reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells

Estimating the proportion of true null hypotheses when the statistics are discrete

(2015) Isaac Dialsingh et al.   BIOINFORMATICS

Single molecule and single cell epigenomics

(2015) Byung-Ryool Hyun et al.   METHODS

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs

(2015) Kyung-Min Noh et al.   MOLECULAR CELL

The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4

(2015) Valeria Ranzani et al.   NATURE IMMUNOLOGY

Detecting differential peaks in ChIP-seq signals with ODIN

(2014) Manuel Allhoff et al.   BIOINFORMATICS

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

(2014) Elisabeth Wachter et al.   eLife

Histone H3K27 Trimethylation Inhibits H3 Binding and Function of SET1-Like H3K4 Methyltransferase Complexes

(2013) D.-H. Kim et al.   MOLECULAR AND CELLULAR BIOLOGY

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Asymmetrically Modified Nucleosomes

(2012) Philipp Voigt et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

(2011) Frank W. Schmitges et al.   MOLECULAR CELL

Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome

(2010) Ed Luk et al.   CELL

Cooperative interaction between retinoic acid receptor-  and estrogen receptor in breast cancer

(2010) C. S. Ross-Innes et al.   GENES & DEVELOPMENT

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

(2010) Eric M. Mendenhall et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

High Throughput Characterization of Combinatorial Histone Codes

(2009) Nicolas L. Young et al.   MOLECULAR & CELLULAR PROTEOMICS

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

The N-terminus of histone H3 is required for de novo DNA methylation in chromatin

(2009) Jia-Lei Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY