Modeling gene expression using chromatin features in various cellular contexts

Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models

(2011) Ivan G Costa et al.   BMC BIOINFORMATICS

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

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

(2011) Jason Ernst et al.   NATURE

Evidence That Gene Activation and Silencing during Stem Cell Differentiation Requires a Transcriptionally Paused Intermediate State

(2011) Jonathan L. Golob et al.   PLoS One

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

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

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

(2009) Yasuto Araki et al.   IMMUNITY

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Discovery and Annotation of Functional Chromatin Signatures in the Human Genome

(2009) Gary Hon et al.   PLoS Computational Biology

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Defining the chromatin signature of inducible genes in T cells

(2009) Pek S Lim et al.   GENOME BIOLOGY

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

DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells

(2008) D. J. Steger et al.   MOLECULAR AND CELLULAR BIOLOGY

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