Genome Biology

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Differential expression analysis for sequence count data

Simon Anders* and Wolfgang Huber

Genome Biology 2010, 11:R106 doi:10.1186/gb-2010-11-10-r106

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BioMed Central: 16 citations

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A normalization strategy for comparing tag count data

Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu Algorithms for Molecular Biology 2012, 7:5 (5 April 2012)

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Genome-wide dynamic transcriptional profiling in Clostridium beijerinckii NCIMB 8052 using single-nucleotide resolution RNA-Seq

Yi Wang, Xiangzhen Li, Yuejian Mao, Hans P Blaschek BMC Genomics 2012, 13:102 (20 March 2012)

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Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

Pablo Peláez, Minerva S Trejo, Luis P Iñiguez, Georgina Estrada-Navarrete, Alejandra A Covarrubias, José L Reyes, Federico Sanchez BMC Genomics 2012, 13:83 (6 March 2012)

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Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Kelly J Vining, Kyle R Pomraning, Larry J Wilhelm, Henry D Priest, Matteo Pellegrini, Todd C Mockler, Michael Freitag, Steven H Strauss BMC Genomics 2012, 13:27 (17 January 2012)

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Expression divergence measured by transcriptome sequencing of four yeast species

Michele A Busby, Jesse M Gray, Allen M Costa, Chip Stewart, Michael P Stromberg, Derek Barnett, Jeffrey H Chuang, Michael Springer, Gabor T Marth BMC Genomics 2011, 12:635 (29 December 2011)

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GC-Content Normalization for RNA-Seq Data

Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit BMC Bioinformatics 2011, 12:480 (17 December 2011)

The combination of three different strategies for GC-content normalization of RNA-seq data leads to more accurate estimations of gene expression levels and fold-changes, making statistical inference of differential expression less prone to false discoveries.

Software   Open Access

NanoStriDE: normalization and differential expression analysis of NanoString nCounter data

Christopher D Brumbaugh, Hyunsung J Kim, Mario Giovacchini, Nader Pourmand BMC Bioinformatics 2011, 12:479 (16 December 2011)

Research article   Open Access

Chemical and transcriptional responses of Norway spruce genotypes with different susceptibility to Heterobasidion spp. infection

Marie Danielsson, Karl Lundén, Malin Elfstrand, Jiang Hu, Tao Zhao, Jenny Arnerup, Katarina Ihrmark, Gunilla Swedjemark, Anna-Karin Borg-Karlson, Jan Stenlid BMC Plant Biology 2011, 11:154 (8 November 2011)

Research article   Open Access

Transcript profiling reveals expression differences in wild-type and glabrous soybean lines

Matt Hunt, Navneet Kaur, Martina Stromvik, Lila Vodkin BMC Plant Biology 2011, 11:145 (26 October 2011)

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SpeCond: a method to detect condition-specific gene expression

Florence MG Cavalli, Richard Bourgon, Wolfgang Huber, Juan M Vaquerizas, Nicholas M Luscombe Genome Biology 2011, 12:R101 (18 October 2011)

A method to detect condition-specific gene expression from microarray data

Research article   Open Access

Effect of the down-regulation of the high Grain Protein Content (GPC) genes on the wheat transcriptome during monocarpic senescence

Dario Cantu, Stephen P Pearce, Assaf Distelfeld, Michael W Christiansen, Cristobal Uauy, Eduard Akhunov, Tzion Fahima, Jorge Dubcovsky BMC Genomics 2011, 12:492 (7 October 2011)

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Cistrome: an integrative platform for transcriptional regulation studies

Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011)

A Galaxy-based web application for integrative analysis of ChIP data

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The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Thomas Sandmann, Matthias C Vogg, Suthira Owlarn, Michael Boutros, Kerstin Bartscherer Genome Biology 2011, 12:R76 (16 August 2011)

Next generation sequencing was used to investigate the transcriptome of head regeneration in the planarian Schmidtea mediterranea

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011)

RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies

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ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011)

A web-based RNA-seq and microarray analysis tool

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rnaSeqMap: a Bioconductor package for RNA sequencing data exploration

Anna Leśniewska, Michał J Okoniewski BMC Bioinformatics 2011, 12:200 (25 May 2011)