A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data

BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets

(2013) Jianrong Wang et al.   BIOINFORMATICS

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data

(2013) Ryuichiro Nakato et al.   GENES TO CELLS

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

A Generalized Linear Model for Peak Calling in ChIP-Seq Data

(2012) Jialin Xu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Optimized detection of transcription factor-binding sites in ChIP-seq experiments

(2011) Laura L. Elo et al.   NUCLEIC ACIDS RESEARCH

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

(2011) Naim U Rashid et al.   GENOME BIOLOGY

Assigning roles to DNA regulatory motifs using comparative genomics

(2010) Fabian A. Buske et al.   BIOINFORMATICS

W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data

(2010) Xun Lan et al.   BIOINFORMATICS

Deep and wide digging for binding motifs in ChIP-Seq data

(2010) I. V. Kulakovskiy et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

(2009) A. A. Sharov et al.   DNA RESEARCH

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Extracting transcription factor targets from ChIP-Seq data

(2009) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH

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

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

F-Seq: a feature density estimator for high-throughput sequence tags

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

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

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

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

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules

(2008) Jean-Valery Turatsinze et al.   Nature Protocols

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

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

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY