Paul Kersey

Paul Kersey

Team Leader - Kersey team: Non-vertebrate genomics

PhD University of Edinburgh 1992. Postdoctoral work at University of Edinburgh and MRC Human Genetics Unit, Edinburgh. At EMBL-EBI since 1999.

ORCID iD: 0000-0002-7054-800X

Tel:+44 (0)1223 494 601 / Fax:+44 (0)1223 494 468

Kersey team

The Non-vertebrate Genomics team, led by Dr Paul Kersey, develops Ensembl Genomes and related resources. Ensembl Genomes provides portals for bacteria, protists, fungi, plants and invertebrate metazoa, offering access to genome-scale data through a set of programmatic and interactive interfaces, exploiting developments originating in the vertebrate-focused Ensembl project.

Our major areas of interest include broad-range comparative genomics and the visualisation and interpretation of genomic variation, which is being increasingly studied in species throughout the taxonomy. Even small communities with little informatics infrastructure can now perform highly complex and data generative experiments that were once the sole domain of large, internationally coordinated sequencing projects. Through collaborating with EMBL-EBI and re-using our established toolset, such small communities can store, analyse and disseminate data more cheaply and powerfully than if they develop their own tools.

Collaborations

We collaborate closely with VectorBase, a resource focused on the annotation of invertebrate vectors; WormBase, a resource for nematode biology; and PomBase, focused on the fission yeast Schizosaccharomyces pombe. Plant science collaborations include Gramene in the US and several European groups in the transPLANT project. We developed PhytoPath, a new portal for plant pathogen data, and are involved in the development of Microme, a resource for bacterial metabolic pathways.

Publications

2015

PomBase 2015: updates to the fission yeast database.
McDowall MD, Harris MA, Lock A, Rutherford K, Staines DM, Bähler J, Kersey PJ, Oliver SG, Wood V.
Nucleic Acids Res Volume 43 (2015) p.d656-61
DOI: 10.1093/nar/gku1040

2014

WormBase 2014: new views of curated biology.
Harris TW, Baran J, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, Done J, Grove C, Howe K, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Ozersky P, Paulini M, Raciti D, Schindelman G, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Wong JD, Yook K, Schedl T, Hodgkin J, Berriman M, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic Acids Res Volume 42 (2014) p.d789-93
DOI: 10.1093/nar/gkt1063

Gramene 2013: comparative plant genomics resources.
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
Nucleic Acids Res Volume 42 (2014) p.d1193-9
DOI: 10.1093/nar/gkt1110

De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, Preece J, Tiwari VK, Elser J, Leonard JM, Sage A, Gresham C, Kerhornou A, Bolser D, McCarthy F, Kersey P, Lazo GR, Jaiswal P.
PLoS One Volume 9 (2014) p.e96855
DOI: 10.1371/journal.pone.0096855

Ensembl Genomes 2013: scaling up access to genome-wide data.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, Youens-Clark K, Monaco MK, Stein J, Wei X, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Staines DM.
Nucleic Acids Res Volume 42 (2014) p.d546-52
DOI: 10.1093/nar/gkt979

Ribosomic DNA intergenic spacer 1 region is useful when identifying Candida parapsilosis spp. complex based on high-resolution melting analysis.
Gago S, Alastruey-Izquierdo A, Marconi M, Buitrago MJ, Kerhornou A, Kersey PJ, Mellado E, Cuenca-Estrella M, Rodríguez-Tudela JL, Cuesta I.
Med Mycol Volume 52 (2014) p.472-481
DOI: 10.1093/mmy/myu009

Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
Nayduch D, Cohnstaedt LW, Saski C, Lawson D, Kersey P, Fife M, Carpenter S.
Virus Res Volume 182 (2014) p.43-49
DOI: 10.1016/j.virusres.2013.12.009

2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.
Gigascience Volume 2 (2013) p.10
DOI: 10.1186/2047-217x-2-10

Gene Ontology annotations and resources.
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, 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, Chrisholm 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-, Bonilla C, Bouguerleret 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 C, 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, Porras Millán P, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stutz A, Sundaram S, Tognolli M, Xenarios I, Foulgar R, Lomax J, Roncaglia P, Khodiyar VK, Lovering RC, Talmud PJ, Chibucos M, Giglio MG, Chang H-, 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 DM, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman T, Wang S-, 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, Huala E, Mi H, Thomas PD, Chan J, Kishore R, Sternberg P, Van Auken K, Howe D, Westerfield M.
Nucleic Acids Res Volume 41 (2013) p.d530-5
DOI: 10.1093/nar/gks1050

2012

WormBase: Annotating many nematode genomes
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg P.
Worm Volume 1 (2012) p.15-21

The Gene Ontology: enhancements for 2011.
Gene Ontology Consortium.
Nucleic Acids Res Volume 40 (2012) p.d559-64
DOI: 10.1093/nar/gkr1028

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DS, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E.
Nucleic Acids Res Volume 40 (2012) p.d91-7
DOI: 10.1093/nar/gkr895

Analysis of the bread wheat genome using whole-genome shotgun sequencing.
Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N.
Nature Volume 491 (2012) p.705-710
DOI: 10.1038/nature11650

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.
Heliconius Genome Consortium.
Nature Volume 487 (2012) p.94-98
DOI: 10.1038/nature11041

WormBase 2012: more genomes, more data, new website.
Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R, Ganesan U, Grove C, Howe K, Kadam S, Kishore R, Lee R, Li Y, Muller HM, Nakamura C, Nash B, Ozersky P, Paulini M, Raciti D, Rangarajan A, Schindelman G, Shi X, Schwarz EM, Ann Tuli M, Van Auken K, Wang D, Wang X, Williams G, Hodgkin J, Berriman M, Durbin R, Kersey P, Spieth J, Stein L, Sternberg PW.
Nucleic Acids Res Volume 40 (2012) p.d735-41
DOI: 10.1093/nar/gkr954

PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG.
Nucleic Acids Res Volume 40 (2012) p.d695-9
DOI: 10.1093/nar/gkr853

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.
Megy K, Emrich SJ, Lawson D, Campbell D, Dialynas E, Hughes DS, Koscielny G, Louis C, Maccallum RM, Redmond SN, Sheehan A, Topalis P, Wilson D, VectorBase Consortium.
Nucleic Acids Res Volume 40 (2012) p.d729-34
DOI: 10.1093/nar/gkr1089

WormBase: Annotating many nematode genomes.
Howe K, Davis P, Paulini M, Tuli MA, Williams G, Yook K, Durbin R, Kersey P, Sternberg PW.
Worm Volume 1 (2012) p.15-21
DOI: 10.4161/worm.19574

2011

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfield EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Rätsch G, Mott R.
Nature Volume 477 (2011) p.419-423
DOI: 10.1038/nature10414

Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P.
Database (Oxford) Volume 2011 (2011) p.bar030
DOI: 10.1093/database/bar030

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics Volume 27 (2011) p.2156-2158
DOI: 10.1093/bioinformatics/btr330

Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D.
Nucleic Acids Res Volume 39 (2011) p.d1085-94
DOI: 10.1093/nar/gkq1148

RNAcentral: A vision for an international database of RNA sequences.
Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C.
RNA Volume 17 (2011) p.1941-1946
DOI: 10.1261/rna.2750811

Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.
Genome Res Volume 21 (2011) p.2224-2241
DOI: 10.1101/gr.126599.111

2010

An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium.
Plant Cell Volume 22 (2010) p.2530-2536
DOI: 10.1105/tpc.110.078519

Ensembl Genomes: extending Ensembl across the taxonomic space.
Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A.
Nucleic Acids Res Volume 38 (2010) p.d563-9
DOI: 10.1093/nar/gkp871

Genomic information infrastructure after the deluge.
Parkhill J, Birney E, Kersey P.
Genome Biol Volume 11 (2010) p.402
DOI: 10.1186/gb-2010-11-7-402

2009

The Universal Protein Resource (UniProt) 2009.
UniProt Consortium.
Nucleic Acids Res Volume 37 (2009) p.d169-74
DOI: 10.1093/nar/gkn664

2008

Building a biological space based on protein sequence similarities and biological ontologies.
Kersey P, Lonsdale D, Mulder NJ, Petryszak R, Apweiler R.
Comb Chem High Throughput Screen Volume 11 (2008) p.653-660
DOI: 10.2174/138620708785739925

In silico characterization of proteins: UniProt, InterPro and Integr8.
Mulder NJ, Kersey P, Pruess M, Apweiler R.
Mol Biotechnol Volume 38 (2008) p.165-177
DOI: 10.1007/s12033-007-9003-x

2007

The EMBL Nucleotide Sequence and Genome Reviews Databases.
Sterk P, Kulikova T, Kersey P, Apweiler R.
Methods Mol Biol Volume 406 (2007) p.1-21
DOI: 10.1007/978-1-59745-535-0_1

2006

Linking publication, gene and protein data.
Kersey P, Apweiler R.
Nat Cell Biol Volume 8 (2006) p.1183-1189
DOI: 10.1038/ncb1495

Integr8: Navigating Genome Reviews and the Proteome Analysis Database
Kersey P, Kulikova T, Pruess M.
Volume (2006) p.201-217

Databases and resources for in silico proteome analysis.
Pruess M, Kersey P, Kulikova T, Apweiler R.
Methods Biochem Anal Volume 49 (2006) p.397-414

Genome Reviews: standardizing content and representation of information about complete genomes.
Sterk P, Kersey PJ, Apweiler R.
OMICS Volume 10 (2006) p.114-118
DOI: 10.1089/omi.2006.10.114

Sequence clustering as a method of protein functional annotation
Petryszak R, Kersey P.
Volume (2006) p.11-23

2005

Integr8 and Genome Reviews: integrated views of complete genomes and proteomes.
Kersey P, Bower L, Morris L, Horne A, Petryszak R, Kanz C, Kanapin A, Das U, Michoud K, Phan I, Gattiker A, Kulikova T, Faruque N, Duggan K, Mclaren P, Reimholz B, Duret L, Penel S, Reuter I, Apweiler R.
Nucleic Acids Res Volume 33 (2005) p.d297-302
DOI: 10.1093/nar/gki039

UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs.
Mignone F, Grillo G, Licciulli F, Iacono M, Liuni S, Kersey PJ, Duarte J, Saccone C, Pesole G.
Nucleic Acids Res Volume 33 (2005) p.d141-6
DOI: 10.1093/nar/gki021

Biological Databases: Infrastructure, Content and Integration
Williams AL, Kersey PJ, Pruess M, Apweiler R.
Volume (2005) p.11–28
DOI: 10.1002/0470094419.ch2

The Integr8 project--a resource for genomic and proteomic data.
Pruess M, Kersey P, Apweiler R.
In Silico Biol Volume 5 (2005) p.179-185

2004

The International Protein Index: an integrated database for proteomics experiments.
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R.
Proteomics Volume 4 (2004) p.1985-1988
DOI: 10.1002/pmic.200300721

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
PLoS Biol Volume 2 (2004) p.e162
DOI: 10.1371/journal.pbio.0020162

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.
Nat Biotechnol Volume 22 (2004) p.177-183
DOI: 10.1038/nbt926

2003

Automated annotation of microbial proteomes in SWISS-PROT.
Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A.
Comput Biol Chem Volume 27 (2003) p.49-58
DOI: 10.1016/s1476-9271(02)00094-4

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.
Pruess M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Nucleic Acids Res Volume 31 (2003) p.414-417
DOI: 10.1093/nar/gkg105

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.
Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.203-206
DOI: 10.1002/cfg.279

Integr8: enhanced inter-operability of European molecular biology databases.
Kersey PJ, Morris L, Hermjakob H, Apweiler R.
Methods Inf Med Volume 42 (2003) p.154-160

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data.
Orchard S, Kersey P, Hermjakob H, Apweiler R.
Comp Funct Genomics Volume 4 (2003) p.16-19
DOI: 10.1002/cfg.232

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.
Genome Res Volume 13 (2003) p.662-672
DOI: 10.1101/gr.461403

MCB-mediated regulation of cell cycle-specific cdc22+ transcription in fission yeast.
Maqbool Z, Kersey PJ, Fantes PA, McInerny CJ.
Mol Genet Genomics Volume 269 (2003) p.765-775
DOI: 10.1007/s00438-003-0885-4

2002

Applications of InterPro in protein annotation and genome analysis.
Biswas M, O'Rourke JF, Camon E, Fraser G, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva E, Mittard V, Mulder N, Phan I, Servant F, Apweiler R.
Brief Bioinform Volume 3 (2002) p.285-295
DOI: 10.1093/bib/3.3.285

Computational Methods and Bioinformatic Tools
Cullen P, Lorkowski S, Hennig S, Poustka A, Panopoulou G, Lehrach H, Korsching E, Pickeral O, Herwig R, Kel A, Tchekmenev D, Wingender E, Streicher J, Müller GB, Kawashima T, Makabe KW, Dubchak I, Ji H, Okubo K, Kawamoto S, Fricke E, Karas D, Haubrock M, Land S, Rotert S, Chen X, Pontius J, Eveno E, Auffray C, Decraene C, Chelala C, Piétu G, Devignes M-D, Mariage-Samson R, Imbeaud S, Bortoli S, Amit A, Ringwald M, de Veer MJ, Williams BRG, Walker EM, Davies JA, Grunau C, Baldock R, Davidson DR, Stoeckert CJ Jr., Pizarro A, Manduchi E, Grant GR, Crabtree J, Liu J, Le PV, McWeeney SK, Welle S, Ball CA, Botstein D, Binkley G, Sherlock GJ, Cherry JM, Dolinski K, Issel-Tarver L, Schroeder M, Dwight SS, Wenig S, Matese JC, Jin H, Gollub J, Hebert J, Kaloper M, Brown PO, Hernandez-Boussard T, Kumar A, Cheung K, Marenco L, Snyder M, Tosches N, Bertone P, Miller P, Masiar P, Liu Y, Pesole G, Marc P, Biswas M, Kersey P, Apweiler R, Hoogland C.
Volume (2002) p.769–904
DOI: 10.1002/352760149x.ch7

Interactive InterPro-based comparisons of proteins in whole genomes.
Kanapin A, Apweiler R, Biswas M, Fleischmann W, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Oinn T, Phan I, Servant F, Zdobnov E.
Bioinformatics Volume 18 (2002) p.374-375
DOI: 10.1093/bioinformatics/18.2.374

2001

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Apweiler R, Biswas M, Fleischmann W, Kanapin A, Karavidopoulou Y, Kersey P, Kriventseva EV, Mittard V, Mulder N, Phan I, Zdobnov E.
Nucleic Acids Res Volume 29 (2001) p.44-48
DOI: 10.1093/nar/29.1.44

2000

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL.
Kersey P, Hermjakob H, Apweiler R.
Bioinformatics Volume 16 (2000) p.1048-1049
DOI: 10.1093/bioinformatics/16.11.1048

1996

Cell cycle, DNA damage and heat shock regulate suc22+ expression in fission yeast.
Harris P, Kersey PJ, McInerny CJ, Fantes PA.
Mol Gen Genet Volume 252 (1996) p.284-291
DOI: 10.1007/s004380050230

1995

Positive and negative roles for cdc10 in cell cycle gene expression.
McInerny CJ, Kersey PJ, Creanor J, Fantes PA.
Nucleic Acids Res Volume 23 (1995) p.4761-4768
DOI: 10.1093/nar/23.23.4761