PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

BayesPeak—an R package for analysing ChIP-seq data

(2011) Jonathan Cairns et al.   BIOINFORMATICS

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions

(2011) Jose M Muiño et al.   Plant Methods

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

(2010) Xun Lan et al.   BIOINFORMATICS

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

(2010) Benedikt Zacher et al.   BMC BIOINFORMATICS

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

Orchestration of Floral Initiation by APETALA1

(2010) K. Kaufmann et al.   SCIENCE

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

(2009) Kerstin Kaufmann et al.   PLOS BIOLOGY

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

(2008) M. Cesaroni et al.   BIOINFORMATICS

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS