Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRα

Comprehensive Genomic Analysis Reveals that the Pioneering Function of FOXA1 Is Independent of Hormonal Signaling

(2019) Silvia-E. Glont et al.   Cell Reports

Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver

(2019) Andrew J. Price et al.   AGING CELL

Changes at the nuclear lamina alter binding of pioneer factor Foxa2 in aged liver

(2018) Holly Whitton et al.   AGING CELL

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Minireview: Challenges and Opportunities in Development of PPAR Agonists

(2014) Matthew B. Wright et al.   MOLECULAR ENDOCRINOLOGY

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Changes in Nucleosome Occupancy Associated with Metabolic Alterations in Aged Mammalian Liver

(2014) Irina M. Bochkis et al.   Cell Reports

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Bile acid receptors as targets for drug development

(2013) Frank G. Schaap et al.   Nature Reviews Gastroenterology & Hepatology

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Bile acid-induced inflammatory signaling in mice lacking Foxa2 in the liver leads to activation of mTOR and age-onset obesity

(2013) Irina Mikhailovna Bochkis et al.   Molecular Metabolism

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation

(2012) Zhaoyu Li et al.   CELL

Liver X receptor and peroxisome proliferator-activated receptor as integrators of lipid homeostasis and immunity

(2012) Yoko Kidani et al.   IMMUNOLOGICAL REVIEWS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Pioneer transcription factors: establishing competence for gene expression

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

Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor   in Mouse Liver Reveals Extensive Sharing of Binding Sites

(2011) M. Boergesen et al.   MOLECULAR AND CELLULAR BIOLOGY

The nucleosome map of the mammalian liver

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

Nuclear receptors as drug targets for metabolic disease

(2010) Ira G. Schulman   ADVANCED DRUG DELIVERY REVIEWS

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

(2010) Antoni Hurtado et al.   NATURE GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

p53 Binding to Nucleosomal DNA Depends on the Rotational Positioning of DNA Response Element

(2009) Geetaram Sahu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Foxa2-dependent hepatic gene regulatory networks depend on physiological state

(2009) Irina M. Bochkis et al.   PHYSIOLOGICAL GENOMICS

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

(2008) Mathieu Lupien et al.   CELL

Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress

(2008) Irina M Bochkis et al.   NATURE MEDICINE