Genome Biology

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Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel and Erik van Nimwegen*

Genome Biology 2009, 10:R79 doi:10.1186/gb-2009-10-7-r79

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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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Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding

R Pitts, David C Rinker, Patrick L Jones, Antonis Rokas, Laurence J Zwiebel BMC Genomics 2011, 12:271 (27 May 2011)

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RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

Andrew J Severin, Jenna L Woody, Yung-Tsi Bolon, Bindu Joseph, Brian W Diers, Andrew D Farmer, Gary J Muehlbauer, Rex T Nelson, David Grant, James E Specht, Michelle A Graham, Steven B Cannon, Gregory D May, Carroll P Vance, Randy C Shoemaker BMC Plant Biology 2010, 10:160 (5 August 2010)

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A scaling normalization method for differential expression analysis of RNA-seq data

Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010)

A novel and empirical method for normalization of RNA-seq data is presented