Predictive Models of Gene Regulation from High-Throughput Epigenomics Data

Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

(2011) Zhihua Zhang et al.   BMC BIOINFORMATICS

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells

(2011) Chao Cheng et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

Genomic and chromatin signals underlying transcription start-site selection

(2011) Eivind Valen et al.   TRENDS IN GENETICS

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Reciprocal intronic and exonic histone modification regions in humans

(2010) Jason T Huff et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian network analysis of targeting interactions in chromatin

(2009) B. van Steensel et al.   GENOME RESEARCH

Epigenetics in cancer: Targeting chromatin modifications

(2009) L. Ellis et al.   MOLECULAR CANCER THERAPEUTICS

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

(2009) Leonid Teytelman et al.   PLoS One

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

A glimpse into the epigenetic landscape of gene regulation

(2008) Jane Mellor et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Inferring causal relationships among different histone modifications and gene expression

(2008) H. Yu et al.   GENOME RESEARCH

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology