Difference between revisions of "Publications, Talks, Posters 2007-2009"

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==2009==
 
==2009==
  
===2009 Publications===
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[[GO_2009_Publications,_Tutorials_%26_Workshops,_Presentations,_Posters,_and_Resources]]
 
 
Tyler, BM. 2009. Viewing the microbial world through the lens of the Gene Ontology. Trends in Microbiology. 17(7): 259-261. (July)
 
 
 
Giglio MG, Collmer C.W. Lomax J. Ireland A. 2009. Applying the Gene Ontology in microbial annotation. Trends in Microbiology. 17(7): 262-268. (July)
 
 
 
Hu JC. Karp PD. Keseler, IM. Krummenacker M. Siegele DA. What we can learn about Escherichia coli through application of Gene Ontology. Trends in Microbiology. 17(7): 269-278. (July)
 
 
 
Korves T. Colosimo ME. 2009. Controlled vocabularies for microbial virulence factors. Trends in Microbiology. 17(7): 279-285. (July)
 
 
 
Christie KR, Hong EL, Cherry JM. 2009. Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends in Microbiology. 17(7): 286-294. (July)
 
 
 
Chibucos MC, Tseng T-T, Setubal JC. 2009. Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 17(7): 312-319. (July)
 
 
 
Torto-Alalibo T, Meng S, Dean RA. 2009. Infection strategies of filamentous microbes described with the Gene Ontology. Trends in Microbiology. 17(7): 320-327. (July)
 
 
 
Hill DP, Berardini TZ, Howe DG, Van Auken KM. Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Molecular Reproduction and Development. (submitted)
 
 
 
The Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol 5(7): e1000431. doi:10.1371/journal.pcbi.1000431
 
 
 
Schober D, Smith B, Lewis SE, Kusnierczyk W, Lomax J, Mungall C, Taylor CF, Rocca-Serra P, Sansone SA. Survey-based naming conventions for use in OBO Foundry ontology development. BMC Bioinformatics. 2009 Apr 27;10(1):125. (April)
 
 
 
Wortman J.R., Gilsenan J.M., Joardar V., Deegan J.I., Clutterbuck J., Andersen M.R., Archer D., Bencina M., Braus G., Coutinho P., von Döhren H., Doonan J., Driessen A.J., Durek P., Espeso E., Fekete E., Flipphi M., Estrada C.G., Geysens S., Goldman G., de Groot P.W., Hansen K., Harris S.D., Heinekamp T., Helmstaedt K., Henrissat B., Hofmann G., Homan T., Horio T., Horiuchi H., James S., Jones M., Karaffa L., Karányi Z., Kato M., Keller N., Kelly D.E., Kiel J.A., Kim J.M., van der Klei I.J., Klis F.M., Kovalchuk A., Krasevec N., Kubicek C.P., Liu B., Maccabe A., Meyer V., Mirabito P., Miskei M., Mos M., Mullins J., Nelson D.R., Nielsen J., Oakley B.R., Osmani S.A., Pakula T., Paszewski A., Paulsen I., Pilsyk S., Pócsi I., Punt P.J., Ram A.F., Ren Q., Robellet X., Robson G., Seiboth B., van Solingen P., Specht T., Sun J., Taheri-Talesh N., Takeshita N., Ussery D., vanKuyk P.A., Visser H., van de Vondervoort P.J., de Vries R.P., Walton J., Xiang X., Xiong Y., Zeng A.P., Brandt B.W., Cornell M.J., van den Hondel C.A., Visser J., Oliver S.G., Turner G. The 2008 update of the Aspergillus nidulans genome annotation: A community effort. Fungal Genetics and Biology. 46 (2009) S2–S13.
 
 
 
Barrell D., Dimmer E., Huntley R.P., Binns D., O'Donovan C., Apweiler R. 2009. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res. Jan;37(Database issue):D396-403. (January)
 
 
 
Blake, J.A., Bult, C.J., Eppig, J.T., Kadin, J.A., Richardson, J.E.; Mouse Genome Database Group. 2009. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res. (Database issue):D712-9. (January)
 
 
 
Feltrin E., Campanaro, S., Diehl A.D., Ehler, E., Faulkner, G., Fordham, J., Gardin, C., Harris, M., Hill, D., Knoell, R., Laveder, P., Mittempergher, L., Nori, A., Reggiani, C., Sorrentino V., Volpe P., Zara I., Valle G., Deegan J.  2009.  Muscle Research and Gene Ontology: New standards for improved data integration.  BMC Medical Genomics 2:6 dpo10.1186/1755-8794-2-6. (January)
 
 
 
Tweedie, S., Ashburner, M., Falls, K., Leyland, P., McQuilton, P., Marygold, S., Millburn, G., Osumi-Sutherland, D., Schroeder, A., Seal, R., Zhang, H.; FlyBase Consortium. 2009. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. Jan;37(Database issue):D555-9. (January)
 
 
 
Torto-Alalibo, T, Collmer, CW, Gwinn-Giglio, M. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: Community Development of New Gene Ontology Terms Describing Biological Processes Involved in Microbe-Host Interactions. BMC Microbiology 2009, 9(Suppl 1):S1 (19 February 2009)
 
 
 
Tseng, T-T, Tyler, BM, Setubal, JC. Protein Secretion Systems in Bacterial-Host Associations, and their Description in the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S2 (19 February 2009)
 
 
 
Torto-Alalibo TA, Collmer CW, Lindeberg M, Bird D, Collmer A, Tyler BM. Common and Contrasting Themes in Host Cell-targeted Effectors from Bacterial, Fungal, Oomycete and Nematode Plant Symbionts described using the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S3 (19 February 2009)
 
 
 
Lindeberg M, Biehl BS, Glasner JD, Perna NT, Collmer A, Collmer CW. Gene Ontology Annotation highlights Shared and Divergent Pathogenic Strategies of Type III Effector Proteins deployed by the Plant Pathogen Pseudomonas syringae pv tomato DC3000 and Animal Pathogenic Escherichia coli Strains. BMC Microbiology 2009, 9(Suppl 1):S4 (19 February 2009)
 
 
 
Chibucos MC, Collmer CW, Torto-Alalibo T, Gwinn-Giglio M, Lindeberg M, Li D, Tyler BM. Programmed Cell Death in Host-symbiont Associations, viewed through the Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S5 (19 February 2009)
 
 
 
Chibucos MC, Tyler BM. Common Themes in Nutrient Acquisition by Plant Symbiotic Microbes, described by The Gene Ontology. BMC Microbiology 2009, 9(Suppl 1):S6 (19 February 2009)
 
 
 
Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, Dean RA. Common Processes in Pathogenesis by Fungal and Oomycete Plant Pathogens, described with Gene Ontology Terms. BMC Microbiology 2009, 9(Suppl 1):S7 (19 February 2009)
 
 
 
Meng S, Brown DE, Ebbole DJ, Torto-Alalibo T, Oh YY, Deng J, Mitchell TK, Dean RA. Gene Ontology Annotation of Magnaporthe oryzae. BMC Microbiology 2009, 9(Suppl 1):S8 (19 February 2009)
 
 
 
===2009 Talks===
 
 
 
Invited Speaker and Workshop -'Searching, querying, browsing, downloading and analysing data using GeneDB and the Gene Ontology annotation' Molecular Genetics of the Fission Yeast Schizosaccharomyces pombe. EMBO Workshop. Manchester. (Val Wood)(June)
 
 
 
 
 
Invited Speaker- 'Functional Annotation and the Gene Ontology" 2009 Oomycete Bioinformatics Resources Training Workshop. Virginia Bioinformatics Institute, Virginia Tech. (Torto-Alalibo) USA (June)
 
 
 
Invited Speaker-Introduction to Gene Ontology Annotation (GOA) and The Renal GOA Initiative, GenitoUrinary Development Molecular Anatomy Project (GUDMAP), MRC Human Genetics Unit (HGU), Western General Hospital, Edinburgh (Alam-Faruque) (June)
 
 
 
Invited Speaker-Introduction to the Gene Ontology. Cell Behavior Ontology Workshop, National Institutes of Health, Bethesda, MD. (Diehl) (May)
 
 
 
Invited Speaker-Gene Ontology Recapitulates Ontogeny: Using the Gene Ontology to Study Development. Molecular Reproduction and Development Meeting, Brown University, RI.(Hill) (March)
 
 
 
Invited speaker-Introduction to GO and other Biomedical Ontologies. European Bioinformatics Institute Primer for Predocs Course, Hinxton UK. (Lomax) (Feb)
 
 
 
Invited speaker-'GO for it! Gene Ontology - an essential resource'. Department of Medicine, University College London, UK. (Lovering) (Feb)
 
 
 
Invited speaker-'Microbe-Plant Interactions through the Lens of Gene Ontology'. Research Centre for Plant Biotechnology and Genomics, Madrid, Spain (CW Collmer) (May)
 
 
 
Conference talk - 'The evolution of Sequence Ontology Terms and Relationships' International Conference for Biomedical Ontology, Buffalo NY. (Eilbeck) (July)
 
 
 
===2009 Posters===
 
 
 
2009 Improving Logical Relationship in the Gene Ontology. Third International Biocuration Conference, Berlin, Germany. (Berardini, Harris*, Hill, Lomax, Mungall) (April)
 
 
 
2009 [http://wiki.geneontology.org/index.php/Image:JaneLomaxBiocurators_small.jpg Gene Ontology: Serving the Community]. Third International Biocuration Conference, Berlin, Germany. (Lomax*, Carbon, Hitz, Ireland, the Gene Ontology web-presence WG) (April)
 
 
 
2009 The GO Annotation (GOA) Project. Third International Biocuration Conference, Berlin, Germany. (Rachael Huntley*, Emily Dimmer, Daniel Barrell, David Binns and Rolf Apweiler) (April)
 
 
 
2009 The Gene Ontology: Making Biomedical language Computable. The Hopper Colloquium, British Computer Society, London. (Jennifer I. Deegan*, Michael Bada, Tanya Z. Berardini, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax, Wacek Kusnierczyk, Christopher J. Mungall) (May)
 
 
 
2009 The Gene Ontology's Reference Genome Project: �A Unified Framework for Functional Annotation across Species, Pascale Gaudet for the Reference Genome Group of the Gene Ontology Consortium, Dicty Annual International Meeting, Estes Park, CO (August) (Gaudet)
 
 
 
  
 
==2008==
 
==2008==
  
 
===2008 Publications ===
 
===2008 Publications ===
Alterovitz, G., Xiang, M., Hill, D., Lomax, J., Liu, J., Mungall, C., Harris, M., Dolan, M.E., Blake, J.A., Ramoni, M.F. Engineering Biomedical Ontologies: The Gene Ontology [In Revision, Nature Biotechnology].
 
  
 
Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O’Donoghue, S.I., Peitsch, M, Rebholz-Schumann, D., Shatkay, H., Valencia, A. 2008. Text mining for biology - the way forward: opinions from leading scientists.  Genome Biology 9:S7.  http://genomebiology.com/2008/9/S2/S7  
 
Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O’Donoghue, S.I., Peitsch, M, Rebholz-Schumann, D., Shatkay, H., Valencia, A. 2008. Text mining for biology - the way forward: opinions from leading scientists.  Genome Biology 9:S7.  http://genomebiology.com/2008/9/S2/S7  
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Hill, D., Smith, B. McAndrews-Hill, M., Blake, J.A. 2008. Gene Ontology Annotations: What they mean and where they come from. BMC Bioinformatics 9 Suppl 5: S2.  
 
Hill, D., Smith, B. McAndrews-Hill, M., Blake, J.A. 2008. Gene Ontology Annotations: What they mean and where they come from. BMC Bioinformatics 9 Suppl 5: S2.  
 +
 +
Hong, E.L., Balakrishnan, R., Dong, Q., Christie, K.R., Park, J., Binkley, G., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Krieger, C.J., Livstone, M.S., Miyasato, S.R., Nash, R.S., Oughtred, R., Skrzypek, M.S., Weng, S., Wong, E.D., Zhu, K.K., Dolinski, K., Botstein, D., and J.M. Cherry. (2008) Gene Ontology Annotations at SGD: New Data Sources and Annotation Methods. Nucleic Acids Res., 36:D577-D581
  
 
Lovering, R.C., Camon, E.B., Blake, J.A., Diehl, A.D.  Access to Immunology through the Gene Ontology.  Immunology. 2008 Oct;125(2):154-60.
 
Lovering, R.C., Camon, E.B., Blake, J.A., Diehl, A.D.  Access to Immunology through the Gene Ontology.  Immunology. 2008 Oct;125(2):154-60.
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Lovering R.C., Dimmer E., Khodiyar V.K., Barrell D.G., Scambler P., Hubank M., Apweiler R., Talmud P.J. Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics. 2008 May;8(10):1950-3.
 
Lovering R.C., Dimmer E., Khodiyar V.K., Barrell D.G., Scambler P., Hubank M., Apweiler R., Talmud P.J. Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics. 2008 May;8(10):1950-3.
  
Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. 2008.  A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology. 9:S2. http://genomebiology.com/2008/9/S1/S2  
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Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. 2008.  A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology. 9:S2. http://genomebiology.com/2008/9/S1/S2
 +
 
 +
Rhee SY., Wood V, Dolinski K, Draghici S. Use and misuse of Gene Ontology annotations. Nat Rev Genet. 2008 Jul;9(7):509-15.
  
 
Sam, L.T., Mendonca, EA., Blake, J.A., Friedman, C., Lussier, Y.A. PhenoGO: A Resource for the Multiscale Integration of Clinical and Biological Data. BMC Bioinformatics Suppl 2:S8.
 
Sam, L.T., Mendonca, EA., Blake, J.A., Friedman, C., Lussier, Y.A. PhenoGO: A Resource for the Multiscale Integration of Clinical and Biological Data. BMC Bioinformatics Suppl 2:S8.
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2008 Avian gene Ontology Workshop, Starksville, MI. What is the GO? GO Annotation. (Drabkin) (May)
 
2008 Avian gene Ontology Workshop, Starksville, MI. What is the GO? GO Annotation. (Drabkin) (May)
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2008 WT advanced course. Genome wide approaches with fission yeast fission yeast
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Module GO Tools; a computing workshop (invited talk and workshop) (Wood)
  
 
=== 2008 Posters ===
 
=== 2008 Posters ===
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2003, 2004 Invited speaker Advances in Genome Technology and Bioinformatics. Co-Sponsored by the Marine Biological Laboratory and The Institute for Genomic Research. Woods Hole, MA (Blake).
 
2003, 2004 Invited speaker Advances in Genome Technology and Bioinformatics. Co-Sponsored by the Marine Biological Laboratory and The Institute for Genomic Research. Woods Hole, MA (Blake).
  
[[Category:Reports]]
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[[Category:Publications]]

Latest revision as of 07:18, 9 April 2019

GO publications, Tutorials and Workshops, Presentations, and Posters
For the GO grant HG –02273
2007 – 2009

Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members.

2009

GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources

2008

2008 Publications

Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O’Donoghue, S.I., Peitsch, M, Rebholz-Schumann, D., Shatkay, H., Valencia, A. 2008. Text mining for biology - the way forward: opinions from leading scientists. Genome Biology 9:S7. http://genomebiology.com/2008/9/S2/S7

Arighi, C., Hongfang, L., Natale, D., Barker, W., Drabkin, H., Zhangzhi, H., Blake, J.A., Smith, B., Wu, C. TGF-beta Signaling Proteins and the Protein Ontology. [In Press: BioOntologies SIG 2008.]

Blake, J.A. and Harris, M. “The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis.” Current Protocols in Bioinformatics, Chapter 7, Unit 7.2. Wiley Inc.

Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA., Mouse Genome Database Group. 2008. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 36(Database):D724-8.

Degtyarenko, K., de Matos, P., Ennis, M., Hastings, J., Zbinden, M., McNaught, A., Alcantara, R., Guedj, M., Ashburner, M. 2008. ChEBI: A database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36 (Database Issue): D344-50.

Diehl, A.D., Camon, E.B., Lovering, R.C., Immunology On the GO, Immunology News, issue 15.2 May 2008.

Dimmer E. The GOA@EBI resource. EMBnet News 14(1): 22-27.

Dimmer, E.C., Huntley, R.P., Barrell, D.G., Binns, D., Camon, E., Hubank, M., Blake, J.A., Apweiler, R., Talmud, P.J., Lovering, R.C. The Gene Ontology - Providing a Functional Role in Proteomic Studies. Proteomics. 2008 Jul 17. [Epub ahead of print].

Dolan, M.E., and Blake, J.A., Using ontology visualization to facilitate access to knowledge about human disease genes [In press: Applied Ontology].

Drabkin, H.J., Arighi, C.N., Wu, C. H., Blake, J.A. Functional Annotation of Protein Isoforms and Modified Forms. Proceedings of the 2008 International Conference on Bioinformatics & Computational Biology. Volume 2, 701-707.

Field, D., Garrity, G., Gray, T., Morrison, N., Selengut, J., Sterk, P., Tatusova, T., Thomson, N., Allen, M.J., Angiuoli, S.V., Ashburner, M., Axelrod, N., Baldauf, S., Ballard, S., Boore, J., Cochrane, G., Cole, J., Dawyndt, P., de Vos, P., dePamphilis, C., Edwards, R., Faruque, N., Feldman, R., Gilbert, J., Gilna, P., Glöckner, F.O., Goldstein, P., Guralnick, R., Haft, D., Hancock, D., Hermjakob, H., Hertz-Fowler, C., Hugenholtz, P., Joint, I., Kagan, L., Kane, M., Kennedy, J., Kowalchuk, G., Kottmann, R., Kolker, E., Kravitz, S., Kyrpides, N., Leebens-Mack, J., Lewis, S.E., Li, K., Lister, A., Lord, P., Maltsev, N., Markowitz, V., Martiny, J., Methe, B., Moxon, R., Nelson, K., Parkhill, J., Proctor, L., Sansone, S.-A., Spiers, A., Stevens, R., Swift, P., Taylor, C., Tateno, Y., Tett, A., Turner, S., Ussery, D., Vaughan, B., Ward, N., Whetzel, T. Wilson, G., and Wipat, A. 2008. Minimum Information about a Genome Sequence (MIGS) specification. Nature Biotechnology 26: 541-7.

Harris MA. 2008. Developing an ontology. Methods Mol Biol. 452: 111-124.

Harris MA, Feltrin E. 2008. Browsing and searching Gene Ontology resources using AmiGO. EMBnet News 14(1): 17-21.

Hill, D., Smith, B. McAndrews-Hill, M., Blake, J.A. 2008. Gene Ontology Annotations: What they mean and where they come from. BMC Bioinformatics 9 Suppl 5: S2.

Hong, E.L., Balakrishnan, R., Dong, Q., Christie, K.R., Park, J., Binkley, G., Costanzo, M.C., Dwight, S.S., Engel, S.R., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Krieger, C.J., Livstone, M.S., Miyasato, S.R., Nash, R.S., Oughtred, R., Skrzypek, M.S., Weng, S., Wong, E.D., Zhu, K.K., Dolinski, K., Botstein, D., and J.M. Cherry. (2008) Gene Ontology Annotations at SGD: New Data Sources and Annotation Methods. Nucleic Acids Res., 36:D577-D581

Lovering, R.C., Camon, E.B., Blake, J.A., Diehl, A.D. Access to Immunology through the Gene Ontology. Immunology. 2008 Oct;125(2):154-60.

Lovering R.C., Dimmer E., Khodiyar V.K., Barrell D.G., Scambler P., Hubank M., Apweiler R., Talmud P.J. Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO? Proteomics. 2008 May;8(10):1950-3.

Pena-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP. 2008. A critical assessment of M. musculus gene function prediction using integrated genomic evidence. Genome Biology. 9:S2. http://genomebiology.com/2008/9/S1/S2

Rhee SY., Wood V, Dolinski K, Draghici S. Use and misuse of Gene Ontology annotations. Nat Rev Genet. 2008 Jul;9(7):509-15.

Sam, L.T., Mendonca, EA., Blake, J.A., Friedman, C., Lussier, Y.A. PhenoGO: A Resource for the Multiscale Integration of Clinical and Biological Data. BMC Bioinformatics Suppl 2:S8.

Tasan, M., Tian, W., Hill, D.P., Gibbons, F.D., Blake, J.A., and Roth F.P. 2008. An en masse phenotype and function prediction system for M. musculus. Genome Biology. 9:S8. http://genomebiology.com/2008/9/S1/S8

Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novere N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, Wiemann S. 2008. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotech 26: 889-96.

The Gene Ontology Consortium*. 2008. The Gene Ontology (GO) Project in 2008. Nucleic Acids Res. 36(Database issue): D440-4.

2008 Talks

2008 Keynote speaker: Plant and Animal Genomes Conference, San Diego. (Ashburner) (January)

2008 Invited speaker: Ontology workshop, Plant and Animal Genomes Conference, San Diego. (Ashburner) (January)

2008 Organiser and speaker: Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Dagstuhl, Germany. March 24-28th. (Ashburner) (March)

2008 Invited talk. Introduction to the Gene Ontology. Making Small Facts Travel: Labels, Packages and Vehicles workshop, London School of Economics and Political Science, UK. (Harris) (March)

2008 Invited Speaker. Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives. Dagstuhl, Germany. March 24-28, 2008. Talk: What makes text mining useful. (Blake)(March)

2008 Invited speaker. Royal Society Discussion Meeting, Environmental eScience. (Ashburner) (April)

2008 Keynote speaker. European Bioinfomatics Institute, Chemi-Informatics Meeting. Hinxton. (Ashburner) (May)

2008 Plenary Speaker. International Conference: Delivering Value from Avian Genomics. Mississippi State University, Starkville, Mississippi. May 19-20, 2008. Talk: Ontologies for Biology. (Blake)(May)

2008 Invited speaker. Royal Society of Chemistry, Cambridge, UK. The Gene Ontology Project. (Harris) (June)

2008 Invited speaker. Wellcome Trust Advanced courses, Functional Genomics and Systems Biology, Wellcome Trust Genome Campus, Hinxton, Cambridge. (Lomax) (June)

2008 Invited Seminar speaker. Universität Bonn, B-IT. (Ashburner) (July)

2008 Invited speaker. Cardiovascular Initiative Workshop, Human Proteome Organisation 7th Annual World Congress, Amsterdam, Netherlands. Talk: The Cardiovascular Gene Ontology Annotation Initiative. (Lovering) (August)

2008 Keynote speaker. German Conference on Bioinformatics -2008 - Dresden. (Ashburner) (September)

2008 Plenary Speaker. British Society for Immunology Annual Congress, Glasgow, UK. Talk: Immunology's time to GO. (Lovering) (November)

2008 Workshops

2008 Avian gene Ontology Workshop, Starksville, MI. What is the GO? GO Annotation. (Drabkin) (May)

2008 WT advanced course. Genome wide approaches with fission yeast fission yeast Module GO Tools; a computing workshop (invited talk and workshop) (Wood)

2008 Posters

2008 Describing Biological Regulations In The Gene Ontology. Biology of Genomes, Cold Spring Harbor, NY. (Dolan) (May)

2008 Data Management and Biological Knowledge Representation in the Mouse, ISMB 2008 Conference, Toronto, CA. (Ni) (July)

2008 The Cardiovascular Gene Ontology Initiative, 77th European Atherosclerosis Society Meeting, Istanbul, Turkey. (Talmud) (April)

2008 The Cardiovascular Gene Ontology Initiative, UCL Cardiovascular Science and Medicine day, London, UK. (Lovering, Khodiyar, Talmud) (June)

2008 Participate in the Cardiovascular Gene Ontology Annotation Initiative, Human Proteome Organisation 7th Annual World Congress, Amsterdam, Netherlands. (Lovering) (August)

2008 Gene Ontology - a way forwards, British Society for Immunology Annual Congress, Glasgow, UK. (Lovering) (November)

2008 Using the Universal Language of Gene Ontology to Annotate Gene Products involved in the Interactions between Microbes and their Hosts, American Phyopathological Society annual meeting, Minneapolis, MN (CW Collmer) (July)

2007

2007 Publications

Day-Richter J, Harris MA, Haendel M, The Gene Ontology OBO-Edit Working Group, Lewis S. 2007. OBO-Edit--an ontology editor for biologists. Bioinformatics. 23(16): 2198-2200.

Diehl A.D., Lee J.A., Scheuermann R.H., Blake J.A. 2007. Ontology development for biological systems: immunology. Bioinformatics. 23(7):913-5.

Dimmer, E., Berardini, T. Z., Barrell, D., Camon, E. Methods for Gene Ontology Annotation. Plant Bioinformatics: Methods and Protocols, Ed. D. Edwards. Published by Humana Press: Series Methods in Molecular Biology 31 July 2007.

Dolan, M.E., and Blake, J.A., Using ontology visualization to facilitate access to knowledge about human disease genes (in press: Applied Ontology).

Mabee, P.M., Ashburner, M., Cronk, Q., Gkoutos, G.V., Haendel, M., Segerdell, E., Mungall, C. and Westerfield, M. 2007. Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22(7): 345—350.

Natale DA, Arighi CN, Barker WC, Blake JA, Chang T-C, Hu Z, Liu H, Smith B, Wu CH. 2007. Framework for a Protein Ontology. BMC Bioinformatics 8(Suppl 9):S1.

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. 2007. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25: 1251-1255.

The Gene Ontology Consortium. 2007. The Gene Ontology (GO) project in 2008. Nucleic Acids Res. Epub 2007 Nov 4.

Zhong, W., Sternberg P.W. Automated data integration for developmental biological research. Development. 2007 Sep;134(18):3227-38.


2007 Talks

2007 Gene Ontology Annotation (GOA) at the EBI: Update. EBI Sequence Database group, EBI, Cambridge, UK. (Huntley)(January)

2007 What's New in GO? Chicken and Cow Meeting, Hinxton, UK. (Clark)(January)

2007 The Gene Ontology Project. CRIBI, University of Padua, Italy (Clark)(January)

2007 Plant-Associated Microbe Gene Ontology (PAMGO): A community resource of Gene Ontology (GO) terms describing gene products involved in microbe-host interactions. Plant and Animal Genome XV Conference. San Diego. CA. USA. (Gwinn-Giglio, Collmer, Torto-Alalibo) (January)

2007 Sharing immunological knowledge with Gene Ontology. St. Vincents Hospital Research Centre, Dublin. (Camon)(February)

2007 Invited seminar. Ontologies for all. Babraham Institute, Cambridge. (Ashburner)(February)

2007 Invited Speaker and Participant. Alignment of Ontologies for Biological Research. Dagstuhl Seminar: Towards Interoperability of Biomedical Ontologies. Wadern, Germany. (Blake)(March)

2007 Invited talk. SO and Biological Sequence. Towards interoperability of biomedical ontologies, Schloss Dagstuhl, Germany. (Eilbeck)(March)

2007 Real-life Ontology Development: Lessons from the Gene Ontology. Ontogenesis Meeting, Manchester, UK. (Lomax) (March)

2007 Invited seminar. The Gene Ontology, Department of Biology, University of Cyprus. (Ashburner)(April)

2007 Presentation on ontologies. GAIA Workshop, Gournadis GAIA Centre, Athens. (Ashburner)(April)

2007 Invited seminar. Ontologies and biological knowledge. Max-Plank Institute for Cell Biology, Dresden. (Ashburner)(April)

2007 Presentation on ontologies. EU-US Workshop on Infrastructure Needs of Systems Biology, Boston. (Ashburner)(May)

2007 Invited Participant. US-EU Workshop on Infrastructure Needs of Systems Biology. US-EC Task Force on Biotechnology Research: NSF, NIH, and Research Directorate of the European Commission. Boston, MA. (Blake)(May)

2007 Invited talk. Representing Immunology in the GO: Ontology Development and Annotation. DAIT Bioinformatics Summit 2007, Gaithersburg, MD. (Diehl)(May)

2007 Invited talk. Gene Ontology for Immunology: an Overview. 94th Annual Meeting of the The American Association of Immunologists, Miami Beach, FL.(Diehl)(May)

2007 Invited talk. SO meets RNAO. RNA Ontology Consortium meeting, Madison. (Eilbeck)(May)

2007 Introduction to the Gene Ontology and GOA projects, and an overview of other ontology developments at the EBI. Boehringer-Ingelheim, Biberach an der Riss, Germany. (Dimmer)(May)

2007 Introduction to the Gene Ontology and GOA projects, EMBO/SPINE2 Conference on Intrinsically Unstructured Proteins, Budapest, Hungary. (Camon)(May)

2007 Immune Gene Classification Using Gene Ontology, Bovine & Avian Immunogenomics Workshop, Dublin, Ireland. (Dimmer)(May)

2007 Using Ontology to Represent Biological Knowledge, Dept. of Physiology, Medical College of Wisconsin, Milwaukee, WI (Hill)(May)

2007 Sharing Knowledge with Gene Ontology Annotation: An Immunology Update. Institute for Animal Health (IAH), Compton, Berkshire, England, UK. (Camon)(June)

2007 Gene Ontology in WormBase. WormBase Workshop. 16th International C. elegans Meeting, University of California at Los Angeles. (Kishore)(June).

2007 Presentation on ontologies. Drosophila Neuroinformatics Workshop. HHMI, Janelia Farm Research Campus. (Ashburner)(July)

2007 Gene Ontology Annotation Database, Almac Group Ltd., Craigavon, Northern Ireland. (Camon)(July)

2007 GO and GOA. Royal Society of Chemistry, Cambridge, UK. (Dimmer)(July)

2007 GOA database Project. Swiss Institute of Bioinformatics, Geneva, Switzerland. (Dimmer and Barrell)(July)

2007 GOA: Looking after GO annotations, International Workshop on Genomic Databases, Rio de Janeiro, Brazil. (Foulger)(August)

2007 Presentation on ontologies. Infectious Disease Ontology Meeting, Cold Spring Harbor. (Ashburner)(September)

2007 Invited talk. Ontologies for all. ESF-EMBO Symposium on Comparative Genomics, Spain. (Ashburner)(September)

2007 Presentation on ontologies. Expanding the Genetic Toolkit in Drosophila, HHMI, Janelia Farm Research Campus. (Ashburner)(September)

2007 Gene Ontology Annotation for Immune System Genes. Irish Society of Immunology, Annual Symposium, Dublin, Ireland. (Camon)(September)

2007 Invited seminar. Center for Molecular and Biomolecular Informatics, Radboud University, Nijmegen. (Ashburner)(October)

2007 Plenary Speaker. Evidence and Influence: Paths to Curation. Second International Biocurator Meeting, San Jose (Blake)(October)

2007 Good habits in Ontology Development, a GO perspective. 2nd International Biocurator Meeting, San Jose (Hill)(October)

2007 Invited talk. Introduction to the Gene Ontology. EMBRACE workshop on Applied GO, Bari, Italy. (Harris) (November)

2007 Invited talk. Introduction to GOA. EMBRACE workshop on Applied GO, Bari, Italy. (Dimmer)(November)

2007 Seminar and tutorial: Introduction to GOA. Wellcome Trust Advanced Courses Proteomics Workshop, EBI, Cambridge, UK. (Dimmer and Huntley)(November)

2007 Cardiovascular GO annotation initiative. Centre for Cardiovascular Genetics, University College London, UK. (Lovering)(November)

2007 Invited talk. Protein features in SO. The inaugural meeting of the Protein Ontology project, Georgetown University, Washington DC. (Eilbeck)(December)

2007 Workshops and Tutorials

2007 Browsing and Searching Gene Ontology Resources Using AmiGO: A Tutorial. EMBRACE workshop on Applied GO, Bari, Italy. (Harris, Feltrin)

2007 The Gene Ontology project and its application to fission yeast functional genomics data. Wellcome Trust fission yeast functional genomics workshop. Hinxton, UK (Wood)

2007 The Gene Ontology (GO) Project. GO tutorial at Interactome Networks meeting, Hinxton, UK. (Deegan, Hitz)

2007 Using GO for Analysis of Gene Expression Data. Talk and demo on GO at Wellcome Trust Advanced Course on Functional Genomics, Hinxton, UK. (Lomax)

2007 Gene Ontology (GO) Project. Talk and demo on GO at Agro-genomics workshop on plant annotation, Ghent, Belgium. (Lomax)

2007 GO demonstration at MSc student open day at EBI, Hinxton, UK. (Clark)

2007 Gene Ontology Project. GO tutorial at Royal Society of Chemistry, Cambridge, UK. (Lomax, Clark)

2007 Making Gene Ontology Annotations for Fungal Genomes. GO Workshop at 24th Fungal Genetics Conference, Asilomar, Pacific Grove, CA. (Christie, Balakrishnan, Costanzo)

2007 Arabidopsis gene function annotation using controlled vocabularies. Part of the TAIR workshop. Plant and Animal Genome Conference, San Diego, CA. (Donghui) (January)

2007 TAIR/Gramene/SGN Workshop I: Gene Ontology and Plant Metabolic Databases. American Society of Plant Biologists Plant Biology and Botany Joint Congress, Chicago, IL (Tanya) (July)

2007 Invited workshop. Getting started with PAMGO: Theory and practice of creating new GO terms. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Collmer)(July)

2007. Invited workshop. GO annotation of experimentally characterized genes from Pseudomonas syringae. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Lindeberg) (July)

2007. Invited workshop. GO annotation of oomycete genomes: bioinformatic approaches. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Chibucos) (July)

2007. Invited workshop. Overview of ontology-based comparative genomics of microbes and their hosts. XIII International Congress on Molecular Plant-Microbe Interactions. Sorrento, Italy. (Torto-Alalibo) (July)

2007. Introduction to Functional Annotation. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Hannick) (August)

2007. The Gene Ontology. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Gwinn-Giglio)(August)

2007. Introduction to PAMGO. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Collmer)(August)

2007. Introduction to GO tools. PAMGO Workshop at the Virginia Bioinformatics Institute, Virginia Tech. Blacksburg VA. USA. (Torto-Alalibo)(August)

2007. Faculty, Graduate Course in Functional Genomics. UMaine-Orono and The Jackson Laboratory, Bar Harbor, ME. (Blake)

2007 Posters

2007 Does your species show in GO? Therapeutic Applications of Computational Biology and Chemistry meeting, Hinxton, UK. (Clark)

2007 The Cardiovascular Gene Ontology Initiative, University College London Cardiovascular Science and Medicine Day, London, UK. (Talmud, Lovering, Khodiyar)

2007 The Cardiovascular Gene Ontology Initiative, Genomics of Common Diseases, Wellcome Trust Genome Campus, Cambridge, UK (Talmud, Dimmer)

2007 The GO Reference Genome Annotation Project. Second International Biocurator Meeting, San Jose, CA, US. (Tweedie)

2007 PAMGO: A Community Resource for Gene Ontology (GO) Term Development and Annotation of Gene Products Involved in Microbe-Host Interactions. 107th American Society for Microbiology. Toronto, Canada. (Torto-Alalibo)

2007 Gene Ontology (GO) for microbe-host interactions and its use in ongoing annotation of three Pseudomonas syringae genomes. 7th International Conference on Pseudomonas syringae Pathovars and Related Pathogens (ICPSPRP), Agadir, Morocco. (Collmer)

2007 Ortholog detection and transfer of Gene Ontology annotations in related oomycete genomes. Oomycete Molecular Genetics Network Workshop, Pacific Grove, CA. USA.(Chibucos)

2007 Computing on Development. Society for Developmental Biology Annual Meeting, Cancun, Mexico (Hill)

2007 The Comprehensive Functional Annotation of Mouse Genes and Gene Products Using The Gene Ontology (GO). Genome Informatics Meeting, Cold Spring Harbor, NY. (Ni) (November)

2007 Fliers/literature created

University College London Cardiovascular Science and Medicine Day, May 2007, London, UK: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)

76th European Atherosclerosis Society Meeting, June 2007, Helsinki, Finland: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)

Genomics of Common Diseases, July 2007, Wellcome Trust Genome Campus, Cambridge, UK: Distributed a one-page flyer titled ‘The Cardiovascular Gene Ontology Initiative’ (P Talmud, P Scambler, M Hubank, R Apweiler, R Lovering and V Khodiyar)


All Years

Course Lectures on GO in the following courses

2007 Faculty, Graduate Course in Bioinformatics. Nanjing Agricultural University, China (Tyler)

2004 Faculty, Graduate Course in Functional Genomics. University of Maine and The Jackson Laboratory, Bar Harbor, ME (Blake).

2004 Faculty, Assessing gene function using the GO and MGI, Short Course on Gene Microarray Development and Analysis: Approaches to Heart, Lung, Blood and Sleep Disorders.(Blake).

2002-2004 Faculty, Short Course on Genome Sequence Analysis: Theory and Practice. Bar Harbor, ME. (Blake, Lewis)

2002-2004 Faculty, Short Course on Gene Microarray Development and Analysis: Approach to Heart, Lung, Blood and Sleep Disorders. Bar Harbor, ME. (Blake)

2003 Faculty, Toxicogenomics. Gordon Research Conference. Bates College, Lewiston, ME.(Blake).

2003, 2004 Invited speaker Advances in Genome Technology and Bioinformatics. Co-Sponsored by the Marine Biological Laboratory and The Institute for Genomic Research. Woods Hole, MA (Blake).