ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

Embryonic stem cell-derived hemangioblasts remain epigenetically plastic and require PRC1 to prevent neural gene expression

(2010) L. Mazzarella et al.   BLOOD

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

ESCs Require PRC2 to Direct the Successful Reprogramming of Differentiated Cells toward Pluripotency

(2010) Carlos F. Pereira et al.   Cell Stem Cell

Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment

(2010) O. Alder et al.   DEVELOPMENT

A unique H3K4me2 profile marks tissue-specific gene regulation

(2010) A. Pekowska et al.   GENOME RESEARCH

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Ezh2 Orchestrates Gene Expression for the Stepwise Differentiation of Tissue-Specific Stem Cells

(2009) Elena Ezhkova et al.   CELL

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

Differential chromatin marking of introns and expressed exons by H3K36me3

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

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

(2009) Cizhong Jiang et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Stem cell regulation by polycomb repressors: postponing commitment

(2008) Alexandra M Pietersen et al.   CURRENT OPINION IN CELL BIOLOGY

Chromatin state maps: new technologies, new insights

(2008) Eric M Mendenhall et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

(2008) Fabio Mohn et al.   MOLECULAR CELL

Stat3 and c-Myc Genome-Wide Promoter Occupancy in Embryonic Stem Cells

(2008) Benjamin L. Kidder et al.   PLoS One

Polycomb Repressive Complex 2 (PRC2) Restricts Hematopoietic Stem Cell Activity

(2008) Ian J Majewski et al.   PLOS BIOLOGY

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

(2008) Gary Hon et al.   PLoS Computational Biology

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY