PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

(2011) Li Chen et al.   BIOINFORMATICS

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

Discovering homotypic binding events at high spatial resolution

(2010) Yuchun Guo et al.   BIOINFORMATICS

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data

(2010) Zhaohui S Qin et al.   BMC BIOINFORMATICS

MM Algorithms for Some Discrete Multivariate Distributions

(2010) Hua Zhou et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs

(2010) Morten Beck Rye et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou 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

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

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

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY