Deconvolving sequence features that discriminate between overlapping regulatory annotations

Discovery and validation of information theory-based transcription factor and cofactor binding site motifs

(2016) Ruipeng Lu et al.   NUCLEIC ACIDS RESEARCH

Jointly characterizing epigenetic dynamics across multiple human cell types

(2016) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo

(2016) Anthony Mathelier et al.   Cell Systems

BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data

(2015) Juhani Kähärä et al.   BIOINFORMATICS

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps

(2015) Manu Setty et al.   PLoS Computational Biology

ETS transcription factor ETV2 directly converts human fibroblasts into functional endothelial cells

(2014) Rimpei Morita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hippo Signaling Influences HNF4A and FOXA2 Enhancer Switching during Hepatocyte Differentiation

(2014) Olivia Alder et al.   Cell Reports

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

(2014) Shaun Mahony et al.   PLoS Computational Biology

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

(2013) Esteban O Mazzoni et al.   NATURE NEUROSCIENCE

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour et al.   NUCLEIC ACIDS RESEARCH

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey 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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells

(2011) A. DeLaForest et al.   DEVELOPMENT

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee 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

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

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH