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Annotating genomes with massive-scale RNA sequencing
France Denoeud, Jean-Marc Aury, Corinne Da Silva, Benjamin Noel, Odile Rogier, Massimo Delledonne, Michele Morgante, Giorgio Valle, Patrick Wincker, Claude Scarpelli, Olivier Jaillon, François Artiguenave
Genome Biol. 2008; 9(12): R175. Published online 2008 December 16. doi: 10.1186/gb-2008-9-12-r175
PMCID:
PMC2646279
Abstract Full Text PDF–511K Supplementary Material

Is Cited by the Following 34 Articles in this Archive:

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian Gu, Kelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui
PLoS Comput Biol. 2012 April; 8(4): e1002464. Published online 2012 April 5. doi: 10.1371/journal.pcbi.1002464
PMCID:
PMC3320572
Abstract Full Text PDF–701K Supplementary Material
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney
Bioinformatics. 2012 April 15; 28(8): 1086–1092. Published online 2012 February 24. doi: 10.1093/bioinformatics/bts094
PMCID:
PMC3324515
Abstract Full Text PDF–291K Supplementary Material
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade
Joseph A Christie-Oleza, Guylaine Miotello, Jean Armengaud
BMC Genomics. 2012; 13: 73. Published online 2012 February 15. doi: 10.1186/1471-2164-13-73
PMCID:
PMC3305630
Abstract Full Text PDF–472K Supplementary Material
RNASEQR—a streamlined and accurate RNA-seq sequence analysis program
Leslie Y. Chen, Kuo-Chen Wei, Abner C.-Y. Huang, Kai Wang, Chiung-Yin Huang, Danielle Yi, Chuan Yi Tang, David J. Galas, Leroy E. Hood
Nucleic Acids Res. 2012 March; 40(6): e42. Published online 2011 December 22. doi: 10.1093/nar/gkr1248
PMCID:
PMC3315322
Abstract Full Text PDF–9.9M Supplementary Material
RNA-Seq improves annotation of protein-coding genes in the cucumber genome
Zhen Li, Zhonghua Zhang, Pengcheng Yan, Sanwen Huang, Zhangjun Fei, Kui Lin
BMC Genomics. 2011; 12: 540. Published online 2011 November 2. doi: 10.1186/1471-2164-12-540
PMCID:
PMC3219749
Abstract Full Text PDF–1.4M Supplementary Material
The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach
Jun Odawara, Akihito Harada, Tomohiko Yoshimi, Kazumitsu Maehara, Taro Tachibana, Seiji Okada, Koichi Akashi, Yasuyuki Ohkawa
BMC Genomics. 2011; 12: 516. Published online 2011 October 20. doi: 10.1186/1471-2164-12-516
PMCID:
PMC3209707
Abstract Full Text PDF–2.0M Supplementary Material
Defective photoreceptor phagocytosis in a mouse model of enhanced S-cone syndrome causes progressive retinal degeneration
Debarshi Mustafi, Brian M. Kevany, Christel Genoud, Kiichiro Okano, Artur V. Cideciyan, Alexander Sumaroka, Alejandro J. Roman, Samuel G. Jacobson, Andreas Engel, Mark D. Adams, Krzysztof Palczewski
FASEB J. 2011 September; 25(9): 3157–3176. doi: 10.1096/fj.11-186767
PMCID:
PMC3157681
Free in PMC on 2012/09/01
IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V Davuluri
BMC Bioinformatics. 2011; 12: 305. Published online 2011 July 27. doi: 10.1186/1471-2105-12-305
PMCID:
PMC3180389
Abstract Full Text PDF–323K Supplementary Material
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length
Shao-Ke Lou, Jing-Woei Li, Hao Qin, Aldrin Kay-Yuen Yim, Leung-Yau Lo, Bing Ni, Kwong-Sak Leung, Stephen Kwok-Wing Tsui, Ting-Fung Chan
BMC Bioinformatics. 2011; 12(Suppl 5): S2. Published online 2011 July 27. doi: 10.1186/1471-2105-12-S5-S2
PMCID:
PMC3226252
Abstract Full Text PDF–1.0M Supplementary Material
Querying large read collections in main memory: a versatile data structure
Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, Eric Rivals
BMC Bioinformatics. 2011; 12: 242. Published online 2011 June 17. doi: 10.1186/1471-2105-12-242
PMCID:
PMC3163563
Abstract Full Text PDF–599K Supplementary Material
The Drosophila melanogaster transcriptome by paired-end RNA sequencing
Bryce Daines, Hui Wang, Liguo Wang, Yumei Li, Yi Han, David Emmert, William Gelbart, Xia Wang, Wei Li, Richard Gibbs, Rui Chen
Genome Res. 2011 February; 21(2): 315–324. doi: 10.1101/gr.107854.110
PMCID:
PMC3032934
Abstract Full Text PDF–770K
Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing
Fatih Ozsolak, Patrice M. Milos
Methods Mol Biol. Author manuscript; available in PMC 2012 February 5.
Published in final edited form as: Methods Mol Biol. 2011; 733: 51–61. doi: 10.1007/978-1-61779-089-8_4
PMCID:
PMC3272358
Abstract Full Text PDF–403K
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
Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)
Hiroshi Mizuno, Yoshihiro Kawahara, Hiroaki Sakai, Hiroyuki Kanamori, Hironobu Wakimoto, Harumi Yamagata, Youko Oono, Jianzhong Wu, Hiroshi Ikawa, Takeshi Itoh, Takashi Matsumoto
BMC Genomics. 2010; 11: 683. Published online 2010 December 2. doi: 10.1186/1471-2164-11-683
PMCID:
PMC3016417
Abstract Full Text PDF–4.7M Supplementary Material
Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z. Levin, Moran Yassour, Xian Adiconis, Chad Nusbaum, Dawn Anne Thompson, Nir Friedman, Andreas Gnirke, Aviv Regev
Nat Methods. Author manuscript; available in PMC 2011 March 1.
Published in final edited form as: Nat Methods. 2010 September; 7(9): 709–715. Published online 2010 August 15. doi: 10.1038/nmeth.1491
PMCID:
PMC3005310
Abstract Full Text PDF–1.8M Supplementary Material
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 Biol. 2010; 10: 160. Published online 2010 August 5. doi: 10.1186/1471-2229-10-160
PMCID:
PMC3017786
Abstract Full Text PDF–1.8M Supplementary Material
Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly
Reginaldo M. Kuroshu, Junichi Watanabe,, Sumio Sugano, Shinichi Morishita, Yutaka Suzuki, Masahiro Kasahara
PLoS One. 2010; 5(5): e10517. Published online 2010 May 7. doi: 10.1371/journal.pone.0010517
PMCID:
PMC2866332
Abstract Full Text PDF–1.1M Supplementary Material
A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
James R Bradford, Yvonne Hey, Tim Yates, Yaoyong Li, Stuart D Pepper, Crispin J Miller
BMC Genomics. 2010; 11: 282. Published online 2010 May 5. doi: 10.1186/1471-2164-11-282
PMCID:
PMC2877694
Abstract Full Text PDF–1019K Supplementary Material
Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
Mitchell Guttman, Manuel Garber, Joshua Z. Levin, Julie Donaghey, James Robinson, Xian Adiconis, Lin Fan, Magdalena J. Koziol, Andreas Gnirke, Chad Nusbaum, John L. Rinn, Eric S. Lander, Aviv Regev
Nat Biotechnol. Author manuscript; available in PMC 2010 November 2.
Published in final edited form as: Nat Biotechnol. 2010 May; 28(5): 503–510. Published online 2010 May 2. doi: 10.1038/nbt.1633
PMCID:
PMC2868100
Abstract Full Text PDF–1.8M Supplementary Material
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. van Baren, Steven L. Salzberg, Barbara J. Wold, Lior Pachter
Nat Biotechnol. Author manuscript; available in PMC 2011 July 29.
Published in final edited form as: Nat Biotechnol. 2010 May; 28(5): 511–515. Published online 2010 May 2. doi: 10.1038/nbt.1621
PMCID:
PMC3146043
Abstract Full Text PDF–1.1M Supplementary Material
Supersplat—spliced RNA-seq alignment
Douglas W. Bryant, Jr, Rongkun Shen, Henry D. Priest, Weng-Keen Wong, Todd C. Mockler
Bioinformatics. 2010 June 15; 26(12): 1500–1505. Published online 2010 April 21. doi: 10.1093/bioinformatics/btq206
PMCID:
PMC2881391
Abstract Full Text PDF–426K
Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing
Ernesto Picardi, David S. Horner, Matteo Chiara, Riccardo Schiavon, Giorgio Valle, Graziano Pesole
Nucleic Acids Res. 2010 August; 38(14): 4755–4767. Published online 2010 April 10. doi: 10.1093/nar/gkq202
PMCID:
PMC2919710
Abstract Full Text PDF–772K Supplementary Material
Global and unbiased detection of splice junctions from RNA-seq data
Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Genome Biol. 2010; 11(3): R34. Published online 2010 March 17. doi: 10.1186/gb-2010-11-3-r34
PMCID:
PMC2864574
Abstract Full Text PDF–725K Supplementary Material
Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè, David S Horner
BMC Genomics. 2010; 11: 109. Published online 2010 February 12. doi: 10.1186/1471-2164-11-109
Corrects:
BMC Genomics. 2009; 10: 558.
PMCID:
PMC2831844
Correction PDF–1.0M Supplementary Material Original Article
The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines
Courtney Coleman, Dario Copetti, Guido Cipriani, Sarolta Hoffmann, Pál Kozma, László Kovács, Michele Morgante, Raffaele Testolin, Gabriele Di Gaspero
BMC Genet. 2009; 10: 89. Published online 2009 December 30. doi: 10.1186/1471-2156-10-89
PMCID:
PMC2814809
Abstract Full Text PDF–3.0M Supplementary Material
Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis
Yinan Yuan, Jeng-Der Chung, Xueyan Fu, Virgil E. Johnson, Priya Ranjan, Sarah L. Booth, Scott A. Harding, Chung-Jui Tsai
Proc Natl Acad Sci U S A. 2009 December 22; 106(51): 22020–22025. Published online 2009 December 8. doi: 10.1073/pnas.0906869106
PMCID:
PMC2790362
Abstract Full Text PDF–1.6M Supplementary Material
High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera
Erica Mica, Viviana Piccolo, Massimo Delledonne, Alberto Ferrarini, Mario Pezzotti, Cesare Casati, Cristian Del Fabbro, Giorgio Valle, Alberto Policriti, Michele Morgante, Graziano Pesole, M Enrico Pè, David S Horner
BMC Genomics. 2009; 10: 558. Published online 2009 November 25. doi: 10.1186/1471-2164-10-558
Correction in:
BMC Genomics. 2010; 11: 109.
PMCID:
PMC2822795
Abstract Full Text PDF–1.5M Supplementary Material Correction
Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
Diana Bellin, Alberto Ferrarini, Antonio Chimento, Olaf Kaiser, Natasha Levenkova, Pascal Bouffard, Massimo Delledonne
BMC Genomics. 2009; 10: 555. Published online 2009 November 24. doi: 10.1186/1471-2164-10-555
PMCID:
PMC2790472
Abstract Full Text PDF–357K Supplementary Material
Proteomics-based Refinement of Deinococcus deserti Genome Annotation Reveals an Unwonted Use of Non-canonical Translation Initiation Codons
Mathieu Baudet, Philippe Ortet, Jean-Charles Gaillard, Bernard Fernandez, Philippe Guérin, Christine Enjalbal, Gilles Subra, Arjan de Groot, Mohamed Barakat, Alain Dedieu, Jean Armengaud
Mol Cell Proteomics. 2010 February; 9(2): 415–426. Published online 2009 October 29. doi: 10.1074/mcp.M900359-MCP200
PMCID:
PMC2830850
Abstract Full Text Supplementary Material
RNA-seq: from technology to biology
Samuel Marguerat, Jürg Bähler
Cell Mol Life Sci. 2010 February; 67(4): 569–579. Published online 2009 October 27. doi: 10.1007/s00018-009-0180-6
PMCID:
PMC2809939
Abstract Full Text PDF–313K
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