My NCBISign In
Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack
Genome Biol. 2010; 11(2): R14. Published online 2010 February 4. doi: 10.1186/gb-2010-11-2-r14
PMCID:
PMC2872874
Abstract Full Text PDF–1.4M Supplementary Material

Is Cited by the Following 21 Articles in this Archive:

Personalized Pathway Enrichment Map of Putative Cancer Genes from Next Generation Sequencing Data
Peilin Jia, Zhongming Zhao
PLoS One. 2012; 7(5): e37595. Published online 2012 May 18. doi: 10.1371/journal.pone.0037595
PMCID:
PMC3356304
Abstract Full Text PDF–1.6M Supplementary Material
Transcriptome Characterization by RNA-seq Unravels the Mechanisms of Butyrate-Induced Epigenomic Regulation in Bovine Cells
Sitao Wu, Robert W. Li, Weizhong Li, Cong-jun Li
PLoS One. 2012; 7(5): e36940. Published online 2012 May 15. doi: 10.1371/journal.pone.0036940
PMCID:
PMC3352864
Abstract Full Text PDF–2.0M Supplementary Material
Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia
Jing Qin Wu, Xi Wang, Natalie J. Beveridge, Paul A. Tooney, Rodney J. Scott, Vaughan J. Carr, Murray J. Cairns
PLoS One. 2012; 7(4): e36351. Published online 2012 April 27. doi: 10.1371/journal.pone.0036351
PMCID:
PMC3338678
Abstract Full Text PDF–1.0M Supplementary Material
pcaGoPromoter - An R Package for Biological and Regulatory Interpretation of Principal Components in Genome-Wide Gene Expression Data
Morten Hansen, Thomas Alexander Gerds, Ole Haagen Nielsen, Jakob Benedict Seidelin, Jesper Thorvald Troelsen, Jørgen Olsen
PLoS One. 2012; 7(2): e32394. Published online 2012 February 27. doi: 10.1371/journal.pone.0032394
PMCID:
PMC3288097
Abstract Full Text PDF–599K
Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds
Wen Huang, Asif Nadeem, Bao Zhang, Masroor Babar, Morris Soller, Hasan Khatib
PLoS One. 2012; 7(1): e30244. Published online 2012 January 23. doi: 10.1371/journal.pone.0030244
PMCID:
PMC3264571
Abstract Full Text PDF–392K Supplementary Material
Statistical methods on detecting differentially expressed genes for RNA-seq data
Zhongxue Chen, Jianzhong Liu, Hon Keung Tony Ng, Saralees Nadarajah, Howard L Kaufman, Jack Y Yang, Youping Deng
BMC Syst Biol. 2011; 5(Suppl 3): S1. Published online 2011 December 23. doi: 10.1186/1752-0509-5-S3-S1
PMCID:
PMC3287564
Abstract Full Text PDF–623K
GC-Content Normalization for RNA-Seq Data
Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
BMC Bioinformatics. 2011; 12: 480. Published online 2011 December 17. doi: 10.1186/1471-2105-12-480
PMCID:
PMC3315510
Abstract Full Text PDF–1.2M Supplementary Material
A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Young-Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
PLoS Negl Trop Dis. 2011 December; 5(12): e1409. Published online 2011 December 13. doi: 10.1371/journal.pntd.0001409
PMCID:
PMC3236722
Abstract Full Text PDF–375K Supplementary Material
Differential expression in RNA-seq: A matter of depth
Sonia Tarazona, Fernando García-Alcalde, Joaquín Dopazo, Alberto Ferrer, Ana Conesa
Genome Res. 2011 December; 21(12): 2213–2223. doi: 10.1101/gr.124321.111
PMCID:
PMC3227109
Abstract Full Text PDF–2.2M
RNA-Seq analysis in MeV
Eleanor A. Howe, Raktim Sinha, Daniel Schlauch, John Quackenbush
Bioinformatics. 2011 November 15; 27(22): 3209–3210. Published online 2011 October 5. doi: 10.1093/bioinformatics/btr490
PMCID:
PMC3208390
Abstract Full Text PDF–215K
Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases
Frank Emmert-Streib, Galina V. Glazko
PLoS Comput Biol. 2011 May; 7(5): e1002053. Published online 2011 May 26. doi: 10.1371/journal.pcbi.1002053
PMCID:
PMC3102754
Full Text PDF–305K
Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Valerio Costa, Claudia Angelini, Luciana D'Apice, Margherita Mutarelli, Amelia Casamassimi, Linda Sommese, Maria Assunta Gallo, Marianna Aprile, Roberta Esposito, Luigi Leone, Aldo Donizetti, Stefania Crispi, Monica Rienzo, Berardo Sarubbi, Raffaele Calabrò, Marco Picardi, Paola Salvatore, Teresa Infante, Piergiuseppe De Berardinis, Claudio Napoli, Alfredo Ciccodicola
PLoS One. 2011; 6(4): e18493. Published online 2011 April 20. doi: 10.1371/journal.pone.0018493
PMCID:
PMC3080369
Abstract Full Text PDF–1.0M Supplementary Material
Single-molecule direct RNA sequencing without cDNA synthesis
Fatih Ozsolak, Patrice M. Milos
Wiley Interdiscip Rev RNA. Author manuscript; available in PMC 2012 February 5.
Published in final edited form as: Wiley Interdiscip Rev RNA. 2011 Jul-Aug; 2(4): 565–570. Published online 2011 March 14. doi: 10.1002/wrna.84
PMCID:
PMC3272359
Abstract Full Text PDF–597K
Length bias correction for RNA-seq data in gene set analyses
Liyan Gao, Zhide Fang, Kui Zhang, Degui Zhi, Xiangqin Cui
Bioinformatics. 2011 March 1; 27(5): 662–669. Published online 2011 January 19. doi: 10.1093/bioinformatics/btr005
PMCID:
PMC3042188
Abstract Full Text PDF–599K Supplementary Material
De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits
Shuang Chen, Pengcheng Yang, Feng Jiang, Yuanyuan Wei, Zongyuan Ma, Le Kang
PLoS One. 2010; 5(12): e15633. Published online 2010 December 30. doi: 10.1371/journal.pone.0015633
PMCID:
PMC3012706
Abstract Full Text PDF–1.4M Supplementary Material
RNA sequencing: advances, challenges and opportunities
Fatih Ozsolak, Patrice M. Milos
Nat Rev Genet. Author manuscript; available in PMC 2011 May 1.
Published in final edited form as: Nat Rev Genet. 2011 February; 12(2): 87–98. Published online 2010 December 30. doi: 10.1038/nrg2934
PMCID:
PMC3031867
Abstract Full Text PDF–633K
From RNA-seq reads to differential expression results
Alicia Oshlack, Mark D Robinson, Matthew D Young
Genome Biol. 2010; 11(12): 220. Published online 2010 December 22. doi: 10.1186/gb-2010-11-12-220
PMCID:
PMC3046478
Abstract Full Text PDF–435K
Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays
Mark B. Stead, Sarah Marshburn, Bijoy K. Mohanty, Joydeep Mitra, Lourdes Peňa Castillo, Debashish Ray, Harm van Bakel, Timothy R. Hughes, Sidney R. Kushner
Nucleic Acids Res. 2011 April; 39(8): 3188–3203. Published online 2010 December 11. doi: 10.1093/nar/gkq1242
PMCID:
PMC3082872
Abstract Full Text PDF–7.5M Supplementary Material
Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
Fabrizio Costa, Rob Alba, Henk Schouten, Valeria Soglio, Luca Gianfranceschi, Sara Serra, Stefano Musacchi, Silviero Sansavini, Guglielmo Costa, Zhangjun Fei, James Giovannoni
BMC Plant Biol. 2010; 10: 229. Published online 2010 October 25. doi: 10.1186/1471-2229-10-229
PMCID:
PMC3095317
Abstract Full Text PDF–1.5M Supplementary Material
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control
Yuling Jiao, Elliot M Meyerowitz
Mol Syst Biol. 2010; 6: 419. Published online 2010 October 5. doi: 10.1038/msb.2010.76
PMCID:
PMC2990639
Abstract Full Text PDF–2.4M Supplementary Material
Gene set enrichment; a problem of pathways
Matthew N. Davies, Emma L. Meaburn, Leonard C. Schalkwyk
Brief Funct Genomics. 2010 December; 9(5-6): 385–390. Published online 2010 September 22. doi: 10.1093/bfgp/elq021
PMCID:
PMC3080747
Abstract Full Text PDF–84K
You are here: NCBI > Literature > PubMed Central (PMC)
Write to the Help Desk