My NCBISign In
Full-length messenger RNA sequences greatly improve genome annotation
Brian J Haas, Natalia Volfovsky, Christopher D Town, Maxim Troukhan, Nickolai Alexandrov, Kenneth A Feldmann, Richard B Flavell, Owen White, Steven L Salzberg
Genome Biol. 2002; 3(6): research0029.1–research0029.12. Published online 2002 May 30.
PMCID:
PMC116726
Abstract Full Text PDF–123K Supplementary Material

Is Cited by the Following 33 Articles in this Archive:

Approaches to Fungal Genome Annotation
Brian J. Haas, Qiandong Zeng, Matthew D. Pearson, Christina A. Cuomo, Jennifer R. Wortman
Mycology. Author manuscript; available in PMC 2012 October 3.
Published in final edited form as: Mycology. 2011 October 3; 2(3): 118–141. doi: 10.1080/21501203.2011.606851
PMCID:
PMC3207268
Free in PMC on 2012/10/03
Twenty-First Century Plant Biology: Impacts of the Arabidopsis Genome on Plant Biology and Agriculture
C. Robin Buell, Robert L. Last
Plant Physiol. 2010 October; 154(2): 497–500. Published online 2010 October 6. doi: 10.1104/pp.110.159541
PMCID:
PMC2948998
Full Text PDF–66K
Identification and analysis of in planta expressed genes of Magnaporthe oryzae
Soonok Kim, Jongsun Park, Sook-Young Park, Thomas K Mitchell, Yong-Hwan Lee
BMC Genomics. 2010; 11: 104. Published online 2010 February 10. doi: 10.1186/1471-2164-11-104
PMCID:
PMC2832786
Abstract Full Text PDF–1.0M Supplementary Material
Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana
Xiaoping Gou, Kai He, Hui Yang, Tong Yuan, Honghui Lin, Steven D Clouse, Jia Li
BMC Genomics. 2010; 11: 19. Published online 2010 January 11. doi: 10.1186/1471-2164-11-19
PMCID:
PMC2817689
Abstract Full Text PDF–1.7M Supplementary Material
A new set of ESTs and cDNA clones from full-length and normalized libraries for gene discovery and functional characterization in citrus
M Carmen Marques, Hugo Alonso-Cantabrana, Javier Forment, Raquel Arribas, Santiago Alamar, Vicente Conejero, Miguel A Perez-Amador
BMC Genomics. 2009; 10: 428. Published online 2009 September 11. doi: 10.1186/1471-2164-10-428
PMCID:
PMC2754500
Abstract Full Text PDF–757K Supplementary Material
Splign: algorithms for computing spliced alignments with identification of paralogs
Yuri Kapustin, Alexander Souvorov, Tatiana Tatusova, David Lipman
Biol Direct. 2008; 3: 20. Published online 2008 May 21. doi: 10.1186/1745-6150-3-20
PMCID:
PMC2440734
Abstract Full Text PDF–731K
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman
Genome Biol. 2008; 9(1): R7. Published online 2008 January 11. doi: 10.1186/gb-2008-9-1-r7
PMCID:
PMC2395244
Abstract Full Text PDF–722K Supplementary Material
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome
Françoise Thibaud-Nissen, Matthew Campbell, John P Hamilton, Wei Zhu, C Robin Buell
BMC Genomics. 2007; 8: 388. Published online 2007 October 25. doi: 10.1186/1471-2164-8-388
PMCID:
PMC2151081
Abstract Full Text PDF–804K Supplementary Material
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
Mihaela Pertea, Stephen M Mount, Steven L Salzberg
BMC Bioinformatics. 2007; 8: 159. Published online 2007 May 21. doi: 10.1186/1471-2105-8-159
PMCID:
PMC1892810
Abstract Full Text PDF–446K Supplementary Material
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome
Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante, Maria Luisa Chiusano
BMC Bioinformatics. 2007; 8(Suppl 1): S9. Published online 2007 March 8. doi: 10.1186/1471-2105-8-S1-S9
PMCID:
PMC1885861
Abstract Full Text PDF–252K
Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome
William A Moskal, Jr, Hank C Wu, Beverly A Underwood, Wei Wang, Christopher D Town, Yongli Xiao
BMC Genomics. 2007; 8: 18. Published online 2007 January 17. doi: 10.1186/1471-2164-8-18
PMCID:
PMC1783852
Abstract Full Text PDF–492K Supplementary Material
Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis
Matthew A Campbell, Brian J Haas, John P Hamilton, Stephen M Mount, C Robin Buell
BMC Genomics. 2006; 7: 327. Published online 2006 December 28. doi: 10.1186/1471-2164-7-327
PMCID:
PMC1769492
Abstract Full Text PDF–1.0M Supplementary Material
The Arabidopsis thaliana PARTING DANCERS Gene Encoding a Novel Protein Is Required for Normal Meiotic Homologous Recombination
Asela J. Wijeratne, Changbin Chen, Wei Zhang, Ljudmilla Timofejeva, Hong Ma
Mol Biol Cell. 2006 March; 17(3): 1331–1343. doi: 10.1091/mbc.E05-09-0902
PMCID:
PMC1382321
Abstract Full Text PDF–993K Supplementary Material
Tiling microarray analysis of rice chromosome 10 to identify the transcriptome and relate its expression to chromosomal architecture
Lei Li, Xiangfeng Wang, Mian Xia, Viktor Stolc, Ning Su, Zhiyu Peng, Songgang Li, Jun Wang, Xiping Wang, Xing Wang Deng
Genome Biol. 2005; 6(6): R52. Published online 2005 May 27. doi: 10.1186/gb-2005-6-6-r52
Correction in:
Genome Biol. 2005; 6(8): 403.
PMCID:
PMC1175972
Abstract Full Text PDF–1.9M Supplementary Material Correction
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
Mulu Ayele, Brian J. Haas, Nikhil Kumar, Hank Wu, Yongli Xiao, Susan Van Aken, Teresa R. Utterback, Jennifer R. Wortman, Owen R. White, Christopher D. Town
Genome Res. 2005 April; 15(4): 487–495. doi: 10.1101/gr.3176505
PMCID:
PMC1074363
Abstract Full Text PDF–588K
Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana
Manpreet S. Katari, Vivekanand Balija, Richard K. Wilson, Robert A. Martienssen, W. Richard McCombie
Genome Res. 2005 April; 15(4): 496–504. doi: 10.1101/gr.3239105
PMCID:
PMC1074364
Abstract Full Text PDF–297K
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Jr, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town
BMC Biol. 2005; 3: 7. Published online 2005 March 22. doi: 10.1186/1741-7007-3-7
PMCID:
PMC1082884
Abstract Full Text PDF–588K
Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes
Alexandra V Andreeva, Mikhail A Kutuzov
BMC Evol Biol. 2004; 4: 47. Published online 2004 November 19. doi: 10.1186/1471-2148-4-47
PMCID:
PMC535813
Abstract Full Text PDF–495K Supplementary Material
Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
Pierre Hilson, Joke Allemeersch, Thomas Altmann, Sébastien Aubourg, Alexandra Avon, Jim Beynon, Rishikesh P. Bhalerao, Frédérique Bitton, Michel Caboche, Bernard Cannoot, Vasil Chardakov, Cécile Cognet-Holliger, Vincent Colot, Mark Crowe, Caroline Darimont, Steffen Durinck, Holger Eickhoff, Andéol Falcon de Longevialle, Edward E. Farmer, Murray Grant, Martin T.R. Kuiper, Hans Lehrach, Céline Léon, Antonio Leyva, Joakim Lundeberg, Claire Lurin, Yves Moreau, Wilfried Nietfeld, Javier Paz-Ares, Philippe Reymond, Pierre Rouzé, Goran Sandberg, Maria Dolores Segura, Carine Serizet, Alexandra Tabrett, Ludivine Taconnat, Vincent Thareau, Paul Van Hummelen, Steven Vercruysse, Marnik Vuylsteke, Magdalena Weingartner, Peter J. Weisbeek, Valtteri Wirta, Floyd R.A. Wittink, Marc Zabeau, Ian Small
Genome Res. 2004 October; 14(10b): 2176–2189. doi: 10.1101/gr.2544504
PMCID:
PMC528935
Abstract Full Text PDF–465K
The Use of MPSS for Whole-Genome Transcriptional Analysis in Arabidopsis
Blake C. Meyers, Shivakundan Singh Tej, Tam H. Vu, Christian D. Haudenschild, Vikas Agrawal, Steve B. Edberg, Hassan Ghazal, Shannon Decola
Genome Res. 2004 August; 14(8): 1641–1653. doi: 10.1101/gr.2275604
PMCID:
PMC509274
Abstract Full Text PDF–246K
Formin homology 2 domains occur in multiple contexts in angiosperms
Fatima Cvrčková, Marian Novotný, Denisa Pícková, Viktor Žárský
BMC Genomics. 2004; 5: 44. Published online 2004 July 15. doi: 10.1186/1471-2164-5-44
PMCID:
PMC509240
Abstract Full Text PDF–1.9M Supplementary Material
Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
Vanina Castelli, Jean-Marc Aury, Olivier Jaillon, Patrick Wincker, Christian Clepet, Manuella Menard, Corinne Cruaud, Francis Quétier, Claude Scarpelli, Vincent Schächter, Gary Temple, Michel Caboche, Jean Weissenbach, Marcel Salanoubat
Genome Res. 2004 March; 14(3): 406–413. doi: 10.1101/gr.1515604
PMCID:
PMC353228
Abstract Full Text PDF–434K
Numerous Novel Annotations of the Human Genome Sequence Supported by a 5′-End–Enriched cDNA Collection
Betina M. Porcel, Olivier Delfour, Vanina Castelli, Veronique De Berardinis, Lucie Friedlander, Corinne Cruaud, Abel Ureta-Vidal, Claude Scarpelli, Patrick Wincker, Vincent Schächter, William Saurin, Gabor Gyapay, Marcel Salanoubat, Jean Weissenbach
Genome Res. 2004 March; 14(3): 463–471. doi: 10.1101/gr.1481104
PMCID:
PMC353234
Abstract Full Text PDF–593K
Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping
Wei Zhu, Shannon D. Schlueter, Volker Brendel
Plant Physiol. 2003 June; 132(2): 469–484. doi: 10.1104/pp.102.018101
PMCID:
PMC166990
Abstract Full Text PDF–919K
Towards Interoperability in Genome Databases: The MAtDB (MIPS Arabidopsis Thaliana Database) Experience
Heiko Schoof
Comp Funct Genomics. 2003 April; 4(2): 255–258. doi: 10.1002/cfg.278
PMCID:
PMC2447410
Summary PDF–76K
Powdery Mildew-Induced Mla mRNAs Are Alternatively Spliced and Contain Multiple Upstream Open Reading Frames
Dennis A. Halterman, Fusheng Wei, Roger P. Wise
Plant Physiol. 2003 February; 131(2): 558–567. doi: 10.1104/pp.014407
PMCID:
PMC166832
Abstract Full Text PDF–369K
CATMA: a complete Arabidopsis GST database
Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, Martin Trick
Nucleic Acids Res. 2003 January 1; 31(1): 156–158.
PMCID:
PMC165518
Abstract Full Text PDF–357K
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis
Genome Biol. 2002; 3(12): research0083.1–83.22. Published online 2002 December 31. doi: 10.1186/gb-2002-3-12-research0083
PMCID:
PMC151185
Abstract Full Text PDF–1.1M Supplementary Material
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker
Genome Biol. 2002; 3(12): research0086.1–86.2. Published online 2002 December 30. doi: 10.1186/gb-2002-3-12-research0086
PMCID:
PMC151188
Abstract Full Text PDF–505K Supplementary Material
An integrated computational pipeline and database to support whole-genome sequence annotation
CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis
Genome Biol. 2002; 3(12): research0081.1–81.11. Published online 2002 December 23. doi: 10.1186/gb-2002-3-12-research0081
PMCID:
PMC151183
Abstract Full Text PDF–143K
You are here: NCBI > Literature > PubMed Central (PMC)
Write to the Help Desk