Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

(2011) Chao Cheng et al.   BIOINFORMATICS

Discovering transcription factor regulatory targets using gene expression and binding data

(2011) Mark Maienschein-Cline et al.   BIOINFORMATICS

A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms

(2011) Rebecca Hannah et al.   EXPERIMENTAL HEMATOLOGY

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

(2011) Chao Cheng et al.   PLoS Computational Biology

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-Seq data

(2010) Song Wu et al.   Theoretical Biology and Medical Modelling

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression

(2010) Kenzie D. MacIsaac et al.   PLoS Computational Biology

Predicting functionality of protein-DNA interactions by integrating diverse evidence

(2009) D. Ucar et al.   BIOINFORMATICS

Role of the Murine Reprogramming Factors in the Induction of Pluripotency

(2009) Rupa Sridharan et al.   CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State

(2009) Alice Gerrits et al.   PLoS Genetics

Prioritization of gene regulatory interactions from large-scale modules in yeast

(2008) Ho-Joon Lee et al.   BMC BIOINFORMATICS

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

(2008) Yuji Zhang et al.   BMC BIOINFORMATICS

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

(2008) Xi Chen et al.   CELL

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

(2008) Anton Valouev et al.   NATURE METHODS

Associating transcription factor-binding site motifs with target GO terms and target genes

(2008) Mikael Bodén et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY