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The past, present and future of genome-wide re-annotation
Christos A Ouzounis, Peter D Karp
Genome Biol. 2002; 3(2): comment2001.1–comment2001.6. Published online 2002 January 31.
PMCID:
PMC139008
Abstract Full Text PDF–175K
 Is Cited by the Following 19 Articles in this Archive:
Solving the Problem: Genome Annotation Standards before the Data Deluge
William Klimke, Claire O'Donovan, Owen White, J. Rodney Brister, Karen Clark, Boris Fedorov, Ilene Mizrachi, Kim D. Pruitt, Tatiana Tatusova
Stand Genomic Sci. 2011 October 15; 5(1): 168–193. Published online 2011 October 1. doi: 10.4056/sigs.2084864
PMCID:
PMC3236044
Abstract Full Text PDF–909K
An Integrative Method for Identifying the Over-Annotated Protein-Coding Genes in Microbial Genomes
Jia-Feng Yu, Ke Xiao, Dong-Ke Jiang, Jing Guo, Ji-Hua Wang, Xiao Sun
DNA Res. 2011 December; 18(6): 435–449. Published online 2011 September 8. doi: 10.1093/dnares/dsr030
PMCID:
PMC3223076
Abstract Full Text PDF–396K Supplementary Material
A proteogenomic update to Yersinia: enhancing genome annotation
Samuel H Payne, Shih-Ting Huang, Rembert Pieper
BMC Genomics. 2010; 11: 460. Published online 2010 August 5. doi: 10.1186/1471-2164-11-460
PMCID:
PMC3091656
Abstract Full Text PDF–612K Supplementary Material
More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology
Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber
PLoS Comput Biol. 2010 July; 6(7): e1000867. Published online 2010 July 29. doi: 10.1371/journal.pcbi.1000867
PMCID:
PMC2912341
Abstract Full Text PDF–620K Supplementary Material
Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data
Bart H. J. van den Berg, Fiona M. McCarthy, Susan J. Lamont, Shane C. Burgess
PLoS One. 2010; 5(5): e10642. Published online 2010 May 14. doi: 10.1371/journal.pone.0010642
PMCID:
PMC2871057
Abstract Full Text PDF–425K
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt
PLoS Comput Biol. 2009 December; 5(12): e1000605. Published online 2009 December 11. doi: 10.1371/journal.pcbi.1000605
PMCID:
PMC2781113
Abstract Full Text PDF–1.3M Supplementary Material
Genome reannotation of Escherichia coli CFT073 with new insights into virulence
Chengwei Luo, Gang-Qing Hu, Huaiqiu Zhu
BMC Genomics. 2009; 10: 552. Published online 2009 November 22. doi: 10.1186/1471-2164-10-552
PMCID:
PMC2785843
Abstract Full Text PDF–713K Supplementary Material
A Statistical Model of Protein Sequence Similarity and Function Similarity Reveals Overly-Specific Function Predictions
Brenton Louie, Roger Higdon, Eugene Kolker
PLoS One. 2009; 4(10): e7546. Published online 2009 October 21. doi: 10.1371/journal.pone.0007546
PMCID:
PMC2760442
Abstract Full Text PDF–667K Supplementary Material
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning
Adrian K Arakaki, Ying Huang, Jeffrey Skolnick
BMC Bioinformatics. 2009; 10: 107. Published online 2009 April 13. doi: 10.1186/1471-2105-10-107
PMCID:
PMC2670841
Abstract Full Text PDF–334K Supplementary Material
FINDSITE: a combined evolution/structure-based approach to protein function prediction
Jeffrey Skolnick, Michal Brylinski
Brief Bioinform. 2009 July; 10(4): 378–391. Published online 2009 March 26. doi: 10.1093/bib/bbp017
PMCID:
PMC2691936
Abstract Full Text PDF–475K
Matching curated genome databases: a non trivial task
Stéphane Descorps-Declère, Matthieu Barba, Bernard Labedan
BMC Genomics. 2008; 9: 501. Published online 2008 October 24. doi: 10.1186/1471-2164-9-501
PMCID:
PMC2596144
Abstract Full Text PDF–555K
Probability landscapes for integrative genomics
Annick Lesne, Arndt Benecke
Theor Biol Med Model. 2008; 5: 9. Published online 2008 May 20. doi: 10.1186/1742-4682-5-9
PMCID:
PMC2409305
Abstract Full Text PDF–447K
Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data
Randall Hulshizer, Eric M Blalock
BMC Bioinformatics. 2007; 8: 240. Published online 2007 July 5. doi: 10.1186/1471-2105-8-240
PMCID:
PMC1934919
Abstract Full Text PDF–1.8M Supplementary Material
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence
Ozan Gundogdu, Stephen D Bentley, Matt T Holden, Julian Parkhill, Nick Dorrell, Brendan W Wren
BMC Genomics. 2007; 8: 162. Published online 2007 June 12. doi: 10.1186/1471-2164-8-162
PMCID:
PMC1899501
Abstract Full Text PDF–306K Supplementary Material
CORRIE: enzyme sequence annotation with confidence estimates
Benjamin Audit, Emmanuel D Levy, Wally R Gilks, Leon Goldovsky, Christos A Ouzounis
BMC Bioinformatics. 2007; 8(Suppl 4): S3. Published online 2007 May 22. doi: 10.1186/1471-2105-8-S4-S3
PMCID:
PMC1892082
Abstract Full Text PDF–412K
A kingdom-specific protein domain HMM library for improved annotation of fungal genomes
Intikhab Alam, Simon J Hubbard, Stephen G Oliver, Magnus Rattray
BMC Genomics. 2007; 8: 97. Published online 2007 April 10. doi: 10.1186/1471-2164-8-97
PMCID:
PMC1854895
Abstract Full Text PDF–379K Supplementary Material
High precision multi-genome scale reannotation of enzyme function by EFICAz
Adrian K Arakaki, Weidong Tian, Jeffrey Skolnick
BMC Genomics. 2006; 7: 315. Published online 2006 December 13. doi: 10.1186/1471-2164-7-315
PMCID:
PMC1764738
Abstract Full Text PDF–464K Supplementary Material
The relationship between protein sequences and their gene ontology functions
Zhong-Hui Duan, Brent Hughes, Lothar Reichel, Dianne M Perez, Ting Shi
BMC Bioinformatics. 2006; 7(Suppl 4): S11. Published online 2006 December 12. doi: 10.1186/1471-2105-7-S4-S11
PMCID:
PMC1780109
Abstract Full Text PDF–316K Supplementary Material
PATRIC: The VBI PathoSystems Resource Integration Center
E. E. Snyder, N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, O. R. Crasta, M. J. Czar, A. Dickerman, J. D. Eckart, R. Kenyon, R. Will, J. C. Setubal, B. W. S. Sobral
Nucleic Acids Res. 2007 January; 35(Database issue): D401–D406. Published online 2006 December 6. doi: 10.1093/nar/gkl858
PMCID:
PMC1669763
Abstract Full Text PDF–216K
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