Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

Epigenetic priors for identifying active transcription factor binding sites

(2011) Gabriel Cuellar-Partida 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

MotifClick: prediction of cis-regulatory binding sites via merging cliques

(2011) Shaoqiang Zhang et al.   BMC BIOINFORMATICS

SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model

(2011) Nung Lee et al.   BMC BIOINFORMATICS

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

(2011) Joshua WK Ho et al.   BMC GENOMICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

A Comprehensive Genomic Binding Map of Gene and Chromatin Regulatory Proteins in Saccharomyces

(2011) Bryan J. Venters et al.   MOLECULAR CELL

STEME: efficient EM to find motifs in large data sets

(2011) John E. Reid et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC Genome Browser: update 2012

(2011) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq

(2011) Eloi Mercier et al.   PLoS One

Localized motif discovery in gene regulatory sequences

(2010) V. Narang et al.   BIOINFORMATICS

PriorsEditor: a tool for the creation and use of positional priors in motif discovery

(2010) K. Klepper et al.   BIOINFORMATICS

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

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

GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments

(2010) Simon J. van Heeringen et al.   BIOINFORMATICS

CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

(2010) Lakshmi Kuttippurathu et al.   BIOINFORMATICS

The value of position-specific priors in motif discovery using MEME

(2010) Timothy L Bailey et al.   BMC BIOINFORMATICS

Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts

(2010) A. M. Szalkowski et al.   BRIEFINGS IN BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

On the detection and refinement of transcription factor binding sites using ChIP-Seq data

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

Evidence-ranked motif identification

(2010) Stoyan Georgiev et al.   GENOME BIOLOGY

info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling

(2009) Matthieu Defrance et al.   BIOINFORMATICS

Efficient exact motif discovery

(2009) T. Marschall et al.   BIOINFORMATICS

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

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

GADEM: A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery

(2009) Leping Li   JOURNAL OF COMPUTATIONAL BIOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes

(2009) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Xi Chen et al.   CELL

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

BayesMD: Flexible Biological Modeling for Motif Discovery

(2008) Man-Hung Eric Tang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS

Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation

(2007) Philippe Collas   Frontiers in Bioscience-Landmark