seqMINER: an integrated ChIP-seq data interpretation platform

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

(2009) Cenny Taslim et al.   BIOINFORMATICS

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

GPAT: Retrieval of genomic annotation from large genomic position datasets

(2009) Arnaud Krebs et al.   BMC BIOINFORMATICS

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

LookSeq: A browser-based viewer for deep sequencing data

(2009) H. M. Manske et al.   GENOME RESEARCH

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

(2009) Kimberly R. Blahnik et al.   NUCLEIC ACIDS RESEARCH

EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data

(2009) Christoph Bock et al.   GENOME BIOLOGY

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

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