOGY

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Species-Specific Transcription in Mice Carrying Human Chromosome 21

(2008) M. D. Wilson et al.   SCIENCE