The logic of transcriptional regulator recruitment architecture at cis -regulatory modules controlling liver functions

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

High-throughput functional comparison of promoter and enhancer activities

(2016) Thomas A. Nguyen et al.   GENOME RESEARCH

Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic

(2016) Annelien Verfaillie et al.   GENOME RESEARCH

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

(2016) Cosmas D Arnold et al.   NATURE BIOTECHNOLOGY

Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer

(2016) Swneke D Bailey et al.   NATURE GENETICS

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

Mutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis

(2016) Natalia Gomez-Ospina et al.   Nature Communications

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

Ketone Body Therapy Protects From Lipotoxicity and Acute Liver Failure UponPparα Deficiency

(2015) Michal Pawlak et al.   MOLECULAR ENDOCRINOLOGY

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

GEEQBOX: AMATLABToolbox for Generalized Estimating Equations and Quasi-Least Squares

(2015) Sarah J. Ratcliffe et al.   Journal of Statistical Software

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

Enhancer Activation Requires trans-Recruitment of a Mega Transcription Factor Complex

(2014) Zhijie Liu et al.   CELL

Nuclear bile acid signaling through the farnesoid X receptor

(2014) Claire Mazuy et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Metformin interferes with bile acid homeostasis through AMPK-FXR crosstalk

(2014) Fleur Lien et al.   JOURNAL OF CLINICAL INVESTIGATION

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Creating and validating cis-regulatory maps of tissue-specific gene expression regulation

(2014) Timothy R. O'Connor et al.   NUCLEIC ACIDS RESEARCH

A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

(2014) Julie Dubois-Chevalier et al.   NUCLEIC ACIDS RESEARCH

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

(2014) Samuel Beck et al.   Nature Communications

Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers

(2014) Rasmus Siersbæk et al.   Cell Reports

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Dynamic trans-Acting Factor Colocalization in Human Cells

(2013) Dan Xie et al.   CELL

The Hepatic Orosomucoid/α1-Acid Glycoprotein Gene Cluster Is Regulated by the Nuclear Bile Acid Receptor FXR

(2013) Geoffrey Porez et al.   ENDOCRINOLOGY

Classification of topological domains based on gene expression and regulation

(2013) Jingjing Zhao et al.   GENOME

Glucose sensing O-GlcNAcylation pathway regulates the nuclear bile acid receptor farnesoid X receptor (FXR)

(2013) Wahiba Berrabah et al.   HEPATOLOGY

Peroxisome Proliferator-activated Receptor γ Regulates Genes Involved in Insulin/Insulin-like Growth Factor Signaling and Lipid Metabolism during Adipogenesis through Functionally Distinct Enhancer Classes

(2013) Frédérik Oger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Peroxisome Proliferator-Activated Receptor   and C/EBP  Synergistically Activate Key Metabolic Adipocyte Genes by Assisted Loading

(2013) M. S. Madsen et al.   MOLECULAR AND CELLULAR BIOLOGY

Hepatocyte Nuclear Factor 4 Alpha and Farnesoid X Receptor Co-regulates Gene Transcription in Mouse Livers on a Genome-Wide Scale

(2013) Ann M. Thomas et al.   PHARMACEUTICAL RESEARCH

A Comprehensive Nuclear Receptor Network for Breast Cancer Cells

(2013) Ralf Kittler et al.   Cell Reports

Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR

(2012) Hansook Chong et al.   BMC GENOMICS

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Pioneer transcription factors: establishing competence for gene expression

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

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

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

(2011) Jason Ernst et al.   NATURE

CENTDIST: discovery of co-associated factors by motif distribution

(2011) Zhizhuo Zhang et al.   NUCLEIC ACIDS RESEARCH

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

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

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

FXR Regulates Liver Repair after CCl4-Induced Toxic Injury

(2010) Zhipeng Meng et al.   MOLECULAR ENDOCRINOLOGY

Clocks not winding down: unravelling circadian networks

(2010) Eric E. Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

(2010) V. Kaimal et al.   NUCLEIC ACIDS RESEARCH

Moderated effect size and P-value combinations for microarray meta-analyses

(2009) G. Marot et al.   BIOINFORMATICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine

(2009) Ann M. Thomas et al.   HEPATOLOGY

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

(2009) Da Wei Huang et al.   Nature Protocols

Role of Bile Acids and Bile Acid Receptors in Metabolic Regulation

(2009) Philippe Lefebvre et al.   PHYSIOLOGICAL REVIEWS

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

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

FXR: a metabolic regulator and cell protector

(2008) Yan-Dong Wang et al.   CELL RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY