Genome-Wide Analysis of Chromatin States Reveals Distinct Mechanisms of Sex-Dependent Gene Regulation in Male and Female Mouse Liver

Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules

(2013) Keunsoo Kang et al.   BMC GENOMICS

Nuclear receptors PXR and CAR: implications for drug metabolism regulation, pharmacogenomics and beyond

(2013) Xiaojuan Chai et al.   Expert Opinion on Drug Metabolism & Toxicology

Foxa1 and Foxa2 Are Essential for Sexual Dimorphism in Liver Cancer

(2012) Zhaoyu Li et al.   CELL

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

(2012) A. Natarajan et al.   GENOME RESEARCH

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

(2012) C. Cheng et al.   GENOME RESEARCH

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

(2012) A. Arvey et al.   GENOME RESEARCH

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics

(2012) Housheng Hansen He et al.   GENOME RESEARCH

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje 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

Impact of CUX2 on the Female Mouse Liver Transcriptome: Activation of Female-Biased Genes and Repression of Male-Biased Genes

(2012) T. L. Conforto et al.   MOLECULAR AND CELLULAR BIOLOGY

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Ligand dependent hepatic gene expression profiles of nuclear receptors CAR and PXR

(2012) Hiroki Tojima et al.   TOXICOLOGY LETTERS

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

Sex-specific mouse liver gene expression: genome-wide analysis of developmental changes from pre-pubertal period to young adulthood

(2012) Tara L Conforto et al.   Biology of Sex Differences

Growth hormone-STAT5 regulation of growth, hepatocellular carcinoma, and liver metabolism

(2011) Myunggi Baik et al.   Annals of the New York Academy of Sciences

Pioneer transcription factors: establishing competence for gene expression

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

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Gadd45β is an inducible coactivator of transcription that facilitates rapid liver growth in mice

(2011) Jianmin Tian et al.   JOURNAL OF CLINICAL INVESTIGATION

Dynamic, Sex-Differential STAT5 and BCL6 Binding to Sex-Biased, Growth Hormone-Regulated Genes in Adult Mouse Liver

(2011) Y. Zhang et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional Profiling of Human Liver Identifies Sex-Biased Genes Associated with Polygenic Dyslipidemia and Coronary Artery Disease

(2011) Yijing Zhang et al.   PLoS One

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

(2010) B. G. Hoffman et al.   GENOME RESEARCH

Cellular and molecular mechanisms involved in hepatocellular carcinoma gender disparity

(2010) Anna Ruggieri et al.   INTERNATIONAL JOURNAL OF CANCER

Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

(2010) G. Ling et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Defining the Epigenetic Actions of Growth Hormone: Acute Chromatin Changes Accompany GH-Activated Gene Transcription

(2010) Dennis J. Chia et al.   MOLECULAR ENDOCRINOLOGY

Intrinsic Sex Differences in the Early Growth Hormone Responsiveness of Sex-Specific Genes in Mouse Liver

(2010) Valerie Wauthier et al.   MOLECULAR ENDOCRINOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Determination of enriched histone modifications in non-genic portions of the human genome

(2009) Jeffrey A Rosenfeld et al.   BMC GENOMICS

Male-Specific Hepatic Bcl6: Growth Hormone-Induced Block of Transcription Elongation in Females and Binding to Target Genes Inversely Coordinated with STAT5

(2009) Rosana D. Meyer et al.   MOLECULAR ENDOCRINOLOGY

Sex Differences in the Expression of Hepatic Drug Metabolizing Enzymes

(2009) D. J. Waxman et al.   MOLECULAR PHARMACOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Transcriptional profiling reveals divergent roles of PPARα and PPARβ/δ in regulation of gene expression in mouse liver

(2009) Linda M. Sanderson et al.   PHYSIOLOGICAL GENOMICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

New Insights on the Xenobiotic-Sensing Nuclear Receptors in Liver Diseases – CAR and PXR-

(2008) Satoru Kakizaki et al.   CURRENT DRUG METABOLISM

Sex-specific differences in CYP450 isoforms in humans

(2008) Marissa J Scandlyn et al.   Expert Opinion on Drug Metabolism & Toxicology

Sex-Specific Early Growth Hormone Response Genes in Rat Liver

(2008) Valerie Wauthier et al.   MOLECULAR ENDOCRINOLOGY

Liver-Specific Hepatocyte Nuclear Factor-4α Deficiency: Greater Impact on Gene Expression in Male than in Female Mouse Liver

(2008) Minita G. Holloway et al.   MOLECULAR ENDOCRINOLOGY

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

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY