Publications

• Kramarz B, Lovering RC. Gene Ontology: A Resource for Analysis and Interpretation of Alzheimer’s Disease Data. In Alzheimer’s Disease. 2019. pp 23-36. (T. Wisniewski, editor), Codon Publications, Brisbane, Australia. PMID: 31895510.
• Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium. FAIR adoption, assessment and challenges at UniProt. Sci Data. 2019. 6(1):175. PMID: 31541106,
• Koopmans F, van Nierop P, Andres-Alonso M, … Kramarz B, Lipstein N, Lovering RC, … Foulger RE, … Thomas PD, Smit AB, Verhage M. SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019. 103(2):217-234. PMID: 31171447.
• Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L. CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics. 2019. pii: btz132. PMID: 30793173.
• Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. Annotation of gene product function from high-throughput studies using the Gene Ontology. Database (Oxford). 2019 doi: 10.1093/database/baz007. PMID: 30715275.
• Vadgama N, Lamont D, Hardy J, Nasir J, Lovering RC. Distinct proteomic profiles in monozygotic twins discordant for ischaemic stroke. Mol. Cell. Biochem. 2019 456(1-2):157-165. PMID:30694515.
• Franceschini N, Giambartolomei C, de Vries PS, Finan C, Bis JC, Huntley RP, Lovering RC, ..., O’Donnell CJ. GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes. Nature Communications. 2018 9(1):5141. PMID:30510157.
• Kramarz B, Roncaglia P, Meldal BHM, Huntley RP, Martin MJ, Orchard S, Parkinson H, Brough D, Bandopadhyay R, Hooper NM, Lovering RC. Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data. Genes(Basel). 2018 9(12). pii: E593. PMID:30501127.
• Köhler S, Carmody L, Vasilevsky N, … Lovering RC, … Haendel MA, Mungall C, Robinson PN. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2018 47(D1):D1018-D1027. PMID:30476213.
• The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. 2018 47(D1):D330-D338. PMID:30395331.
• The RNAcentral Consortium. RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 2018 47(D1):D1250-D1251. PMID:30395267.
• Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea AZ, Acquaah V, Martin MJ, Mayr M, Lovering RC. Expanding the horizons of microRNA bioinformatics. RNA. 2018 24:1005-1017. PMID:29871895.
• Ferrari R, Kia DA, Tomkins JE, Hardy J, Wood NW, Lovering RC, Lewis PA, Manzoni C. Stratification of candidate genes for Parkinson's disease using weighted protein-protein interaction network analysis. BMC Genomics. 2018 19(1):452. PMID:29898659.
• Pichler K, Warner K, Magrane M; UniProt Consortium. SPIN: Submitting Sequences Determined at Protein Level to UniProt. Curr Protoc Bioinformatics. 2018 62(1):e52. PMID:29927080.
• Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics. 2018 19(1):134. PMID:29642841.
• Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Riley PR, Lambiase PD, Elliott PM, Clapp L, Tinker A, Hill DP. Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. Circ. Genom. Precis. Med. 2018 11:e001813. PMID:29440116. Also see the YouTube summary
• Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Exploring autophagy with Gene Ontology. Autophagy. 2018 17:1-18. PMID:29455577.

• Chang D, Nalls MA, Hallgrímsdóttir IB, Hunkapiller J, van der Brug M, Cai F, International Parkinson's Disease Genomics Consortium, 23andMe Research Team, Kerchner GA, Ayalon G, Bingol B, Sheng M, Hinds D, Behrens TW, Singleton AB, Bhangale TR, Graham RR. (2017) A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci. Nat Genet. 49(10):1511-1516. PMID:28892059.
• The Gene Ontology Consortium. (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 4;45(D1):D331-D338. PMID:27899567. 
• Sunderland N, Skroblin P, Barwari T, Huntley RP, Lu R, Joshi A, Lovering RC, Mayr M. (2017) MicroRNA Biomarkers and Platelet Reactivity - the "Clot" Thickens. Circ Res. 120(2):418-435. PMID:28104774.
• Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. (2017) Bioinformatics. 33(21):3454-3460. PMID: 29036270.
• Zaru R, Magrane M, O'Donovan C; UniProt Consortium. From the research laboratory to the database: the Caenorhabditis elegans kinome in UniProtKB. (2017) Biochem J. 474(4):493-515. PMID:28159896.
• Huntley RP, Lovering RC. (2017) Annotation Extensions. Methods Mol Biol. 1446:233-243. PMID:27812947.
• Lovering RC. (2017) How Does the Scientific Community Contribute to Gene Ontology? Methods Mol Biol. 1446:85-93. PMID:27812937.
• Ferrari R, Lovering RC, Hardy J, Lewis P, Manzoni C. (2016) Weighted protein interaction network analysis of Frontotemporal Dementia. Journal of Proteome Research Dec 22. [Epub ahead of print] PMID:28004582.
• Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC. (2016) VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis. Mol Cell Proteomics. 16(2):168-180. PMID:28007913
• Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan  S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F,  Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M,  Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal  S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 17(1):184. PMID:27604469.
• Pundir S, Martin MJ, O'Donovan C; UniProt Consortium. UniProt Tools. (2016) Curr Protoc Bioinformatics. 53:1.29.1-15. PMID:27010333.
• The UniProt Consortium. UniProt: the universal protein knowledgebase. (2017) Nucleic Acids Res. 45(D1):D158-D169. PMID:27899622.
• Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC. (2016). Guidelines for the functional annotation of microRNAs using the Gene Ontology. RNA. 22(5):667-76. PMID:26917558
• Foulger RE, Denny P, Hardy J, Martin MJ, Sawford T, Lovering RC (2016). Using the Gene Ontology to Annotate Key Players in Parkinson's Disease. Neuroinformatics. 14(3):297-304. PMID:26825309
• White J, Sofat R, Hemani G, Shah T, Engmann J, Dale C, Shah S, Kruger FA, Giambartolomei C, Swerdlow DI, Palmer T, McLachlan S, Langenberg C, Zabaneh D, Lovering R, Cavadino A, Jefferis B, Finan C, Wong A, Amuzu A, Ong K, Gaunt TR, Warren H, Davies TL, Drenos F, Cooper J, Ebrahim S, Lawlor DA, Talmud PJ, Humphries SE, Power C, Hypponen E, Richards M, Hardy R, Kuh D, Wareham N, Ben-Shlomo Y, Day IN, Whincup P, Morris R, Strachan MW, Price J, Kumari M, Kivimaki M, Plagnol V, Whittaker JC; International Consortium for Blood Pressure (ICBP), Smith GD, Dudbridge F, Casas JP, Holmes MV, Hingorani AD; UCLEB (University College London-London School of Hygiene & Tropical Medicine-Edinburgh-Bristol Consortium. (2016) Plasma urate concentration and risk of coronary heart disease: a Mendelian randomisation analysis coronary heart disease. Lancet Diabetes Endocrinol. 4(4):327-36. PMID:26781229.

• Manzoni, C., Denny, P., Lovering, R. C., & Lewis, P. A. (2015). Computational analysis of the LRRK2 interactome. PeerJ 3:e778.
• Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Dietze H, Lewis SE, Mungall CJ, Munoz-Torres MC, Feuermann M, Gaudet P, Basu S, Chisholm RL, Dodson RJ, Fey P, Mi H, Thomas PD, Muruganujan A, Poudel S, Hu JC, Aleksander SA, McIntosh BK, Renfro DP, Siegele DA, Attrill H, Brown NH, Tweedie S, Lomax J, Osumi-Sutherland D, Parkinson H, Roncaglia P, Lovering RC, Talmud PJ, Humphries SE, Denny P, Campbell NH, Foulger RE, Chibucos MC, Gwinn Giglio M, Chang HY, Finn R, Fraser M, Mitchell A, Nuka G, Pesseat S, Sangrador A, Scheremetjew M, Young SY, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman GT, Wang SJ, Petri V, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Demeter J, Dwight SS, Engel SR, Hitz BC, Inglis DO, Lloyd P, Miyasato SR, Paskov K, Roe G, Simison M, Nash RS, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Argasinska J, Arighi C, Auchincloss A, Axelsen K, Argoud-Puy G, Bateman A, Bely B, Blatter MC, Bonilla C, Bougueleret L, Boutet E, Breuza L, Bridge A, Britto R, Casals C, Cibrian-Uhalte E, Coudert E, Cusin I, Duek-Roggli P, Estreicher A, Famiglietti L, Gane P, Garmiri P, Gos A, Gruaz-Gumowski N, Hatton-Ellis E, Hinz U, Hulo C, Huntley R, Jungo F, Keller G, Laiho K, Lemercier P, Lieberherr D, MacDougall A, Magrane M, Martin M, Masson P, Mutowo P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Shypitsyna A, Stutz A, Sundaram S, Tognolli M, Wu C, Xenarios I, Chan J, Kishore R, Sternberg PW, Van Auken K, Muller HM, Done J, Li Y, Howe D, Westerfield M. (2015). Gene Ontology Consortium: Going forward. Nucleic Acids Research, 43(Database issue): D1049-D1056.
• Pundir S, Magrane M, Martin MJ, O'Donovan C; UniProt Consortium. Searching and Navigating UniProt Databases. (2015) Curr Protoc Bioinformatics 50:1.27.1-10.
• 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.
• 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 16:186.
• Huntley, R. P., Sawford, T., Mutowo-Meullenet, P., Shypitsyna, A., Bonilla, C., Martin, M. J., & O'Donovan, C. (2015). The GOA database: Gene Ontology annotation updates for 2015. Nucleic Acids Res 43(Database issue): D1057-D1063.
• Bateman A, Martin MJ, O'Donovan C, Magrane M, Apweiler R, Alpi E, Antunes R, Arganiska J, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chavali G, Cibrian-Uhalte E, Da Silva A, De Giorgi M, Dogan T, Fazzini F, Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Saidi R, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Zellner H, Cowley A, Figueira L, Li W, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Argoud-Puy G, Auchincloss A, Axelsen K, Bansal P, Baratin D, Blatter M-C, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, De Castro E, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Jungo F, Keller G, Lara V, Lemercier P, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Nouspikel N, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey A-L, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka CR, Wang Q, Wang Y, Yeh L-S, Yerramalla MS, Zhang J. (2015). UniProt: A hub for protein information. Nucleic Acids Research 43:(Database issue):D204-D212.
• 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. (2015) Key challenges for the creation and maintenance of specialist protein resources. Proteins 83(6):1005-13. PMID: 25820941.
• Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. (2014). The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic acids research 42(Database issue):D358-D363.
• Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. (2014). A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinformatics 15:155.
• Apweiler R, Bateman A, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, Alpi E, Antunes R, Arganiska J, Casanova EB, Bely B, Bingley M, Bonilla C, Britto R, Bursteinas B, Chan WM, Chavali G, Cibrian-Uhalte E, Da Silva A, De Giorgi M, Fazzini F, Gane P, Castro LG, Garmiri P, Hatton-Ellis E, Hieta R, Huntley R, Legge D, Liu W, Luo J, MacDougall A, Mutowo P, Nightingale A, Orchard S, Pichler K, Poggioli D, Pundir S, Pureza L, Qi G, Rosanoff S, Sawford T, Shypitsyna A, Turner E, Volynkin V, Wardell T, Watkins X, Corbett M, Donnelly M, Van Rensburg P, Goujon M, McWilliam H, Lopez R, Xenarios I, Bougueleret L, Bridge A, Poux S, Redaschi N, Aimo L, Auchincloss A, Axelsen K, Bansal P, Baratin D, Binz P-A, Blatter M-C, Boeckmann B, Bolleman J, Boutet E, Breuza L, Casal-Casas C, De Castro E, Cerutti L, Coudert E, Cuche B, Doche M, Dornevil D, Duvaud S, Estreicher A, Famiglietti L, Feuermann M, Gasteiger E, Gehant S, Gerritsen V, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jungo F, Keller G, Lara V, Lemercier P, Lew J, Lieberherr D, Lombardot T, Martin X, Masson P, Morgat A, Neto T, Paesano S, Pedruzzi I, Pilbout S, Pozzato M, Pruess M, Rivoire C, Roechert B, Schneider M, Sigrist C, Sonesson K, Staehli S, Stutz A, Sundaram S, Tognolli M, Verbregue L, Veuthey A-L, Wu CH, Arighi CN, Arminski L, Chen C, Chen Y, Garavelli JS, Huang H, Laiho K, McGarvey P, Natale DA, Suzek BE, Vinayaka CR, Wang Q, Wang Y, Yeh L-S, Yerramalla MS, Zhang J. (2014). Activities at the Universal Protein Resource (UniProt). Nucleic Acids Research 42(Database issue):D191-8.
• Huntley, R. P., Sawford, T., Martin, M. J., & O'Donovan, C. (2014). Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt. Gigascience 3(1):4.

• Pedruzzi I, Rivoire C, Auchincloss AH, Coudert E, Keller G, de Castro E, Baratin D, Cuche BA, Bougueleret L, Poux S, Redaschi N, Xenarios I, Bridge A; UniProt Consortium. (2013). HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 2013 Jan;41(Database issue):D584-9
• Khodiyar, V. K., Howe, D., Talmud, P. J., Breckenridge, R., & Lovering, R. C. (2013). From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. F1000Res, 2, 242-?. doi:10.12688/f1000research.2-242.v2
• Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Bely B, Blatter M-C, Bonilla C, Bougueleret L, Boutet E, Breuza L, Bridge A, Chan WM, Chavali G, Coudert E, Dimmer E, Estreicher A, Famiglietti L, Feuermann M, Gos A, Gruaz-Gumowski N, Hieta R, Hinz U, Hulo C, Huntley R, James J, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Mutowo-Muellenet P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Millan PP, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulger R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-Y, Hunter S, McAnulla C, Mitchell A, Sangrador A, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-J, Petri V, Lowry T, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hitz BC, Hong EL, Karra K, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M, GO Consortium (2013). Gene Ontology Annotations and Resources. NUCLEIC ACIDS RESEARCH, 41 (D1), D530-D535. doi:10.1093/nar/gks1050
• 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
• UniProt Consortium (2013). Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7
• UniProt Consortium (2012). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5.
• Blake JA, Dolan M, Drabkin H, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Lewis SE, Mungall CJ, Gaudet P, Chisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Axelsen K, Argoud-Puy G, Bely B, Blatter M-C, Bougueleret L, Boutet E, Branconi-Quintaje S, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Cusin I, Dimmer E, Duek-Roggli P, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gardner M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, Huntley R, James J, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, Martin MJ, Masson P, Moinat M, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Millan PP, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Sehra H, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulger R, Lomax J, Roncaglia P, Camon E, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Dolinski K, Heinicke S, Livstone MS, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-J, Petri V, Lowry T, D'Eustachio P, Matthews L, Amundsen CD, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Slonim D, Wick H, Thomas P, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M, GO Consortium (2012). The Gene Ontology: enhancements for 2011. NUCLEIC ACIDS RESEARCH, 40 (D1), D559-D564. doi:10.1093/nar/gkr1028
• Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A,Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R. (2012). The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40(Database issue):D565-70.
• UniProt Consortium (2012). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Research, 40 (D1), D71-D75. doi:10.1093/nar/gkr981

• Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. (2011). The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One, 6 (12), e27541. doi:10.1371/journal.pone.0027541
• Khodiyar VK, Hill DP, Howe D, Berardini TZ, Tweedie S, Talmud PJ, Breckenridge R, Bhattarcharya S, Riley P, Scambler P, Lovering RC (2011). The representation of heart development in the gene ontology. Dev Biol, 354 (1), 9-17. doi:10.1016/j.ydbio.2011.03.011
• Stables MJ, Shah S, Camon EB, Lovering RC, Newson J, Bystrom J, Farrow S, Gilroy DW (2011). Transcriptomic analyses of murine resolution-phase macrophages. Blood, 118 (26), e192-e208. doi:10.1182/blood-2011-04-345330
• Khodiyar, V. K., Dimmer, E. C., Huntley, R. P., & Lovering, R. C. (2010). Fundamentals of Gene Ontology Functional Annotation. In G. Alterovitz, M. Ramoni (Eds.), Knowledge-Based Bioinformatics - From analysis to interpretation (pp. 173-208). Wiley.
• GO Consortium (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res, 38 ((Database issue)), D331-D335.
• Berardini TZ, Li DH, Huala E, Bridges S, Burgess S, McCarthy F, Carbon S, Lewis SE, Mungall CJ, Abdulla A, Wood V, Feltrin E, Valle G, Chisholm RL, Fey P, Gaudet P, Kibbe W, Basu S, Bushmanova Y, Eilbeck K, Siegele DA, McIntosh B, Renfro D, Zweifel A, Hu JC, Ashburner M, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Bairoch A, Barrell D, Binns D, Blatter MC, Bougueleret L, Boutet E, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Daugherty L, Dimmer E, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Foulger R, Gruaz-Gumowski N, Hinz U, Huntley R, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, O'Donovan C, Pedruzzi I, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Harris MA, Deegan JI, Ireland A, Lomax J, Jaiswal P, Chibucos M, Giglio MG, Wortman J, Hannick L, Madupu R, Botstein D, Dolinski K, Livstone MS, Oughtred R, Blake JA, Bult C, Diehl AD, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Sitnikov D, Collmer C, Torto-Alalibo T, Laulederkind S, Shimoyama M, Twigger S, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng SA, Wong ED, Aslett M, Chan J, Kishore R, Sternberg P, Van Auken K, Khodiyar VK, Lovering RC, Talmud PJ, Howe D, Westerfield M, Gene Ontology Consortium (2010). The Gene Ontology in 2010: extensions and refinements The Gene Ontology Consortium. NUCLEIC ACIDS RES, 38, D331-D335. doi:10.1093/nar/gkp1018

• Talmud PJ, Drenos F, Shah S, Shah T, Palmen J, Verzilli C, Gaunt TR, Pallas J, Lovering R, Li K, Casas JP, Sofat R, Kumari M, Rodriguez S, Johnson T, Newhouse SJ, Dominiczak A, Samani NJ, Caulfield M, Sever P, Stanton A, Shields DC, Padmanabhan S, Melander O, Hastie C, Delles C, Ebrahim S, Marmot MG, Smith GD, Lawlor DA, Munroe PB, Day IN, Kivimaki M, Whittaker J, Humphries SE, Hingorani AD (2009). Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. American Journal of Human Genetics, 85, 628-642
• Lovering, R. C., Dimmer, E. C., & Talmud, P. J. (2009). Improvements to cardiovascular gene ontology. Atherosclerosis, 205 (1), 9-14. doi:10.1016/j.atherosclerosis.2008.10.014
• Gaudet P, Chisholm R, Berardini T, Dimmer E, Engel SR, Fey P, Hill DP, Howe D, Hu JC, Huntley R, Khodiyar VK, Kishore R, Li D, Lovering RC, McCarthy F, Ni L, Petri V, Siegele DA, Tweedie S, Van Auken K, Wood V, Basu S, Carbon S, Dolan M, Mungall CJ, Dolinski K, Thomas P, Ashburner M, Blake JA, Cherry JM, Lewis SE, 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
• Lovering, R. C., Camon, E. B., Blake, J. A., & Diehl, A. D. (2008). Access to immunology through the Gene Ontology. Immunology, 125 (2), 154-160. doi:10.1111/j.1365-2567.2008.02940.x
• Lovering RC, Dimmer E, Khodiyar VK, Barrell DG, Scambler P, Hubank M, Apweiler R, Talmud PJ (2008). Cardiovascular GO annotation initiative year 1 report: why cardiovascular GO?. Proteomics, 8 (10), 1950-1953.
• Talmud, P. J., Cooper, J. A., Palmen, J., Lovering, R., Drenos, F., Hingorani, A. D., & Humphries, S. E. (2008). Chromosome 9p21.3 coronary heart disease locus genotype and prospective risk of CHD in healthy middle-aged men. Clinical Chemistry, 54 (3), 467-474.
• Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC (2008). The Gene Ontology - Providing a Functional Role in Proteomic Studies. Proteomics.
• Harris MA, Deegan JI, Lomax J, Ashburner M, Tweedie S, Carbon S, Lewis S, Mungall C, Day-Richter J, Eilbeck K, Blake JA, Bult C, Diehl AD, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Dong Q, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Zhu KK, Botstein D, Dolinski K, Livstone MS, Oughtred R, Berardini T, Li DH, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Huntley R, Mulder N, Khodiyar VK, Lovering RC, Povey S, Chisholm R, Fey P, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Van Auken K, Giglio MG, Hannick L, Wortman J, Aslett M, Berriman M, Wood V, Jacob H, Laulederkind S, Petri V, Shimoyama M, Smith J, Twigger S, Jaiswal P, Seigfried T, Howe D, Westerfield M, Collmer C, Torto-Alalibo T, Feltrin E, Valle G, Bromberg S, Burgess S, McCarthy F, Gene Ontology Consortium (2008). The Gene Ontology project in 2008. NUCLEIC ACIDS RES, 36, D440-D444. doi:10.1093/nar/gkm883

Publications supported by a BHF grant, without PubMed Identifiers

• Khodiyar, V. K., Dimmer, E. C., Huntley, R. P., & Lovering, R. C. (2010). Fundamentals of Gene Ontology Functional Annotation. In G. Alterovitz, M. Ramoni (Eds.), Knowledge-Based Bioinformatics - From analysis to interpretation (pp. 173-208). Wiley.
• Diehl AD, Camon EB and Lovering RC. (2008). Immunology on the GO (pdf)  In Immunology News, pp15-21 (the society publication for the British Society for Immunology).
• Dimmer EC, Huntley RP, Barrell DG, Binns D, Draghici S, Camon EB, Hubank M, Talmud PJ, Apweiler R, Lovering RC. (2008). The Gene Ontology - Providing a functional role in proteomic studies (pdf) Proteomics 8 Suppl: Practical Proteomics. 

Reports provided to the Gene Ontology Consortium.

These reports summarise the activities of the UCL annotation team: the staff employed, annotation progress, strategies and priorities and any recent publications and presentations.

• December 2015
• December 2014
• April-June 2014
• January-March 2014
• December 2013
• December 2012
• December 2010
• December 2009
• December 2008