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Genome re-annotation: a wiki solution?
Steven L Salzberg
Genome Biol. 2007; 8(1): 102. Published online 2007 February 1. doi: 10.1186/gb-2007-8-1-102
PMCID:
PMC1839116
Abstract Full Text PDF–706K

Is Cited by the Following 38 Articles in this Archive:

Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae
Alexandra C. Schrimpe-Rutledge, Marcus B. Jones, Sadhana Chauhan, Samuel O. Purvine, James A. Sanford, Matthew E. Monroe, Heather M. Brewer, Samuel H. Payne, Charles Ansong, Bryan C. Frank, Richard D. Smith, Scott N. Peterson, Vladimir L. Motin, Joshua N. Adkins
PLoS One. 2012; 7(3): e33903. Published online 2012 March 27. doi: 10.1371/journal.pone.0033903
PMCID:
PMC3313959
Abstract Full Text PDF–787K Supplementary Material
Tetrahymena genome database Wiki: a community-maintained model organism database
Nicholas A. Stover, Ravinder S. Punia, Michael S. Bowen, Steven B. Dolins, Theodore G. Clark
Database (Oxford) 2012; 2012: bas007. Published online 2012 February 13. doi: 10.1093/database/bas007
PMCID:
PMC3308163
Abstract Full Text PDF–1.0M
WikiBuild: A New Online Collaboration Process For Multistakeholder Tool Development and Consensus Building
Samir Gupta, Flora T Wan, David Newton, Onil K Bhattacharyya, Mark H Chignell, Sharon E Straus
J Med Internet Res. 2011 Oct-Dec; 13(4): e108. Published online 2011 December 8. doi: 10.2196/jmir.1833
PMCID:
PMC3278094
Abstract Full Text
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis
Jing-Woei Li, Keith Robison, Marcel Martin, Andreas Sjödin, Björn Usadel, Matthew Young, Eric C. Olivares, Dan M. Bolser
Nucleic Acids Res. 2012 January; 40(D1): D1313–D1317. Published online 2011 November 15. doi: 10.1093/nar/gkr1058
PMCID:
PMC3245082
Abstract Full Text PDF–2.1M
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
Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris
Lian Zhou, Frank-Jörg Vorhölter, Yong-Qiang He, Bo-Le Jiang, Ji-Liang Tang, Yuquan Xu, Alfred Pühler, Ya-Wen He
BMC Genomics. 2011; 12: 359. Published online 2011 July 12. doi: 10.1186/1471-2164-12-359
PMCID:
PMC3142249
Abstract Full Text PDF–656K Supplementary Material
Next generation models for storage and representation of microbial biological annotation
Daniel J Quest, Miriam L Land, Thomas S Brettin, Robert W Cottingham
BMC Bioinformatics. 2010; 11(Suppl 6): S15. Published online 2010 October 7. doi: 10.1186/1471-2105-11-S6-S15
PMCID:
PMC3026362
Abstract Full Text PDF–982K
Sustainable digital infrastructure
Ruth Bastow, Sabina Leonelli
EMBO Rep. 2010 October; 11(10): 730–734. Published online 2010 September 17. doi: 10.1038/embor.2010.145
PMCID:
PMC2948195
Full Text PDF–299K
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
A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina
Frédérique Bidard, Sandrine Imbeaud, Nancie Reymond, Olivier Lespinet, Philippe Silar, Corinne Clavé, Hervé Delacroix, Véronique Berteaux-Lecellier, Robert Debuchy
BMC Res Notes. 2010; 3: 171. Published online 2010 June 18. doi: 10.1186/1756-0500-3-171
PMCID:
PMC2908635
Abstract Full Text PDF–456K 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
PDBWiki: added value through community annotation of the Protein Data Bank
Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser
Database (Oxford) 2010; 2010: baq009. Published online 2010 April 16. doi: 10.1093/database/baq009
PMCID:
PMC2911844
Abstract Full Text PDF–408K
What is a Wiki, and How Can it be Used in Resident Education?
Marc D. Kohli, John K. Bradshaw
J Digit Imaging. 2011 February; 24(1): 170–175. Published online 2010 April 13. doi: 10.1007/s10278-010-9292-7
PMCID:
PMC3046790
Abstract Full Text PDF–367K
Community annotation in biology
Raja Mazumder, Darren A Natale, Jessica Anne Ecalnir Julio, Lai-Su Yeh, Cathy H Wu
Biol Direct. 2010; 5: 12. Published online 2010 February 18. doi: 10.1186/1745-6150-5-12
PMCID:
PMC2834641
Abstract Full Text PDF–322K
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
MicroScope: a platform for microbial genome annotation and comparative genomics
D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, C. Médigue
Database (Oxford) 2009; 2009: bap021. Published online 2009 November 25. doi: 10.1093/database/bap021
PMCID:
PMC2790312
Abstract Full Text PDF–1022K
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 community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki
Lope A. Flórez, Sebastian F. Roppel, Arne G. Schmeisky, Christoph R. Lammers, Jörg Stülke
Database (Oxford) 2009; 2009: bap012. Published online 2009 September 17. doi: 10.1093/database/bap012
PMCID:
PMC2790307
Abstract Full Text PDF–776K
Automated seeding of specialised wiki knowledgebases with BioKb
Jonathan R Manning, Ann Hedley, John J Mullins, Donald R Dunbar
BMC Bioinformatics. 2009; 10: 291. Published online 2009 September 16. doi: 10.1186/1471-2105-10-291
PMCID:
PMC2753848
Abstract Full Text PDF–590K
JBrowse: A next-generation genome browser
Mitchell E. Skinner, Andrew V. Uzilov, Lincoln D. Stein, Christopher J. Mungall, Ian H. Holmes
Genome Res. 2009 September; 19(9): 1630–1638. doi: 10.1101/gr.094607.109
PMCID:
PMC2752129
Abstract Full Text PDF–1.2M
Diagnostic biomarkers for renal cell carcinoma: selection using novel bioinformatics systems for microarray data analysis
Adeboye O Osunkoya, Qiqin Yin-Goen, John H Phan, Richard A Moffitt, Todd H Stokes, May D Wang, Andrew N Young
Hum Pathol. Author manuscript; available in PMC 2010 December 1.
Published in final edited form as: Hum Pathol. 2009 December; 40(12): 1671–1678. Published online 2009 August 19. doi: 10.1016/j.humpath.2009.05.006
PMCID:
PMC2783948
Abstract Full Text PDF–896K
Seeking Health Information Online: Does Wikipedia Matter?
Michaël R. Laurent, Tim J. Vickers
J Am Med Inform Assoc. 2009 Jul-Aug; 16(4): 471–479. doi: 10.1197/jamia.M3059
PMCID:
PMC2705249
Abstract Full Text PDF–501K
GenBank and PubMed: How connected are they?
Holly Miller, Catherine N Norton, Indra Neil Sarkar
BMC Res Notes. 2009; 2: 101. Published online 2009 June 9. doi: 10.1186/1756-0500-2-101
PMCID:
PMC2704225
Abstract Full Text PDF–483K
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
Tania Lima, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Karine Michoud, Catherine Rivoire, Virginie Bulliard, Edouard de Castro, Corinne Lachaize, Delphine Baratin, Isabelle Phan, Lydie Bougueleret, Amos Bairoch
Nucleic Acids Res. 2009 January; 37(Database issue): D471–D478. Published online 2009 January. doi: 10.1093/nar/gkn661
PMCID:
PMC2686602
Abstract Full Text PDF–2.9M
Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web
Duncan Hull, Steve R. Pettifer, Douglas B. Kell
PLoS Comput Biol. 2008 October; 4(10): e1000204. Published online 2008 October 31. doi: 10.1371/journal.pcbi.1000204
PMCID:
PMC2568856
Abstract Full Text PDF–599K
Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources
Evert Jan Blom, Rainer Breitling, Klaas Jan Hofstede, Jos BTM Roerdink, Sacha AFT van Hijum, Oscar P Kuipers
BMC Genomics. 2008; 9: 495. Published online 2008 October 21. doi: 10.1186/1471-2164-9-495
PMCID:
PMC2585105
Abstract Full Text PDF–1.5M
Bringing Web 2.0 to bioinformatics
Zhang Zhang, Kei-Hoi Cheung, Jeffrey P. Townsend
Brief Bioinform. 2009 January; 10(1): 1–10. Published online 2008 October 8. doi: 10.1093/bib/bbn041
PMCID:
PMC2638627
Abstract Full Text PDF–189K
Search extension transforms Wiki into a relational system: A case for flavonoid metabolite database
Masanori Arita, Kazuhiro Suwa
BioData Min. 2008; 1: 7. Published online 2008 September 17. doi: 10.1186/1756-0381-1-7
PMCID:
PMC2556319
Abstract Full Text PDF–272K
WikiPathways: Pathway Editing for the People
Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo
PLoS Biol. 2008 July; 6(7): e184. Published online 2008 July 22. doi: 10.1371/journal.pbio.0060184
PMCID:
PMC2475545
Full Text PDF–4.2M
Experience using web services for biological sequence analysis
Heinz Stockinger, Teresa Attwood, Shahid Nadeem Chohan, Richard Côté, Philippe Cudré-Mauroux, Laurent Falquet, Pedro Fernandes, Robert D. Finn, Taavi Hupponen, Eija Korpelainen, Alberto Labarga, Aurelie Laugraud, Tania Lima, Evangelos Pafilis, Marco Pagni, Steve Pettifer, Isabelle Phan, Nazim Rahman
Brief Bioinform. 2008 November; 9(6): 493–505. Published online 2008 July 11. doi: 10.1093/bib/bbn029
PMCID:
PMC2989672
Abstract Full Text PDF–299K
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