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UCL Institute of Cardiovascular Science

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Publications

Journals

The full publication list for each of the biocurators is available using the links on the people pages. Note that all of the biocurators have previous research experience and therefore their early publications may be based on their previous work. 

Publications authored by the European Bioinformatics Institute (EMBL-EBI)-based software engineers, Alex Ignatchenko (2018-present), Tony Sawford (2009-2018) and Daniel Barrell (2007-2009), as well as any EMBL-EBI publications funded by our collaborative grants, are included in these lists.

2020-2021
  • Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. Gene Ontology representation for transcription factor functions. Biochim Biophys Acta Gene Regul Mech. 2021 Aug 28:194752. Epub ahead of print. PMID: 34461313.
  • Sant DW, Sinclair M, Mungall CJ, Schulz S, Zerbino D, Lovering RC, Logie C, Eilbeck K. Sequence ontology terminology for gene regulation. Biochim Biophys Acta Gene Regul Mech. 2021 Aug 10:194745. doi: 10.1016/j.bbagrm.2021.194745. Epub ahead of print. PMID: 34389511.
  • Lindbohm JV, Mars N, Walker KA, Singh-Manoux A, Livingston G, Brunner EJ, Sipilä PN, Saksela K, Ferrie JE, Lovering RC, Williams SA, Hingorani AD, Gottesman RF, Zetterberg H, Kivimäki M. Plasma proteins, cognitive decline, and 20-year risk of dementia in the Whitehall II and Atherosclerosis Risk in Communities studies. Alzheimers Dement. 2021 Aug 2. doi: 10.1002/alz.12419. Epub ahead of print. PMID: 34338426.
  • Gene Ontology Consortium. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2020 Dec 8:gkaa1113. Epub ahead of print. PMID: 33290552.
  • Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S. Towards a unified open access dataset of molecular interactions. Nat Commun. 2020. 11(1):6144. PMID: 33262342.
  • Lovering RC, Gaudet P, Acencio ML, Ignatchenko A, Jolma A, Fornes O, Kuiper M, Kulakovskiy IV, Laegreid A, Martin MJ, Logie C. A GO catalogue of human DNA-binding transcription factors. bioRxiv 2020 2020.10.28.359232.
  • RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 2020 Oct 27:gkaa921. Epub ahead of print. PMID: 33106848.
  • Wood V, Carbon S, Harris MA, Lock A, Engel SR, Hill DP, Van Auken K, Attrill H, Feuermann M, Gaudet P, Lovering RC, Poux S, Rutherford KM, Mungall CJ. Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. Open Biol. 2020 Sep;10(9):200149. PMID: 32875947.
  • Breuza L, Arighi CN, Argoud-Puy G, Casals-Casas C, Estreicher A, Famiglietti ML, Georghiou G, Gos A, Gruaz-Gumowski N, Hinz U, Hyka-Nouspikel N, Kramarz B, Lovering RC, Lussi Y, Magrane M, Masson P, Perfetto L, Poux S, Rodriguez-Lopez M, Stoeckert C, Sundaram S, Wang LS, Wu E, Orchard S; IMEx Consortium, UniProt Consortium. A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. J Alzheimers Dis. 2020. 77(1):257-273. PMID: 32716361.
  • Mencacci NE, Reynolds R, Ruiz SG, Vandrovcova J, Forabosco P, Sánchez-Ferrer A, Volpato V; UK Brain Expression Consortium; International Parkinson’s Disease Genomics Consortium, Weale ME, Bhatia KP, Webber C, Hardy J, Botía JA, Ryten M. Dystonia genes functionally converge in specific neurons and share neurobiology with psychiatric disorders. Brain. 2020 Sep 1;143(9):2771-2787. doi: 10.1093/brain/awaa217. PMID: 32889528.
  • Touré V, Vercruysse S, Acencio ML, Lovering RC, Orchard S, Bradley G, Casals-Casas C, Chaouiya C, Del-Toro N, Flobak Å, Gaudet P, Hermjakob H, Hoyt CT, Licata L, Lægreid A, Mungall CJ, Niknejad A, Panni S, Perfetto L, Porras P, Pratt D, Saez-Rodriguez J, Thieffry D, Thomas PD, Türei D, Kuiper M. The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics. 2020 Jul 8:btaa622. Epub ahead of print. PMID: 32637990.
  • Tomkins JE, Ferrari R, Vavouraki N, Hardy J, Lovering RC, Lewis PA, McGuffin LJ, Manzoni C. PINOT: an intuitive resource for integrating protein-protein interactions. Cell Commun Signal. 2020. 18(1):92. PMID: 32527260.
  • George MJ, Kleveland O, Garcia-Hernandez J, Palmen J, Lovering R, Wiseth R, Aukrust P, Engmann J, Damås JK, Hingorani AD, Gullestad L, Casas JP, Ueland T. Novel Insights Into the Effects of Interleukin 6 Antagonism in Non-ST-Segment-Elevation Myocardial Infarction Employing the SOMAscan Proteomics Platform. J Am Heart Assoc. 2020. 9(12):e015628. PMID: 32515246.
  • Leonard H, Blauwendraat C, Krohn L, Faghri F, Iwaki H, Ferguson G, Day-Williams AG, Stone DJ, Singleton AB, Nalls MA, Gan-Or Z; International Parkinson's Disease Genomic Consortium (IPDGC). Genetic variability and potential effects on clinical trial outcomes: perspectives in Parkinson's disease. J Med Genet. 2020. 57(5):331-338. PMID: 31784483.
  • Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, Lovering RC. Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. J Alzheimers Dis. 2020. 75(4):1417-1435. PMID: 32417785.
  • Shah S, Henry A, Roselli C, ... Lovering RC, ... Vasan DI, Swerdlow R, Lumbers T. Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure. Nat Commun. 2020. 11:163-185. PMID:31919418
  • Iwaki H, Blauwendraat C, Makarious MB, Bandrés-Ciga S, Leonard HL, Gibbs JR, Hernandez DG, Scholz SW, Faghri F; International Parkinson's Disease Genomics Consortium (IPDGC), Nalls MA, Singleton AB. Penetrance of Parkinson's Disease in LRRK2 p.G2019S Carriers Is Modified by a Polygenic Risk Score. Mov Disord. 2020. 35(5):774-780. PMID: 31958187.
  • Leonard H, Blauwendraat C, Krohn L, Faghri F, Iwaki H, Ferguson G, Day-Williams AG, Stone DJ, Singleton AB, Nalls MA, Gan-Or Z; International Parkinson's Disease Genomic Consortium (IPDGC). Genetic variability and potential effects on clinical trial outcomes: perspectives in Parkinson's disease. J Med Genet. 2020 May;57(5):331-338. PMID: 31784483.
  • Guelfi S, D'Sa K, Botía JA, Vandrovcova J, Reynolds RH, Zhang D, Trabzuni D, Collado-Torres L, Thomason A, Quijada Leyton P, Gagliano Taliun SA, Nalls MA; International Parkinson’s Disease Genomics Consortium (IPDGC); UK Brain Expression Consortium (UKBEC), Small KS, Smith C, Ramasamy A, Hardy J, Weale ME, Ryten M. Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information. Nat Commun. 2020. 11(1):1041. PMID: 32098967.
  • Hall CL, Gurha P, Sabater-Molina M, Asimaki A, Futema M, Lovering RC, Suárez MP, Aguilera B, Molina P, Zorio E, Coarfa C, Robertson MJ, Cheedipudi SM, Ng KE, Delaney P, Hernández JP, Pastor F, Gimeno JR, McKenna WJ, Marian AJ, Syrris P. RNA sequencing-based transcriptome profiling of cardiac tissue implicates novel putative disease mechanisms in FLNC-associated arrhythmogenic cardiomyopathy. Int J Cardiol. 2020. 1;302:124-130. PMID: 31843279.
  • Panni S, Lovering RC, Porras P, Orchard S. Non-coding RNA regulatory networks. Biochim Biophys Acta Gene Regul Mech. 2020. 1863(6):194417. PMID: 31493559.
2018-2019
  • 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.
2016-2017
  • 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.
2014-2015
  • Manzoni, C., Denny, P., Lovering, R. C., & Lewis, P. A. (2015). Computational analysis of the LRRK2 interactomePeerJ 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 forwardNucleic 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 autismBMC 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 UniProtGigascience 3(1):4.
2012-2013
  • 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 systemNucleic 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 developmentF1000Res, 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 ResourcesNUCLEIC 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 lipidsCurr Opin Lipidol, 24 (2), 123-128. doi:10.1097/MOL.0b013e32835df2d6
  • UniProt Consortium (2013). Update on activities at the Universal Protein Resource (UniProt) in 2013Nucleic 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 2011NUCLEIC 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
2010-2011
  • 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 systemsPLoS 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 ontologyDev 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 macrophagesBlood, 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 refinementsNucleic 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 ConsortiumNUCLEIC ACIDS RES, 38, D331-D335. doi:10.1093/nar/gkp1018
    2008-2009
    • 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 StudiesProteomics.
    • 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 2008NUCLEIC ACIDS RES, 36, D440-D444. doi:10.1093/nar/gkm883
    Other Publications

    Publications supported by a BHF grant, without PubMed Identifiers

    Progress reports

    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.