jMOSAiCS: joint analysis of multiple ChIP-seq datasets

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

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

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth

(2011) B. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data

(2011) Yiwen Chen et al.   GENOME BIOLOGY

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

(2010) Frank Johannes et al.   BIOINFORMATICS

JAMIE: joint analysis of multiple ChIP-chip experiments

(2010) Hao Wu et al.   BIOINFORMATICS

Genetic analysis of variation in transcription factor binding in yeast

(2010) Wei Zheng 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

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

(2009) Hyungwon Choi et al.   BIOINFORMATICS

Discovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy

(2009) Tohru Fujiwara et al.   MOLECULAR CELL

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif

(2009) Y.-K. Seo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA