Publications

Publications

2021

Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.
Smyshlyaev G, Bateman A, Barabas O. Molecular systems biology Volume 17 (2021) p.e9880 DOI: 10.15252/msb.20209880
The InterPro protein families and domains database: 20 years on.
Blum M, Chang HY, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S, Richardson L, Salazar GA, Williams L, Bork P, Bridge A, Gough J, Haft DH, Letunic I, Marchler-Bauer A, Mi H, Natale DA, Necci M, Orengo CA, Pandurangan AP, Rivoire C, Sigrist CJA, Sillitoe I, Thanki N, Thomas PD, Tosatto SCE, Wu CH, Bateman A, Finn RD. Nucleic acids research Volume 49 (2021) p.D344-D354 DOI: 10.1093/nar/gkaa977
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UniProt: the universal protein knowledgebase in 2021.
UniProt Consortium. Nucleic acids research Volume 49 (2021) p.D480-D489 DOI: 10.1093/nar/gkaa1100
Pfam: The protein families database in 2021.
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, Tosatto SCE, Paladin L, Raj S, Richardson LJ, Finn RD, Bateman A. Nucleic acids research Volume 49 (2021) p.D412-D419 DOI: 10.1093/nar/gkaa913
Rfam 14: expanded coverage of metagenomic, viral and microRNA families.
Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z, Rivas E, Eddy SR, Finn RD, Bateman A, Petrov AI. Nucleic acids research Volume 49 (2021) p.D192-D200 DOI: 10.1093/nar/gkaa1047
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The Gene Ontology resource: enriching a GOld mine.
Gene Ontology Consortium. Nucleic acids research Volume 49 (2021) p.D325-D334 DOI: 10.1093/nar/gkaa1113
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RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.
RNAcentral Consortium. Nucleic acids research Volume 49 (2021) p.D212-D220 DOI: 10.1093/nar/gkaa921

2020

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Discovery of Fibrillar Adhesins across Bacterial Species
Monzon V, Lafita A, Bateman A. Preprint DOI: 10.1101/2020.12.07.414375
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K, UniProt Consortium. Bioinformatics (Oxford, England) Volume 36 (2020) p.4643-4648 DOI: 10.1093/bioinformatics/btaa485
How to use the MEROPS database and website to help understand peptidase specificity.
Rawlings ND, Bateman A. Protein science : a publication of the Protein Society Volume 30 (2021) p.83-92 DOI: 10.1002/pro.3948
Exploring Non-Coding RNAs in RNAcentral.
Sweeney BA, Tagmazian AA, Ribas CE, Finn RD, Bateman A, Petrov AI. Current protocols in bioinformatics Volume 71 (2020) p.e104 DOI: 10.1002/cpbi.104
Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase.
Pearson CR, Tindall SN, Herman R, Jenkins HT, Bateman A, Thomas GH, Potts JR, Van der Woude MW. mBio Volume 11 (2020) DOI: 10.1128/mbio.01364-20
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Modelling structural rearrangements in proteins using Euclidean distance matrices
Lafita A, Bateman A. Preprint DOI: 10.12688/f1000research.25235.1
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Cryo-EM structures of human RNA polymerase III in its unbound and transcribing states
Girbig M, Misiaszek AD, Vorländer MK, Lafita A, Grötsch H, Baudin F, Bateman A, Müller CW. Preprint DOI: 10.1101/2020.06.29.177642
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression.
Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Genetics Volume 215 (2020) p.1039-1054 DOI: 10.1534/genetics.120.302923
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Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research
Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild A, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki E, O'Toole ÁN, Palacios-Ontiveros N, Petrov AI, Rangel-Piñeros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Preprint DOI: 10.20944/preprints202005.0376.v1
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The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.
Drysdale R, Cook CE, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E, Gruhl F, Haas J, Lanfear J, Lopez R, Redaschi N, Stockinger H, Teixeira D, Venkatesan A, Elixir Core Data Resource Forum, Blomberg N, Durinx C, McEntyre J. Bioinformatics (Oxford, England) Volume 36 (2020) p.2636-2642 DOI: 10.1093/bioinformatics/btz959
The thrombospondin module 1 domain of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers.
Xu ER, Lafita A, Bateman A, Hyvönen M. Acta crystallographica. Section D, Structural biology Volume 76 (2020) p.124-134 DOI: 10.1107/s2059798319016747

2019

Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.
Whelan F, Lafita A, Griffiths SC, Cooper REM, Whittingham JL, Turkenburg JP, Manfield IW, St John AN, Paci E, Bateman A, Potts JR. Proceedings of the National Academy of Sciences of the United States of America (2019) DOI: 10.1073/pnas.1911776116
Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.
Bortnov V, Tonelli M, Lee W, Lin Z, Annis DS, Demerdash ON, Bateman A, Mitchell JC, Ge Y, Markley JL, Mosher DF. Nature communications Volume 10 (2019) p.5612 DOI: 10.1038/s41467-019-13577-5
Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing.
Chihara K, Bischler T, Barquist L, Monzon VA, Noda N, Vogel J, Tsuneda S. mSystems Volume 4 (2019) DOI: 10.1128/msystems.00590-19
Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases.
Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Nucleic acids research Volume 47 (2019) p.10994-11006 DOI: 10.1093/nar/gkz841
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Caenorhabditis elegansAF4/FMR2 family homologaffl-2is required for heat shock induced gene expression
Walton SJ, Wang H, Quintero-Cadena P, Bateman A, Sternberg PW. Preprint DOI: 10.1101/817833
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Thrombospondin module 1 domain (TSP1) of the matricellular protein CCN3 shows an atypical disulfide pattern and incomplete CWR layers
Xu E, Lafita A, Bateman A, Hyvönen M. Preprint DOI: 10.1101/779553
FAIR adoption, assessment and challenges at UniProt.
Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium. Scientific data Volume 6 (2019) p.175 DOI: 10.1038/s41597-019-0180-9
Origins of peptidases.
Rawlings ND, Bateman A. Biochimie Volume 166 (2019) p.4-18 DOI: 10.1016/j.biochi.2019.07.026
TADOSS: computational estimation of tandem domain swap stability.
Lafita A, Tian P, Best RB, Bateman A. Bioinformatics (Oxford, England) Volume 35 (2019) p.2507-2508 DOI: 10.1093/bioinformatics/bty974
Tandem domain swapping: determinants of multidomain protein misfolding.
Lafita A, Tian P, Best RB, Bateman A. Current opinion in structural biology Volume 58 (2019) p.97-104 DOI: 10.1016/j.sbi.2019.05.012
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Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes
Smyshlyaev G, Barabas O, Bateman A. Preprint DOI: 10.1101/542381
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D1250-D1251 DOI: 10.1093/nar/gky1206
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UniProt: a worldwide hub of protein knowledge.
UniProt Consortium. Nucleic acids research Volume 47 (2019) p.D506-D515 DOI: 10.1093/nar/gky1049
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The Gene Ontology Resource: 20 years and still GOing strong.
The Gene Ontology Consortium. Nucleic acids research Volume 47 (2019) p.D330-D338 DOI: 10.1093/nar/gky1055
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RNAcentral: a hub of information for non-coding RNA sequences.
The RNAcentral Consortium. Nucleic acids research Volume 47 (2019) p.D221-D229 DOI: 10.1093/nar/gky1034
The Pfam protein families database in 2019.
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, Sonnhammer ELL, Hirsh L, Paladin L, Piovesan D, Tosatto SCE, Finn RD. Nucleic acids research Volume 47 (2019) p.D427-D432 DOI: 10.1093/nar/gky995

2018

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Rapid identification of novel protein families using similarity searches
Jeffryes M, Bateman A. Preprint DOI: 10.12688/f1000research.17315.1
Rapid identification of novel protein families using similarity searches.
Jeffryes M, Bateman A. F1000Research Volume 7 (2018) DOI: 10.12688/f1000research.17315.1
The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest.
Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Cell Volume 176 (2019) p.391-403.e19 DOI: 10.1016/j.cell.2018.11.004
Non-Coding RNA Analysis Using the Rfam Database.
Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI. Current protocols in bioinformatics Volume 62 (2018) p.e51 DOI: 10.1002/cpbi.51
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The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest
Trendel J, Schwarzl T, Prakash A, Bateman A, Hentze MW, Krijgsveld J. Preprint DOI: 10.1101/329995
Gene Unprediction with Spurio: A tool to identify spurious protein sequences.
Höps W, Jeffryes M, Bateman A. F1000Research Volume 7 (2018) p.261 DOI: 10.12688/f1000research.14050.1
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.
Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. Nucleic acids research Volume 46 (2018) p.D624-D632 DOI: 10.1093/nar/gkx1134
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Nucleic acids research Volume 46 (2018) p.D335-D342 DOI: 10.1093/nar/gkx1038

2017

The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Current protocols in bioinformatics Volume 60 (2017) p.3.15.1-3.15.23 DOI: 10.1002/cpbi.40
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
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. Bioinformatics (Oxford, England) Volume 33 (2017) p.3454-3460 DOI: 10.1093/bioinformatics/btx439
The yeast noncoding RNA interaction network.
Panni S, Prakash A, Bateman A, Orchard S. RNA (New York, N.Y.) Volume 23 (2017) p.1479-1492 DOI: 10.1261/rna.060996.117
Eros is a novel transmembrane protein that controls the phagocyte respiratory burst and is essential for innate immunity.
Thomas DC, Clare S, Sowerby JM, Pardo M, Juss JK, Goulding DA, van der Weyden L, Storisteanu D, Prakash A, Espéli M, Flint S, Lee JC, Hoenderdos K, Kane L, Harcourt K, Mukhopadhyay S, Umrania Y, Antrobus R, Nathan JA, Adams DJ, Bateman A, Choudhary JS, Lyons PA, Condliffe AM, Chilvers ER, Dougan G, Smith KG. The Journal of experimental medicine Volume 214 (2017) p.1111-1128 DOI: 10.1084/jem.20161382
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Data management: A global coalition to sustain core data.
Anderson WP, Global Life Science Data Resources Working Group. Nature Volume 543 (2017) p.179 DOI: 10.1038/543179a
Structure of the Escherichia coli ProQ RNA-binding protein.
Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW. RNA (New York, N.Y.) Volume 23 (2017) p.696-711 DOI: 10.1261/rna.060343.116

2016

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On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study
Poux S, Arighi CN, Magrane M, Bateman A, Wei C, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, The UniProt Consortium. Preprint DOI: 10.1101/094011
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Nucleic acids research Volume 45 (2017) p.D190-D199 DOI: 10.1093/nar/gkw1107
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RNAcentral: a comprehensive database of non-coding RNA sequences.
The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME. Nucleic acids research Volume 45 (2017) p.D128-D134 DOI: 10.1093/nar/gkw1008
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB.
Doğan T, MacDougall A, Saidi R, Poggioli D, Bateman A, O'Donovan C, Martin MJ. Bioinformatics (Oxford, England) Volume 32 (2016) p.2264-2271 DOI: 10.1093/bioinformatics/btw114
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources.
Bousfield D, McEntyre J, Velankar S, Papadatos G, Bateman A, Cochrane G, Kim JH, Graef F, Vartak V, Alako B, Blomberg N. F1000Research Volume 5 (2016) DOI: 10.12688/f1000research.7911.1

2015

The Pfam protein families database: towards a more sustainable future.
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. Nucleic acids research Volume 44 (2016) p.D279-85 DOI: 10.1093/nar/gkv1344
The Importance of Biological Databases in Biological Discovery.
Baxevanis AD, Bateman A. Current protocols in bioinformatics Volume 50 (2015) p.1.1.1-1.1.8 DOI: 10.1002/0471250953.bi0101s50
HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. Nucleic acids research Volume 43 (2015) p.W30-8 DOI: 10.1093/nar/gkv397
Domain atrophy creates rare cases of functional partial protein domains.
Prakash A, Bateman A. Genome biology Volume 16 (2015) p.88 DOI: 10.1186/s13059-015-0655-8
Key challenges for the creation and maintenance of specialist protein resources.
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. Proteins Volume 83 (2015) p.1005-1013 DOI: 10.1002/prot.24803

2014

Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.
Rawlings ND, Barrett AJ, Bateman A. Current protocols in bioinformatics Volume 48 (2014) p.1.25.1-33 DOI: 10.1002/0471250953.bi0125s48
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Gene Ontology Consortium: going forward.
Gene Ontology Consortium. Nucleic acids research Volume 43 (2015) p.D1049-56 DOI: 10.1093/nar/gku1179
The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. Nucleic acids research Volume 43 (2015) p.D213-21 DOI: 10.1093/nar/gku1243
Rfam 12.0: updates to the RNA families database.
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD. Nucleic acids research Volume 43 (2015) p.D130-7 DOI: 10.1093/nar/gku1063
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RNAcentral: an international database of ncRNA sequences.
RNAcentral Consortium, Petrov AI, Kay SJE, Gibson R, Kulesha E, Staines D, Bruford EA, Wright MW, Burge S, Finn RD, Kersey PJ, Cochrane G, Bateman A, Griffiths-Jones S, Harrow J, Chan PP, Lowe TM, Zwieb CW, Wower J, Williams KP, Hudson CM, Gutell R, Clark MB, Dinger M, Quek XC, Bujnicki JM, Chua NH, Liu J, Wang H, Skogerbø G, Zhao Y, Chen R, Zhu W, Cole JR, Chai B, Huang HD, Huang HY, Cherry JM, Hatzigeorgiou A, Pruitt KD. Nucleic acids research Volume 43 (2015) p.D123-9 DOI: 10.1093/nar/gku991
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UniProt: a hub for protein information.
UniProt Consortium. Nucleic acids research Volume 43 (2015) p.D204-12 DOI: 10.1093/nar/gku989
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Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis.
Das D, Murzin AG, Rawlings ND, Finn RD, Coggill P, Bateman A, Godzik A, Aravind L. BMC bioinformatics Volume 15 (2014) p.75 DOI: 10.1186/1471-2105-15-75
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K, UniProt Consortium. Database : the journal of biological databases and curation Volume 2014 (2014) p.bau016 DOI: 10.1093/database/bau016

2013

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.
Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat077 DOI: 10.1093/database/bat077
iPfam: a database of protein family and domain interactions found in the Protein Data Bank.
Finn RD, Miller BL, Clements J, Bateman A. Nucleic acids research Volume 42 (2014) p.D364-73 DOI: 10.1093/nar/gkt1210
Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Nucleic acids research Volume 42 (2014) p.D222-30 DOI: 10.1093/nar/gkt1223
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LUD, a new protein domain associated with lactate utilization.
Hwang WC, Bakolitsa C, Punta M, Coggill PC, Bateman A, Axelrod HL, Rawlings ND, Sedova M, Peterson SN, Eberhardt RY, Aravind L, Pascual J, Godzik A. BMC bioinformatics Volume 14 (2013) p.341 DOI: 10.1186/1471-2105-14-341
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Filling out the structural map of the NTF2-like superfamily.
Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L. BMC bioinformatics Volume 14 (2013) p.327 DOI: 10.1186/1471-2105-14-327
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Activities at the Universal Protein Resource (UniProt).
UniProt Consortium. Nucleic acids research Volume 42 (2014) p.D191-8 DOI: 10.1093/nar/gkt1140
TreeFam v9: a new website, more species and orthology-on-the-fly.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A. Nucleic acids research Volume 42 (2014) p.D922-5 DOI: 10.1093/nar/gkt1055
MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Waller M, Barrett AJ, Bateman A. Nucleic acids research Volume 42 (2014) p.D503-9 DOI: 10.1093/nar/gkt953
ISCB computational biology Wikipedia competition.
Bateman A, Kelso J, Mietchen D, Macintyre G, Di Domenico T, Abeel T, Logan DW, Radivojac P, Rost B. PLoS computational biology Volume 9 (2013) p.e1003242 DOI: 10.1371/journal.pcbi.1003242
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Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila.
Coggill P, Eberhardt RY, Finn RD, Chang Y, Jaroszewski L, Godzik A, Das D, Xu Q, Axelrod HL, Aravind L, Murzin AG, Bateman A. BMC bioinformatics Volume 14 (2013) p.265 DOI: 10.1186/1471-2105-14-265
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The COMBREX project: design, methodology, and initial results.
Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S. PLoS biology Volume 11 (2013) p.e1001638 DOI: 10.1371/journal.pbio.1001638
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Alternative splicing of intrinsically disordered regions and rewiring of protein interactions.
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. Current opinion in structural biology Volume 23 (2013) p.443-450 DOI: 10.1016/j.sbi.2013.03.006
The challenge of increasing Pfam coverage of the human proteome.
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD, Bateman A, Punta M. Database : the journal of biological databases and curation Volume 2013 (2013) p.bat023 DOI: 10.1093/database/bat023
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.
Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Nucleic acids research Volume 41 (2013) p.e121 DOI: 10.1093/nar/gkt263
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A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium.
Barquist L, Langridge GC, Turner DJ, Phan MD, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP. Nucleic acids research Volume 41 (2013) p.4549-4564 DOI: 10.1093/nar/gkt148
The SHOCT domain: a widespread domain under-represented in model organisms.
Eberhardt RY, Bartholdson SJ, Punta M, Bateman A. PloS one Volume 8 (2013) p.e57848 DOI: 10.1371/journal.pone.0057848
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Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.
Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Bürglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ. Genome biology Volume 14 (2013) p.R11 DOI: 10.1186/gb-2013-14-2-r11
The challenge of increasing Pfam coverage of the human proteome
Mistry J, Coggill P, Eberhardt R, Deiana A, Giansanti A, Finn R, Bateman A, Punta M. Database: The Journal of Biological Databases and Curation Volume 2013 (2013)

2012

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Rfam 11.0: 10 years of RNA families.
Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Nucleic acids research Volume 41 (2013) p.D226-32 DOI: 10.1093/nar/gks1005
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Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference.
Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas036 DOI: 10.1093/database/bas036
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Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks.
Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM. Molecular cell Volume 46 (2012) p.871-883 DOI: 10.1016/j.molcel.2012.05.039
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The YARHG domain: an extracellular domain in search of a function.
Coggill P, Bateman A. PloS one Volume 7 (2012) p.e35575 DOI: 10.1371/journal.pone.0035575
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InterPro in 2011: new developments in the family and domain prediction database
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood T, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn R, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn A, Rivoire C, Sangrador-Vegas A, Selengut J, Sigrist C, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas P, Wu C, Yeats C, Yong S. Nucleic acids research Volume 40 (2012) p.4725-4725 DOI: 10.1093/nar/gks456
Biocurators and biocuration: surveying the 21st century challenges.
Burge S, Attwood TK, Bateman A, Berardini TZ, Cherry M, O'Donovan C, Xenarios L, Gaudet P. Database : the journal of biological databases and curation Volume 2012 (2012) p.bar059 DOI: 10.1093/database/bar059
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AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A. Database : the journal of biological databases and curation Volume 2012 (2012) p.bas003 DOI: 10.1093/database/bas003
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Bioimage informatics: a new category in Bioinformatics.
Peng H, Bateman A, Valencia A, Wren JD. Bioinformatics (Oxford, England) Volume 28 (2012) p.1057 DOI: 10.1093/bioinformatics/bts111

2011

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Making your database available through Wikipedia: the pros and cons.
Finn RD, Gardner PP, Bateman A. Nucleic acids research Volume 40 (2012) p.D9-12 DOI: 10.1093/nar/gkr1195
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The Pfam protein families database.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. Nucleic acids research Volume 40 (2012) p.D290-301 DOI: 10.1093/nar/gkr1065
InterPro in 2011: new developments in the family and domain prediction database.
Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY. Nucleic acids research Volume 40 (2012) p.D306-12 DOI: 10.1093/nar/gkr948
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MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.
Rawlings ND, Barrett AJ, Bateman A. Nucleic acids research Volume 40 (2012) p.D343-50 DOI: 10.1093/nar/gkr987