Target analysis by integration of transcriptome and ChIP-seq data with BETA

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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 Comprehensive View of Nuclear Receptor Cancer Cistromes

(2011) Q. Tang et al.   CANCER RESEARCH

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor

(2011) Jing Qin et al.   NUCLEIC ACIDS RESEARCH

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

(2010) Carmen G Palii et al.   EMBO JOURNAL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

(2010) Ming Hu et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

Model-based method for transcription factor target identification with limited data

(2010) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

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

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Reactivation of Androgen Receptor-Regulated TMPRSS2:ERG Gene Expression in Castration-Resistant Prostate Cancer

(2009) C. Cai et al.   CANCER RESEARCH

TFCat: the curated catalog of mouse and human transcription factors

(2009) Debra L Fulton et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor

(2008) Chang S. Chan et al.   CANCER RESEARCH

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval

(2008) Naomi Habib et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY