Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Alzheimer's disease is associated with altered expression of genes involved in immune response and mitochondrial processes in astrocytes

(2015) Shobana Sekar et al.   NEUROBIOLOGY OF AGING

Association of Genetic Variants in and Promoter Hypermethylation of CDH1 With Gastric Cancer

(2014) Huiquan Jing et al.   MEDICINE

A protective factor for the ageing brain

(2014) Li-Huei Tsai et al.   NATURE

REST and stress resistance in ageing and Alzheimer’s disease

(2014) Tao Lu et al.   NATURE

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

(2014) Shaun Mahony et al.   PLoS Computational Biology

Enabling interspecies epigenomic comparison with CEpBrowser

(2013) Xiaoyi Cao et al.   BIOINFORMATICS

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Polycomb Repressive Complex 2 Regulates Normal Hematopoietic Stem Cell Function in a Developmental-Stage-Specific Manner

(2013) Huafeng Xie et al.   Cell Stem Cell

Topoisomerases facilitate transcription of long genes linked to autism

(2013) Ian F. King et al.   NATURE

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome

(2013) Miyake Kunio et al.   PLoS One

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential principal component analysis of ChIP-seq

(2013) H. Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

jMOSAiCS: joint analysis of multiple ChIP-seq datasets

(2013) Xin Zeng et al.   GENOME BIOLOGY

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models

(2011) C. Taslim et al.   BIOINFORMATICS

Identifying dispersed epigenomic domains from ChIP-Seq data

(2011) Qiang Song et al.   BIOINFORMATICS

Dependency on the polycomb gene Ezh2 distinguishes fetal from adult hematopoietic stem cells

(2011) M. Mochizuki-Kashio et al.   BLOOD

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

(2011) Jason Ernst et al.   NATURE

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Mass univariate analysis of event-related brain potentials/fields II: Simulation studies

(2011) David M. Groppe et al.   PSYCHOPHYSIOLOGY

Mass univariate analysis of event-related brain potentials/fields I: A critical tutorial review

(2011) David M. Groppe et al.   PSYCHOPHYSIOLOGY

How to obtain the P value from a confidence interval

(2011) D. G. Altman et al.   BMJ-British Medical Journal

Allelic Skewing of DNA Methylation Is Widespread across the Genome

(2010) Leonard C. Schalkwyk et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq

(2010) Frank Johannes et al.   BIOINFORMATICS

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Genetics of early-onset obsessive–compulsive disorder

(2010) Susanne Walitza et al.   EUROPEAN CHILD & ADOLESCENT PSYCHIATRY

Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program

(2010) J. van Arensbergen et al.   GENOME RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

seqMINER: an integrated ChIP-seq data interpretation platform

(2010) Tao Ye et al.   NUCLEIC ACIDS RESEARCH

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Alternative Epigenetic Chromatin States of Polycomb Target Genes

(2010) Yuri B. Schwartz et al.   PLoS Genetics

Robustness of multiple testing procedures against dependence

(2009) Sandy Clarke et al.   ANNALS OF STATISTICS

Comparative study on ChIP-seq data: normalization and binding pattern characterization

(2009) Cenny Taslim et al.   BIOINFORMATICS

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

(2008) Han Xu et al.   BIOINFORMATICS

Effects of dependence in high-dimensional multiple testing problems

(2008) Kyung In Kim et al.   BMC BIOINFORMATICS

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

(2008) Gary Hon et al.   PLoS Computational Biology

Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers

(2008) Kamila Naxerova et al.   GENOME BIOLOGY