Identification and analysis of murine pancreatic islet enhancers

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

(2012) Yin Shen et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data

(2012) Xuekui Zhang et al.   PLoS One

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

(2011) Phillippa C. Taberlay et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

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

(2011) Jason Ernst et al.   NATURE

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

The nucleosome map of the mammalian liver

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

Chromatin "Prepattern" and Histone Modifiers in a Fate Choice for Liver and Pancreas

(2011) C.-R. Xu et al.   SCIENCE

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Pancreatic β Cells Require NeuroD to Achieve and Maintain Functional Maturity

(2010) Chunyan Gu et al.   Cell Metabolism

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

(2010) Michael L. Stitzel et al.   Cell Metabolism

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

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Serotonin regulates pancreatic beta cell mass during pregnancy

(2010) Hail Kim et al.   NATURE MEDICINE

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

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

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Nathaniel D. Heintzman et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

(2008) A. G. Robertson et al.   GENOME RESEARCH

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

(2008) F. M. Pauler et al.   GENOME RESEARCH

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Genetic programming of liver and pancreas progenitors: lessons for stem-cell differentiation

(2008) Kenneth S. Zaret   NATURE REVIEWS GENETICS

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

(2008) Elizabeth D. Wederell et al.   NUCLEIC ACIDS RESEARCH

Identification of transcripts with enriched expression in the developing and adult pancreas

(2008) Brad G Hoffman et al.   GENOME BIOLOGY