LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data

A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes

(2012) Russell Bonneville et al.   BIOINFORMATICS

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages

(2012) Xun Lan et al.   NUCLEIC ACIDS RESEARCH

Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

(2012) Seth Frietze et al.   GENOME BIOLOGY

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

Inference of hierarchical regulatory network of estrogen-dependent breast cancer through ChIP-based data

(2011) Fei Gu et al.   BMC Systems Biology

A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer

(2011) Changyu Shen et al.   BMC Systems Biology

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

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

(2010) Xun Lan et al.   BIOINFORMATICS

PICS: Probabilistic Inference for ChIP-seq

(2010) Xuekui Zhang et al.   BIOMETRICS

Investigating repetitively matching short sequencing reads: The enigmatic nature of H3K9me3

(2010) Jeffrey A. Rosenfeld et al.   Epigenetics

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

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

ZNF274 Recruits the Histone Methyltransferase SETDB1 to the 3′ Ends of ZNF Genes

(2010) Seth Frietze et al.   PLoS One

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

(2009) Chongzhi Zang et al.   BIOINFORMATICS

W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data

(2009) V. X. Jin et al.   BIOINFORMATICS

ChIP-Seq of ERα and RNA polymerase II defines genes differentially responding to ligands

(2009) Willem-Jan Welboren et al.   EMBO JOURNAL

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

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

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

Modeling ChIP Sequencing In Silico with Applications

(2008) Zhengdong D. Zhang et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY