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From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data

auteur

Chad E Niederhuth

Thomas P Mawhinney

Jianlin Cheng

James Birchler

1950 -

gepubliceerd in: PLOS ONE

publicatiedatum: 2015-04-22

taal: Engels

belangrijk thema: bio-informatica, RNA-sequencing, transcriptoom, transcriptomics, RNA-Seq

Cites articles 42

Date

Titel

Auteurs

2018-07-01

KBase: The United States Department of Energy Systems Biology Knowledgebase

Adam Arkin, Robert Cottingham, Nomi L Harris, Sergei Maslov, Doreen Ware, Fernando Pérez, Benjamin H Allen, John-Marc Chandonia, José P Faria, Mark Bender Gerstein, Fei He, Miriam Land, Folker Meyer, Taeyun Oh, Michael C Schatz, Daifeng Wang, William Riehl, David J Weston, Marcin P Joachimiak, Pamela Ronald
2013-09-23

Differential effect of aneuploidy on the X chromosome and genes with sex-biased expression in Drosophila

Adam F Johnson, Jianlin Cheng
2013-09-22

Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data

Gary Stacey
2013

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Harold Pimentel, Steven Salzberg, Cole Trapnell
2013-04-15

Dosage compensation and inverse effects in triple X metafemales of Drosophila

James Birchler
2013-02-28

Three-level prediction of protein function by combining profile-sequence search, profile-profile search, and domain co-occurrence networks
2013-03-09

A comparison of methods for differential expression analysis of RNA-seq data

Charlotte Soneson
2013-02-04

Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation

James Birchler
2013-03

A large-scale evaluation of computational protein function prediction

Amos Bairoch, Christine Orengo, Burkhard Rost, Predrag Radivojac, Rita Casadio, Iddo Friedberg, Domenico Cozzetto, Steven E. Brenner, Tapio Salakoski, Petri Törönen, Julian Gough, Jari Björne, Esmeralda Vicedo, Maximilian Hecht, Yannick Mahlich, Peter Hönigschmid, Kiley Graim, Stefan Seemayer, Alfonso E. Romero, Avik Datta, Robert Rentzsch, Panče Panov, Kevin Bryson, Fran Supek, Damiano Piovesan, Mark N Wass, Marco Falda, Hai Fang, Serkan Erdin, Stefano Toppo, Karin Verspoor, Michal Linial, Patricia Babbitt, Olivier Lichtarge, Daisuke Kihara, Saso Dzeroski, Asa Ben-Hur, Susanna Repo, Sean D Mooney, Hagit Shatkay, Thomas A Hopf, David Tudor Jones, Michael Sternberg, Tal Ronnen Oron, Wyatt T Clark, Christopher Ronald Funk, Patrik Koskinen, Prajwal Bhat, Haixuan Yang, Tobias Hamp, Yuanpeng Zhou, Paolo Fontana, Aalt van Dijk, Enrico Lavezzo, Alexandra M. Schnoes
2013-01-17

Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq

Chad E Niederhuth, John C Walker
2012-09-17

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors

Gwénaël Leday, Håvard Rue
2012-08-31

Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells

Trupti Joshi, Gary Stacey
2012-07-31

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
2012-03-04

Fast gapped-read alignment with Bowtie 2

Steven Salzberg, Ben Langmead
2012-02

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data
2011

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Lincoln Stein, Pamela Soltis, Alexandros Stamatakis, Jim Leebens-Mack, Naim Matasci, Christos Noutsos, Karen Cranston, Sheldon McKay, Rion Dooley, Ann E Stapleton, Matthew Vaughn, Brian C O'Meara, Todd Vision, Brian J. Enquist, Christopher R. Myers, Liya Wang, Eric Lyons, Brad Boyle, Edwin J Skidmore, Nirav Merchant, Chris E. Jordan, Douglas Soltis, Michael John Donoghue
2011-12-01

Overview of available methods for diverse RNA-Seq data analyses
2011-09-08

Differential expression in RNA-seq: a matter of depth

Joaquín Dopazo, Ana Conesa, Sonia Tarazona, A. Ferrer
2011-03-24

A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny

Gary Stacey
2011-06

Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

Gerton Lunter
2010-12-22

From RNA-seq reads to differential expression results

Alicia Oshlack, Mark D Robinson
2010

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber
2010-10-10

De novo assembly and analysis of RNA-seq data

Shaun Jackman, Malachi Griffith, Timothee Cezard, Steven Jones, Pamela A Hoodless, Inanc Birol, Readman Chiu
2010-08-10

baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

Thomas J Hardcastle
2010-05

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

Steven Salzberg, Lior Pachter, Cole Trapnell, Barbara Wold
2010-02-10

Fast and SNP-tolerant detection of complex variants and splicing in short reads
2010-02-03

Exploring plant transcriptomes using ultra high-throughput sequencing

Thomas Brutnell
2009-08-15

The Sequence Alignment/Map format and SAMtools

Richard M. Durbin, Heng Li, Gonçalo Abecasis, Jue Ruan
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
2008-05-30

Mapping and quantifying mammalian transcriptomes by RNA-Seq

Barbara Wold
2007-01

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

Tatiana Tatusova, Kim D. Pruitt, Donna R. Maglott

Artike - wd:Q30938549

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