A genome-wide interactome of DNA-associated proteins in the human liver

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

LS-GKM: a new gkm-SVM for large-scale datasets

(2016) Dongwon Lee   BIOINFORMATICS

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk

(2016) Ashley K. Tehranchi et al.   CELL

The Genetics of Transcription Factor DNA Binding Variation

(2016) Bart Deplancke et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

Distinct gene regulatory programs define the inhibitory effects of liver X receptors and PPARG on cancer cell proliferation

(2016) Daniel Savic et al.   Genome Medicine

Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types

(2016) Vera B. Kaiser et al.   PLoS Genetics

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

(2015) Daniel Savic et al.   GENOME RESEARCH

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

KPNβ1 promotes palmitate-induced insulin resistance via NF-κB signaling in hepatocytes

(2015) Suxin Wang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

EGR1 Functions as a Potent Repressor of MEF2 Transcriptional Activity

(2015) Yi Feng et al.   PLoS One

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

(2015) Nergiz Dogan et al.   Epigenetics & Chromatin

Reciprocal Interaction of Wnt and RXR-α Pathways in Hepatocyte Development and Hepatocellular Carcinoma

(2015) Jinyu Li et al.   PLoS One

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Jian Yan et al.   CELL

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

(2013) A. Mortazavi et al.   GENOME RESEARCH

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

(2013) Jason Gertz et al.   MOLECULAR CELL

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

(2013) Christopher Fletez-Brant et al.   NUCLEIC ACIDS RESEARCH

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

Mapping genome-wide transcription factor binding sites in frozen tissues

(2013) Daniel Savic et al.   Epigenetics & Chromatin

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

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

Predicting cell-type-specific gene expression from regions of open chromatin

(2012) A. Natarajan et al.   GENOME RESEARCH

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner

(2012) J. Gertz et al.   GENOME RESEARCH

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

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

Suppression of Hepatocyte Proliferation by Hepatocyte Nuclear Factor 4α in Adult Mice

(2012) Jessica A. Bonzo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multiple roles of COUP-TFII in cancer initiation and progression

(2012) Lacey M Litchfield et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

The Hypersensitive Glucocorticoid Response Specifically Regulates Period 1 and Expression of Circadian Genes

(2012) T. E. Reddy et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2011) A. DeLaForest et al.   DEVELOPMENT

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

Mechanisms and functions of Hedgehog signalling across the metazoa

(2011) Philip W. Ingham et al.   NATURE REVIEWS GENETICS

Hepatocyte Nuclear Factor 4  Suppresses the Development of Hepatocellular Carcinoma

(2010) B.-F. Ning et al.   CANCER RESEARCH

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

Biological, clinical and population relevance of 95 loci for blood lipids

(2010) Tanya M. Teslovich et al.   NATURE

Hepatocyte Nuclear Factor 4  Coordinates a Transcription Factor Network Regulating Hepatic Fatty Acid Metabolism

(2009) C. P. Martinez-Jimenez et al.   MOLECULAR AND CELLULAR BIOLOGY

TFCat: the curated catalog of mouse and human transcription factors

(2009) Debra L Fulton et al.   GENOME BIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY