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

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

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

(2009) Iwanka Kozarewa et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Genome-Wide Analysis of Genes Targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during Seed Germination in Arabidopsis

(2009) E. Oh et al.   PLANT CELL

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

A Systems Approach Reveals Regulatory Circuitry for Arabidopsis Trichome Initiation by the GL3 and GL1 Selectors

(2009) Kengo Morohashi et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

(2008) D. S. Johnson et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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

(2008) Michael A Quail et al.   NATURE METHODS

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5

(2008) Moussa Benhamed et al.   PLANT JOURNAL

Serial ChIP as a tool to investigate the co-localization or exclusion of proteins on plant genes

(2008) Zidian Xie et al.   Plant Methods

Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana

(2008) Yana V. Bernatavichute et al.   PLoS One

Genome-Scale Validation of Deep-Sequencing Libraries

(2008) Dominic Schmidt et al.   PLoS One