The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding

Shape-based peak identification for ChIP-Seq

(2011) Valerie Hower et al.   BMC BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

Selective changes of retroelement expression in human prostate cancer

(2011) Wolfgang Goering et al.   CARCINOGENESIS

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

PICS: Probabilistic Inference for ChIP-seq

(2010) Xuekui Zhang et al.   BIOMETRICS

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

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Derepression of an endogenous long terminal repeat activates the CSF1R proto-oncogene in human lymphoma

(2010) Björn Lamprecht et al.   NATURE MEDICINE

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

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

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

(2010) Christoph D. Schmid et al.   PLoS One

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

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

(2009) Teemu D Laajala et al.   BMC GENOMICS

Regulation by c-Myc of ncRNA expression

(2009) Niall S Kenneth et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

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

Endogenous retroviral LTRs as promoters for human genes: A critical assessment

(2009) Carla J. Cohen et al.   GENE

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

(2009) J. Boros et al.   GENOME RESEARCH

Genomic location analysis by ChIP-Seq

(2009) Artem Barski et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

(2009) Ken Daigoro Yokoyama et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

c-Myc Accelerates S-Phase and Requires WRN to Avoid Replication Stress

(2009) Kristin Robinson et al.   PLoS One

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

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

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko 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

A role for Myc in facilitating transcription activation by E2F1

(2008) J Y Leung et al.   ONCOGENE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY