Inventaire - your friends and communities are your best library

Computation for ChIP-seq and RNA-seq studies

author

Barbara J. Wold

published in: Nature Methods

date of publication: 2009-11-01

main subject: RNA sequencing, RNA-Seq

Cites articles 47

Date

Title

Authors

2009-08-09

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis
2009-06-24

Extracting transcription factor targets from ChIP-Seq data
2009-06-15

De novo transcriptome assembly with ABySS.

Randy D Gascoyne, Joseph M Connors, Ryan D Morin, Marco Marra, Shaun Jackman, Yongjun Zhao, Inanc Birol, Jacqueline E. Schein, Doug E Horsman
2009-06-15

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq
2009-06-08

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

Chongzhi Zang
2009-05-01

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing

Erez Y. Levanon, George M. Church
2009-05

How to map billions of short reads onto genomes

Steven Salzberg, Cole Trapnell
2009-05-05

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level
2009

Transcript length bias in RNA-seq data confounds systems biology

Alicia Oshlack, Matthew Wakefield
2009-04-01

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
2009-05-01

TopHat: discovering splice junctions with RNA-Seq

Steven Salzberg, Lior Pachter, Cole Trapnell
2009

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

Mihai Pop, Steven Salzberg, Ben Langmead, Cole Trapnell
2009-02-26

RNA Pol II accumulates at promoters of growth genes during developmental arrest

L. Ryan Baugh, Paul W. Sternberg
2009-02-25

Statistical inferences for isoform expression in RNA-Seq
2009-01

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

Joel Rozowsky, Mark Bender Gerstein, Michael P. Snyder
2009-07-30

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

Nicole Cloonan, Dave Tang, Sean Grimmond
2008-09

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

Richard M. Myers, Serafim Batzoglou
2008

Annotating genomes with massive-scale RNA sequencing

Patrick Wincker, Jean-Marc Aury, Corinne Da Silva, Olivier Jaillon, Claude Scarpelli, François Artiguenave, France Denoeud, Benjamin Noel, Odile Rogier, Giorgio Valle, Corinne Da Silva, Michele Morgante
2008-12-05

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

Kenneth Boucher
2008-11-02

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

Hui Jiang, Wenxiu Ma
2008-10-17

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome
2008

Model-based analysis of ChIP-Seq (MACS)

Chad Nusbaum, Richard M. Myers, Tao Liu, Yong Zhang, Myles Brown, Wei Li, Bradley Bernstein
2008-09-10

F-Seq: a feature density estimator for high-throughput sequence tags

Terrence S. Furey, Alan P. Boyle, Gregory E. Crawford, Justin Guinney
2008-08-01

Optimal spliced alignments of short sequence reads

Stephan Ossowski, Gunnar Rätsch
2008-08-06

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

Suresh Cuddapah, Artem Barski
2008-07-29

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
2008-07-03

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

Stefan Haas, Hans Lehrach, Marie-Laure Yaspo
2008-07-03

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

Steven Jones
2008-09

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

Yoav Gilad, John Marioni, Christopher E. Mason
2008-07

Stem cell transcriptome profiling via massive-scale mRNA sequencing

Kevin McKernan, Nicole Cloonan, Andrew C Perkins, Sean Grimmond
2008-05-30

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Barbara J. Wold
2008-05-18

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

Jürg Bähler, Ian Goodhead, Valerie Wood

Article - wd:Q33999125

Welcome to Inventaire

the library of your friends and communities

learn more