Efficiently identifying genome-wide changes with next-generation sequencing data

MAP3K4/CBP-Regulated H2B Acetylation Controls Epithelial-Mesenchymal Transition in Trophoblast Stem Cells

(2011) Amy N. Abell et al.   Cell Stem Cell

PICS: Probabilistic Inference for ChIP-seq

(2010) Xuekui Zhang et al.   BIOMETRICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Assessing serotonin receptor mRNA editing frequency by a novel ultra high-throughput sequencing method

(2010) A. I. Abbas et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

(2009) Nicole Cloonan et al.   BIOINFORMATICS

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) Teemu D Laajala et al.   BMC GENOMICS

High-resolution analysis of epigenetic changes associated with X inactivation

(2009) H. Marks et al.   GENOME RESEARCH

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

(2009) Sika Zheng et al.   NUCLEIC ACIDS RESEARCH

Optimal spliced alignments of short sequence reads

(2008) F. De Bona et al.   BIOINFORMATICS

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

(2008) Han Xu et al.   BIOINFORMATICS

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

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

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

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi 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

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

ChromaSig: A Probabilistic Approach to Finding Common Chromatin Signatures in the Human Genome

(2008) Gary Hon et al.   PLoS Computational Biology

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY