Publications, Talks, Posters 2015

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List of papers published by GOC in 2015

Please list all article publications below in chronological order; the most recent publication should appear first.

Acknowledge funding by GOC NHGRI grant

  • Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 2015 Nov 3. pii: gkv1116. [Epub ahead of print] PubMed PMID: 26538599.
  • Drabkin HJ, Christie KR, Dolan ME, Hill DP, Ni L, Sitnikov D, Blake JA. Application of comparative biology in GO functional annotation: the mouse model. Mamm Genome. 2015 Jul 4. [Epub ahead of print] PubMed PMID: 26141960.
  • Dolan ME, Baldarelli RM, Bello SM, Ni L, McAndrews MS, Bult CJ, Kadin JA, Richardson JE, Ringwald M, Eppig JT, Blake JA. Orthology for comparative genomics in the mouse genome database. Mamm Genome. 2015 Aug;26(7-8):305-13. doi:10.1007/s00335-015-9588-5. Epub 2015 Jul 30. PubMed PMID: 26223881; PubMed Central PMCID: PMC4534493.
  • Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. Genesis. 2015 Aug;53(8):474-85. doi: 10.1002/dvg.22877. Epub 2015 Aug 4. PubMed PMID: 26201819; PubMed Central PMCID: PMC4545719.
  • Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL. dictyBase 2015: Expanding data and annotations in a new software environment. Genesis. 2015 Aug;53(8):523-34. doi: 10.1002/dvg.22867. Epub 2015 Jul 8. PubMed PMID: 26088819; PubMed Central PMCID: PMC4545684.
  • Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121. PubMed PMID: 26133389; PubMed Central PMCID: PMC4524488.
  • Patel S, Roncaglia P, Lovering RC. Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. BMC Bioinformatics. 2015 Jun 6;16:186. doi: 10.1186/s12859-015-0622-0. PubMed PMID: 26047810; PubMed Central PMCID: PMC4458007.
  • Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford). 2015 May 9;2015:bav043. doi:10.1093/database/bav043. Print 2015. PubMed PMID: 25957950; PubMed Central PMCID:PMC4425939.
  • Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Manning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbitt PC, Bateman A. Key challenges for the creation and maintenance of specialist protein resources. Proteins. 2015 Jun;83(6):1005-13. doi: 10.1002/prot.24803. Epub 2015 Apr 22. PubMed PMID: 25820941; PubMed Central PMCID: PMC4446195.
  • Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ. TermGenie - a web-application for pattern-based ontology class generation. J Biomed Semantics. 2014 Dec 11;5:48. doi: 10.1186/2041-1480-5-48. eCollection 2014. PubMed PMID: 25937883; PubMed Central PMCID: PMC4417543.
  • Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol. 2014 Dec 3;5:634. doi: 10.3389/fmicb.2014.00634. eCollection 2014. PubMed PMID: 25520705; PubMed Central PMCID: PMC4253957.
  • Ascensao JA, Dolan ME, Hill DP, Blake JA. Methodology for the inference of gene function from phenotype data. BMC Bioinformatics. 2014 Dec 12;15:405. doi:10.1186/s12859-014-0405-z. PubMed PMID: 25495798; PubMed Central PMCID:PMC4302099.
  • Gene Ontology Consortium. Gene Ontology Consortium: going forward. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26. PubMed PMID: 25428369; PubMed Central PMCID: PMC4383973.
  • Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C. The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res. 2015 Jan;43(Database issue):D1057-63. doi:10.1093/nar/gku1113. Epub 2014 Nov 6. PubMed PMID: 25378336; PubMed Central PMCID: PMC4383930.
  • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015 Jan;43(Database issue):D204-12. doi: 10.1093/nar/gku989. Epub 2014 Oct 27. PubMed PMID: 25348405; PubMed Central PMCID: PMC4384041.

Substantial GO involvement reported by broader GOC community

  • Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: Automating Patient Matching Through the Exchange of Structured Phenotypic and Genotypic Profiles. Hum Mutat. 2015 Oct;36(10):922-7. doi: 10.1002/humu.22850. PubMed PMID: 26255989.
  • Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858. PubMed PMID: 26295439; PubMed Central PMCID: PMC4610002.
  • Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct;26(9-10):548-55. doi:10.1007/s00335-015-9577-8. Epub 2015 Jun 20. PubMed PMID: 26092691; PubMed Central PMCID: PMC4602072.
  • Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S, Groza T, Shefchek K, Hochheiser H, Robinson PN, Lewis SE, Haendel MA. Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Hum Mutat. 2015 Oct;36(10):979-84. doi: 10.1002/humu.22857. Epub 2015 Sep 8. PubMed PMID:26269093.
  • Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, Oellrich A, Mungall CJ, Washington N, Köhler S, Lewis SE, Robinson PN, Smedley D. Disease insights through cross-species phenotype comparisons. Mamm Genome. 2015 Oct;26(9-10):548-55. doi:10.1007/s00335-015-9577-8. Epub 2015 Jun 20. PubMed PMID: 26092691; PubMed Central PMCID: PMC4602072.
  • Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi:10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25. PubMed PMID: 26119816.
  • Yoshihara M, Ohmiya H, Hara S, Kawasaki S; FANTOM consortium, Hayashizaki Y, Itoh M, Kawaji H, Tsujikawa M, Nishida K. Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS One. 2015 Mar 25;10(3):e0117581. doi:10.1371/journal.pone.0117581. eCollection 2015. Erratum in: PLoS One. 2015;10(5):e0129412. PubMed PMID: 25807145; PubMed Central PMCID: PMC4373821.
  • Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. The complex portal - an encyclopaedia of macromolecular complexes. Nucleic Acids Research 2015, 43(Database issue):D479-84. PMID:25313161 PMCID:PMC4384031
  • Manzoni, C., Denny, P., Lovering, R. C., & Lewis, P. A. (2015). Computational analysis of the LRRK2 interactome. PeerJ, 2015 (2). doi:10.7717/peerj.778
  • Kalea AZ, Hoteit R, Suvan J, Lovering RC, Palmen J, Cooper JA, Khodiyar VK, Harrington Z, Humphries SE, D'Aiuto F. (2015). Upregulation of gingival tissue miR-200b in obese periodontitis subjects. Journal of Dental Research, 94, 59S-69S. doi:10.1177/0022034514568197
  • Patel, S., Roncaglia, P., & Lovering, R. C. (2015). Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. BMC BIOINFORMATICS, 16, UNSP 186. doi:10.1186/s12859-015-0622-0

2015 GO-centric Talks

Presenter Talk Title Date Venue Audience
Donna Slonim Functional Context Matters: Building and Applying a New Dictionary for Human Development 2015-09-01 First GO Symposium Day, GOC Annual Meeting, George Washington University, Washington, DC Open to the general public. Attendees included researchers, faculty, and students from local institutions as well as NIH senior personnel.
Trey Ideker GO as a central reference for automated assembly of multi-scale models of cell biology 2015-09-01 First GO Symposium Day, GOC Annual Meeting, George Washington University, Washington, DC Open to the general public. Attendees included researchers, faculty, and students from local institutions as well as NIH senior personnel.
Monica Munoz-Torres Genome Cartography: tools for precision and depth in the annotation process. (Original title: Cartografía de Genomas: herramientas para anotación con precisión y profundidad) 2015-09-17 Congreso Colombiano Biología Computacional y Bioinformática, Medellín, Colombia Conference attendees.
Monica Munoz-Torres Collaborative Genome Curation: precision and depth in the annotation process 2015-11-13 Dept. of Entomology & Plant Pathology, University of Tennessee, Knoxville Attendees to Departmental Seminar.
Paul Denny (UCL) Parkinson’s Disease and Gene Ontology Annotation 2015-09-12 International Parkinson's Disease Genomics Consortium Meeting, UCL, London Meeting attendees.
Rachael Huntley (UCL) MicroRNA functional annotation 2015-11-03 10th International Meeting on MicroRNAs, non-coding RNAs and Genome Editing, Cambridge, UK Meeting attendees.
Rachael Huntley (UCL) MicroRNA functional annotation 2015-12-01 RNAcentral Consortium and Scientific Advisory Board Meeting, Hinxton, UK Meeting attendees.
Valerie Wood (PomBase) Hidden in plain sight: The eukaryotically conserved unstudied proteins and a framework for their classification and characterisation (using GO to target uncharacterised gene products) June 2015 Fission yeast International meeting, Kobe, Japan Fission yeast biologists x
Kimberly Van Auken (WormBase) Gene Ontology (GO): Finding GO annotations and performing enrichment analysis June 25th and 27th, 2015 International C. elegans Meeting, UCLA WormBase Workshop Attendees
Claire O'Donovan Manual and Automatic annotation of plants and animals in UniProtKB and GO January 2015 Plant & Animal Genome Conference 2015, San Diego
Claire O'Donovan International collaboration in biocuration: projects & data/expertise sharing April 25, 2015 Biocuration Conference 2015, Beijing, China
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2015 GO-centric Posters

Presenter Poster Title Date Venue Audience
Paola Roncaglia and collaborators on vesicle project Refining Gene Ontology to Include Terms and Relationships Relevant to exRNA Communications [1] Apr 2015 ERCC/ISEV meeting, Bethesda, MD, USA Extracellular RNA and vesicle researchers
David Hill, Peter D' Eustachio, Nikolai Renedo, Judith Blake Linking GO Pathways to the Bigger Picture July 2015 ISMB/ECCB Dublin Ireland Computational Biologists
Karen Christie and Judith Blake Comprehensive Gene Ontology annotation of ciliary genes in the laboratory mouse July 2015 FASEB Biology of Cilia & Flagella - Snowmass, CO Cilia researchers
Ruth Lovering The Cardiovascular Gene Annotation Initiative: Current and Future Aims March 2015 83rd European Atherosclerosis Society Congress, Glasgow Atherosclerosis researchers
Paul Denny Autophagy to GO May 2015 First UK Autophagy Network Meeting. Warwick Autophagy researchers
Paul Denny Using Gene Ontology to characterise key participants in Parkinson's disease June 2015 UCL Neuroscience Symposium, London Neuroscience researchers
Melanie Courtot UniProt-GOA: A central resource for data integration and GO annotation December 2015 SWAT4LS, Cambridge UK

2015 GO-centric Workshops

Presenter Workshop Title Date Venue Audience
Various GOC members Workshop on Annotation 2015-09-01 First GO Symposium Day, GOC Annual Meeting, George Washington University, Washington, DC Open to the general public. Attendees included researchers, faculty, and students from local institutions as well as NIH senior personnel.
Paul Thomas Enrichment Analysis using the GO 2015-09-01 First GO Symposium Day, GOC Annual Meeting, George Washington University, Washington, DC Open to the general public. Attendees included researchers, faculty, and students from local institutions as well as NIH senior personnel.
Monica Munoz-Torres Gene Ontology Consortium: tools for functional annotation (Original title: Consorcio Ontología de Genes: herramientas para anotación funcional) 2015-09-22 Centro de Bioinformática y Biología Computacional (BIOS), Manizales, Colombia Science faculty, undergraduate, and graduate students from local institutions.
Ruth Lovering Bioinformatics and Gene Ontology Workshop 2015-04-20-21 University College London graduate students and staff mostly from UCL, but also from other UK universities and Europe.
Valerie Wood (PomBase) Curation workshop 2015-Nov Cambridge University Part III biochemistry undergraduates
Melanie Courtot EMBL-EBI training courses - Introduction to ontologies November 4, 2015 Cambridge, UK
Klemens Pichler EMBL-EBI training courses - Standards and Ontologies November 11-12, 2015 University of Umea, Sweden
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2015 GO Tutoring and Mentoring Activities

  • Paola Roncaglia at the EBI is external advisor of a PhD student in a program on "Foundations and Ethics of Life Sciences" (dissertation completed Oct 2015).
  • Rachael Huntley and Ruth Lovering (UCL) supervised 2 Genetics of Human Disease MSc students to annotate and they each submitted around 300 annotations and received distinctions for their project and MScs.
  • The UCL team taught a ‘bioinformatics’ module for Genetics of Human Disease MSc students (October-December 2015). By focusing on the review of a GWAS risk-associated SNP the students constructively apply their newly acquired knowledge of a variety of online biological resources, including Ensembl, NCBIGene, IntAct, Cytoscape, UniProt, QuickGO, AmiGO and functional analysis tools. In addition, the students learn the importance of including full experimental detail in scientific publications.
  • 1 week teaching GO annotation to VU curators.

2015 GO newsletters, Facebook and twitter

  • The UCL annotation teams continue to circulate quarterly newsletters for both projects and create regular tweets about our project news @UCLGene.