Publications, Talks, Posters 2013

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Journal Publications

Blake JA . 2013 Ten Quick Tips for Using the Gene Ontology. PLoS Comput Biol 9(11): e1003343. doi:10.1371/journal.pcbi.1003343.

Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, & Wilkinson MD. 2013. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of biomedical semantics, 4(1), 2. PMID:23286517

Asselbergs, F. W., Lovering, R. C., & Drenos, F. (2013). Progress in genetic association studies of plasma lipids. Curr Opin Lipidol, 24 (2), 123-128. doi:10.1097/MOL.0b013e32835df2d6 PMID:23385652 (not GOC funded)

Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. 2013. A gene ontology inferred from molecular networks. Nat Biotechnol. 2013 Jan;31(1):38-45. PMID: 23242164

Balakrishnan R, Harris MA, Huntley R, Van Auken K, Cherry JM. 2013. A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford). 2013 Jul 9;2013:bat054. PMC3706743

Blake JA. 2013. Ten Quick Tips for Using the Gene Ontology PMC3828149 PLoS Comput Biol. 2013 November; 9(11):

The Gene Ontology Consortium. 2013. Gene Ontology Annotations and Resources. Nucleic Acids Research, 41(Database issue), D530-535. PMC3531070

Hill DP, Adams N, Bada M, Batchelor C, Berardini TZ, Dietze H, Drabkin HJ, et al. 2013. Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology. BMC genomics, 14(1), 513. PMC3733925

Meehan T, Vasilevsky N, Mungall C, Dougall D, Haendel M, Blake J, & Diehl A. 2013. Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinformatics, 14(1), 263. PMID:24004649

Mutowo-Meullenet P, Huntley RP, Dimmer EC, Alam-Faruque Y, Sawford T, Jesus Martin M, O'Donovan C, Apweiler R. 2013. Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford). 2013 Jan 17;2013:bas062. PMC3548334

Roncaglia P, Martone ME, Hill DP, Berardini TZ, Foulger RE, Imam FT, Drabkin H, et al. 2013. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. Journal of Biomedical Semantics, 4(1), 20. PMID:24093723

Tripathi S, Christie KR, Balakrishnan R, Huntley R, Hill DP, Thommesen L, Blake JA, Kuiper M, Lægreid A. Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. 2013. Database (Oxford). 2013 Aug 27;2013:bat062. PMC3753819

UniProt Consortium. 2013. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. PMC3531094

Talks

Web Apollo: Lessons learned from community based biocuration efforts. 2013 sbvIMPROVER Symposium. Athens, Greece. M. Munoz-Torres (speaker).

TermGenie - Granting Biocurators' Wishes for the Gene Ontology 2013 BioCurators, Cambridge, UK, SlideShare

- Increased Expressivity of Gene Ontology Annotations

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Biocuration April 2013, Cambridge, UK. Prudence Mutowo (talk).

The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany. Rachael Huntley (talk).

Making Gene Ontology Annotations for Transcription Factors. Karen Christie (with Rachael Huntley) - Workshop at the EBI for the NTNU group annotating transcription factors and their target genes (small group workshop). February 7-8 2013, Hinxton, UK.

Increased expressivity of mouse protein function representation using the gene ontology; Drabkin, Harold J; The Jackson Laboratory, USA 2013; Proteomics 2013, July 15-17; Philadelphia PA

Gene Ontology: progress and priorities for annotating the human genome; Ruth Lovering at Annotating the Genome - BCGES Annual Meeting in conjunction with Statistics and South of England Genetic Epidemiology Group. 12th June 2013, London (not GOC funded)

Posters

AmiGO 2: An Adventure in Flatland 2013 International Biocuration Conference, Cambridge, UK.

Representation of apoptosis in the Gene Ontology File:BioCuration2013.pdf 2013 International Biocuration Conference, Cambridge, UK.

Protein2GO: A curation tool for Gene Ontology. 2013 International Biocuration Conference, Cambridge, UK. Rachael Huntley.

The Gene Ontology Resource - Common Misconceptions and Improving Accuracy. Automated Function Prediction SIG at ISMB/ECCB July 20 2013, Berlin, Germany. Rachael Huntley.

The UniProt-GOA resource. EMBL-EBI Open Day, Hinxton. November 7 2013. Prudence Mutowo and Aleks Shypitsyna.

The UniProt-GOA resource. EMBL-EBI Open Day, Hinxton. March 14 2013. Rachael Huntley.

Assessment of comparative functional annotation propagation in mouse. The 27th International Mammalian Genome Conference, 2013. Ni L; Dolan ME; Blake JA

The impact of focused Gene Ontology annotation efforts on high-throughput data analysis. Computational Life & Medical Sciences 3rd Annual Symposium, London. June 28 2013. Ruth Lovering. (Not GOC funded)

The impact of focused Gene Ontology annotation efforts on high-throughput data analysis. Innovations in Cardiovascular Science Symposium, London, April 22 2013. Ruth Lovering. (Not GOC funded)

The impact of focused Gene Ontology annotation efforts on high-throughput data analysis. Biocuration 2013, Cambridge, April 7-10 2013. Ruth Lovering. (Not GOC funded)

Gene Annotation at UCL. RA Fisher Centre Meeting, London, November 8 2013. Nancy Campbell. (Not GOC funded)

Tutorials

EBI Bioinformatics Roadshow January 2013 Zimbabwe. Prudence Mutowo.

Making Gene Ontology Annotations for Transcription Factors. Workshop at the EBI for the NTNU group annotating transcription factors and their target genes. February 7-8 2013, Hinxton, UK. Karen Christie and Rachael Huntley (small group workshop).

Using the Gene Ontology. EMBL-EBI Industry Programme Workshop: "A practical overview of biomedical ontologies". April 17-18 2013, Hinxton, UK. Rachael Huntley (Hands-on tutorial).

Rachael Huntley trained two GeneDB curators in GO annotation. October 18 2013, Hinxton.

2-day GO annotation workshop at UCL. This workshop was attended by 20 UCL scientists who learn how to use some of the freely available biological databases, how to analyse high-throughput datasets and also contributed GO annotations to the GOA database. April 2013. Ruth Lovering and Antonia Lock. (Not GOC funded)