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 Res, 47(d1):D427-D432, 01 Jan 2019

Cited by: 3186 articles | PMID: 30357350 | PMCID: PMC6324024

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 Res, 40(database issue):D290-301, 29 Nov 2011

Cited by: 2799 articles | PMID: 22127870 | PMCID: PMC3245129

The Gene Ontology resource: enriching a GOld mine.

Gene Ontology Consortium

Nucleic Acids Res, 49(d1):D325-D334, 01 Jan 2021

Cited by: 2608 articles | PMID: 33290552 | PMCID: PMC7779012

The Pfam protein families database.

Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR

Nucleic Acids Res, 32(database issue):D138-41, 01 Jan 2004

Cited by: 2598 articles | PMID: 14681378 | PMCID: PMC308855

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Gene Ontology Consortium: going forward.

Gene Ontology Consortium

Nucleic Acids Res, 43(database issue):D1049-56, 26 Nov 2014

Cited by: 2501 articles | PMID: 25428369 | PMCID: PMC4383973

Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2).

Bentley SD, Chater KF, Cerdeño-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, [...] Hopwood DA

Nature, 417(6885):141-147, 01 May 2002

Cited by: 2314 articles | PMID: 12000953

The Pfam protein families database.

Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A

Nucleic Acids Res, 38(database issue):D211-22, 17 Nov 2009

Cited by: 2287 articles | PMID: 19920124 | PMCID: PMC2808889

Highly accurate protein structure prediction for the human proteome.

Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Žídek A, Bridgland A, Cowie A, Meyer C, Laydon A, Velankar S, Kleywegt GJ, Bateman A, Evans R, Pritzel A, Figurnov M, Ronneberger O, Bates R, Kohl SAA, [...] Hassabis D

Nature, 596(7873):590-596, 22 Jul 2021

Cited by: 2038 articles | PMID: 34293799 | PMCID: PMC8387240

InterPro in 2022.

Paysan-Lafosse T, Blum M, Chuguransky S, Grego T, Pinto BL, Salazar GA, Bileschi ML, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunić I, Marchler-Bauer A, Mi H, Natale DA, Orengo CA, Pandurangan AP, Rivoire C, [...] Bateman A

Nucleic Acids Res, 51(d1):D418-D427, 01 Jan 2023

Cited by: 1799 articles | PMID: 36350672 | PMCID: PMC9825450

The Gene Ontology knowledgebase in 2023.

Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, [...] Westerfield M

Genetics, 224(1):iyad031, 01 May 2023

Cited by: 1765 articles | PMID: 36866529 | PMCID: PMC10158837

Review

The Pfam protein families database.

Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A

Nucleic Acids Res, 36(database issue):D281-8, 26 Nov 2007

Cited by: 1691 articles | PMID: 18039703 | PMCID: PMC2238907

The Pfam protein families database.

Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL

Nucleic Acids Res, 30(1):276-280, 01 Jan 2002

Cited by: 1674 articles | PMID: 11752314 | PMCID: PMC99071

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Pfam: clans, web tools and services.

Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A

Nucleic Acids Res, 34(database issue):D247-51, 01 Jan 2006

Cited by: 1656 articles | PMID: 16381856 | PMCID: PMC1347511

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, [...] Finn RD

Nucleic Acids Res, 49(d1):D344-D354, 01 Jan 2021

Cited by: 1589 articles | PMID: 33156333 | PMCID: PMC7778928

InterPro: the integrative protein signature database.

Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, [...] Yeats C

Nucleic Acids Res, 37(database issue):D211-5, 21 Oct 2008

Cited by: 1523 articles | PMID: 18940856 | PMCID: PMC2686546

Rfam: annotating non-coding RNAs in complete genomes.

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A

Nucleic Acids Res, 33(database issue):D121-4, 01 Jan 2005

Cited by: 1209 articles | PMID: 15608160 | PMCID: PMC540035

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

Mistry J, Finn RD, Eddy SR, Bateman A, Punta M

Nucleic Acids Res, 41(12):e121, 17 Apr 2013

Cited by: 1191 articles | PMID: 23598997 | PMCID: PMC3695513

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 Res, 46(d1):D624-D632, 01 Jan 2018

Cited by: 1138 articles | PMID: 29145643 | PMCID: PMC5753285

Rfam: an RNA family database.

Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR

Nucleic Acids Res, 31(1):439-441, 01 Jan 2003

Cited by: 1105 articles | PMID: 12520045 | PMCID: PMC165453

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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, [...] Mitchell AL

Nucleic Acids Res, 45(d1):D190-D199, 29 Nov 2016

Cited by: 1058 articles | PMID: 27899635 | PMCID: PMC5210578

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, [...] Finn RD

Nucleic Acids Res, 43(database issue):D213-21, 26 Nov 2014

Cited by: 971 articles | PMID: 25428371 | PMCID: PMC4383996

Activities at the Universal Protein Resource (UniProt).

UniProt Consortium

Nucleic Acids Res, 42(database issue):D191-8, 18 Nov 2013

Cited by: 913 articles | PMID: 24253303 | PMCID: PMC3965022

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 Res, 43(database issue):D130-7, 11 Nov 2014

Cited by: 818 articles | PMID: 25392425 | PMCID: PMC4383904

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, [...] Yong SY

Nucleic Acids Res, 40(database issue):D306-12, 16 Nov 2011

Cited by: 794 articles | PMID: 22096229 | PMCID: PMC3245097

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 Res, 49(d1):D192-D200, 01 Jan 2021

Cited by: 756 articles | PMID: 33211869 | PMCID: PMC7779021

HMMER web server: 2015 update.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR

Nucleic Acids Res, 43(w1):W30-8, 05 May 2015

Cited by: 699 articles | PMID: 25943547 | PMCID: PMC4489315

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 Res, 46(d1):D335-D342, 01 Jan 2018

Cited by: 698 articles | PMID: 29112718 | PMCID: PMC5753348

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A

Nucleic Acids Res, 37(database issue):D136-40, 25 Oct 2008

Cited by: 680 articles | PMID: 18953034 | PMCID: PMC2686503

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

Rawlings ND, Waller M, Barrett AJ, Bateman A

Nucleic Acids Res, 42(database issue):D503-9, 23 Oct 2013

Cited by: 661 articles | PMID: 24157837 | PMCID: PMC3964991

MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.

Rawlings ND, Barrett AJ, Bateman A

Nucleic Acids Res, 40(database issue):D343-50, 15 Nov 2011

Cited by: 644 articles | PMID: 22086950 | PMCID: PMC3245014

MEROPS: the peptidase database.

Rawlings ND, Barrett AJ, Bateman A

Nucleic Acids Res, 38(database issue):D227-33, 05 Nov 2009

Cited by: 641 articles | PMID: 19892822 | PMCID: PMC2808883

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 Res, 41(database issue):D226-32, 03 Nov 2012

Cited by: 602 articles | PMID: 23125362 | PMCID: PMC3531072

Pfam: multiple sequence alignments and HMM-profiles of protein domains.

Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R

Nucleic Acids Res, 26(1):320-322, 01 Jan 1998

Cited by: 499 articles | PMID: 9399864 | PMCID: PMC147209

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The InterPro Database, 2003 brings increased coverage and new features.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barrell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, [...] Zdobnov EM

Nucleic Acids Res, 31(1):315-318, 01 Jan 2003

Cited by: 473 articles | PMID: 12520011 | PMCID: PMC165493

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A structural biology community assessment of AlphaFold2 applications.

Akdel M, Pires DEV, Pardo EP, Jänes J, Zalevsky AO, Mészáros B, Bryant P, Good LL, Laskowski RA, Pozzati G, Shenoy A, Zhu W, Kundrotas P, Serra VR, Rodrigues CHM, Dunham AS, Burke D, Borkakoti N, Velankar S, [...] Beltrao P

Nat Struct Mol Biol, 29(11):1056-1067, 07 Nov 2022

Cited by: 440 articles | PMID: 36344848 | PMCID: PMC9663297

InterPro: the protein sequence classification resource in 2025.

Blum M, Andreeva A, Florentino LC, Chuguransky SR, Grego T, Hobbs E, Pinto BL, Orr A, Paysan-Lafosse T, Ponamareva I, Salazar GA, Bordin N, Bork P, Bridge A, Colwell L, Gough J, Haft DH, Letunic I, Llinares-López F, [...] Bateman A

Nucleic Acids Res, 53(d1):D444-D456, 01 Jan 2025

Cited by: 406 articles | PMID: 39565202 | PMCID: PMC11701551

The structure of a domain common to archaebacteria and the homocystinuria disease protein.

Bateman A

Trends Biochem Sci, 22(1):12-13, 01 Jan 1997

Cited by: 397 articles | PMID: 9020585

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL

Nucleic Acids Res, 27(1):260-262, 01 Jan 1999

Cited by: 371 articles | PMID: 9847196 | PMCID: PMC148151

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InterPro, progress and status in 2005.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, [...] Wu CH

Nucleic Acids Res, 33(database issue):D201-5, 01 Jan 2005

Cited by: 358 articles | PMID: 15608177 | PMCID: PMC540060

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, 176(1-2):391-403.e19, 06 Dec 2018

Cited by: 334 articles | PMID: 30528433

Non-Coding RNA Analysis Using the Rfam Database.

Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI

Curr Protoc Bioinformatics, 62(1):e51, 05 Jun 2018

Cited by: 328 articles | PMID: 29927072 | PMCID: PMC6754622

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New developments in the InterPro database.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, [...] Yeats C

Nucleic Acids Res, 35(database issue):D224-8, 01 Jan 2007

Cited by: 326 articles | PMID: 17202162 | PMCID: PMC1899100

The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD).

Bateman A, Bycroft M

J Mol Biol, 299(4):1113-1119, 01 Jun 2000

Cited by: 320 articles | PMID: 10843862

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

Mol Cell, 46(6):871-883, 01 Jun 2012

Cited by: 319 articles | PMID: 22749400 | PMCID: PMC3437557

Rfam: Wikipedia, clans and the "decimal" release.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A

Nucleic Acids Res, 39(database issue):D141-5, 09 Nov 2010

Cited by: 303 articles | PMID: 21062808 | PMCID: PMC3013711

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

RNAcentral Consortium

Nucleic Acids Res, 49(d1):D212-D220, 01 Jan 2021

Cited by: 287 articles | PMID: 33106848 | PMCID: PMC7779037

Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain.

Cerutti L, Mian N, Bateman A

Trends Biochem Sci, 25(10):481-482, 01 Oct 2000

Cited by: 269 articles | PMID: 11050429

The tify family previously known as ZIM.

Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G

Trends Plant Sci, 12(6):239-244, 10 May 2007

Cited by: 253 articles | PMID: 17499004

Review

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, [...] Loftus BJ

Genome Biol, 14(2):R11, 01 Feb 2013

Cited by: 237 articles | PMID: 23375108 | PMCID: PMC4053784

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 Res, 47(21):10994-11006, 01 Dec 2019

Cited by: 233 articles | PMID: 31584084 | PMCID: PMC6868369

Review

The systematic functional analysis of Plasmodium protein kinases identifies essential regulators of mosquito transmission.

Tewari R, Straschil U, Bateman A, Böhme U, Cherevach I, Gong P, Pain A, Billker O

Cell Host Microbe, 8(4):377-387, 01 Oct 2010

Cited by: 221 articles | PMID: 20951971 | PMCID: PMC2977076

QuickTree: building huge Neighbour-Joining trees of protein sequences.

Howe K, Bateman A, Durbin R

Bioinformatics, 18(11):1546-1547, 01 Nov 2002

Cited by: 220 articles | PMID: 12424131

Predicting active site residue annotations in the Pfam database.

Mistry J, Bateman A, Finn RD

BMC Bioinformatics, 8:298, 09 Aug 2007

Cited by: 210 articles | PMID: 17688688 | PMCID: PMC2025603

Using deep learning to annotate the protein universe.

Bileschi ML, Belanger D, Bryant DH, Sanderson T, Carter B, Sculley D, Bateman A, DePristo MA, Colwell LJ

Nat Biotechnol, 40(6):932-937, 21 Feb 2022

Cited by: 208 articles | PMID: 35190689

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions.

Finn RD, Marshall M, Bateman A

Bioinformatics, 21(3):410-412, 07 Sep 2004

Cited by: 207 articles | PMID: 15353450

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, [...] Dinger ME

Nucleic Acids Res, 45(d1):D128-D134, 28 Oct 2016

Cited by: 196 articles | PMID: 27794554 | PMCID: PMC5210518

Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, Sigrist CJA, Redaschi N, Bridge A, UniProt Consortium

Bioinformatics, 39(1):btac793, 01 Jan 2023

Cited by: 192 articles | PMID: 36484697 | PMCID: PMC9825770

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium

Nucleic Acids Res, 47(d1):D221-D229, 01 Jan 2019

Cited by: 190 articles | PMID: 30395267 | PMCID: PMC6324050

The CHAP domain: a large family of amidases including GSP amidase and peptidoglycan hydrolases.

Bateman A, Rawlings ND

Trends Biochem Sci, 28(5):234-237, 01 May 2003

Cited by: 190 articles | PMID: 12765834

Review

Large-scale screening for novel low-affinity extracellular protein interactions.

Bushell KM, Söllner C, Schuster-Boeckler B, Bateman A, Wright GJ

Genome Res, 18(4):622-630, 22 Feb 2008

Cited by: 189 articles | PMID: 18296487 | PMCID: PMC2279249

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DUFs: families in search of function.

Bateman A, Coggill P, Finn RD

Acta Crystallogr Sect F Struct Biol Cryst Commun, 66(pt 10):1148-1152, 05 Mar 2010

Cited by: 184 articles | PMID: 20944204 | PMCID: PMC2954198

The PASTA domain: a beta-lactam-binding domain.

Yeats C, Finn RD, Bateman A

Trends Biochem Sci, 27(9):438, 01 Sep 2002

Cited by: 181 articles | PMID: 12217513

Review

The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.

Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C

EMBO J, 18(2):297-305, 01 Jan 1999

Cited by: 154 articles | PMID: 9889186 | PMCID: PMC1171124

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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

Curr Opin Struct Biol, 23(3):443-450, 22 May 2013

Cited by: 146 articles | PMID: 23706950

Review

The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.

Dillon SC, Bateman A

BMC Bioinformatics, 5:109, 12 Aug 2004

Cited by: 136 articles | PMID: 15307895 | PMCID: PMC516016

The evolution of the DLK1-DIO3 imprinted domain in mammals.

Edwards CA, Mungall AJ, Matthews L, Ryder E, Gray DJ, Pask AJ, Shaw G, Graves JA, Rogers J, SAVOIR consortium, Dunham I, Renfree MB, Ferguson-Smith AC

PLoS Biol, 6(6):e135, 01 Jun 2008

Cited by: 134 articles | PMID: 18532878 | PMCID: PMC2408620

The HMMER Web Server for Protein Sequence Similarity Search.

Prakash A, Jeffryes M, Bateman A, Finn RD

Curr Protoc Bioinformatics, 60:3.15.1-3.15.23, 08 Dec 2017

Cited by: 127 articles | PMID: 29220076

Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Karcher N, Kritikos G, Selkrig J, Zietek M, Monzon V, Pfalz B, Garcia-Santamarina S, Galardini M, Sueki A, Kobayashi C, Stein F, Bateman A, Zeller G, Savitski MM, Elfenbein JR, Andrews-Polymenis HL, Typas A

Nature, 609(7925):144-150, 18 Jul 2022

Cited by: 125 articles | PMID: 35850148 | PMCID: PMC11938430

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The Pfam protein families database: embracing AI/ML.

Paysan-Lafosse T, Andreeva A, Blum M, Chuguransky SR, Grego T, Pinto BL, Salazar GA, Bileschi ML, Llinares-López F, Meng-Papaxanthos L, Colwell LJ, Grishin NV, Schaeffer RD, Clementel D, Tosatto SCE, Sonnhammer E, Wood V, Bateman A

Nucleic Acids Res, 53(d1):D523-D534, 01 Jan 2025

Cited by: 123 articles | PMID: 39540428 | PMCID: PMC11701544

The ENTH domain.

De Camilli P, Chen H, Hyman J, Panepucci E, Bateman A, Brunger AT

FEBS Lett, 513(1):11-18, 01 Feb 2002

Cited by: 122 articles | PMID: 11911874

Review

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 Res, 42(database issue):D364-73, 01 Dec 2013

Cited by: 121 articles | PMID: 24297255 | PMCID: PMC3965099

InterPro: an integrated documentation resource for protein families, domains and functional sites.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, [...] InterPro Consortium

Brief Bioinform, 3(3):225-235, 01 Sep 2002

Cited by: 119 articles | PMID: 12230031

TreeFam v9: a new website, more species and orthology-on-the-fly.

Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A

Nucleic Acids Res, 42(database issue):D922-5, 04 Nov 2013

Cited by: 115 articles | PMID: 24194607 | PMCID: PMC3965059

Uncovering new families and folds in the natural protein universe.

Durairaj J, Waterhouse AM, Mets T, Brodiazhenko T, Abdullah M, Studer G, Tauriello G, Akdel M, Andreeva A, Bateman A, Tenson T, Hauryliuk V, Schwede T, Pereira J

Nature, 622(7983):646-653, 13 Sep 2023

Cited by: 109 articles | PMID: 37704037 | PMCID: PMC10584680

Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains.

Sandford R, Sgotto B, Aparicio S, Brenner S, Vaudin M, Wilson RK, Chissoe S, Pepin K, Bateman A, Chothia C, Hughes J, Harris P

Hum Mol Genet, 6(9):1483-1489, 01 Sep 1997

Cited by: 103 articles | PMID: 9285785

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, 33(21):3454-3460, 01 Nov 2017

Cited by: 102 articles | PMID: 29036270 | PMCID: PMC5860168

Membrane-bound progesterone receptors contain a cytochrome b5-like ligand-binding domain.

Mifsud W, Bateman A

Genome Biol, 3(12):RESEARCH0068, 12 Nov 2002

Cited by: 102 articles | PMID: 12537557 | PMCID: PMC151170

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 Res, 41(8):4549-4564, 06 Mar 2013

Cited by: 99 articles | PMID: 23470992 | PMCID: PMC3632133

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 AC, Heider D, Hoffmann M, [...] Marz M

Brief Bioinform, 22(2):642-663, 01 Mar 2021

Cited by: 97 articles | PMID: 33147627 | PMCID: PMC7665365

Review

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, [...] Pruitt KD

Nucleic Acids Res, 43(database issue):D123-9, 28 Oct 2014

Cited by: 94 articles | PMID: 25352543 | PMCID: PMC4384043

Protein interactions in human genetic diseases.

Schuster-Böckler B, Bateman A

Genome Biol, 9(1):R9, 16 Jan 2008

Cited by: 92 articles | PMID: 18199329 | PMCID: PMC2395246

The evolution of protein domain families.

Buljan M, Bateman A

Biochem Soc Trans, 37(pt 4):751-755, 01 Aug 2009

Cited by: 90 articles | PMID: 19614588

Review

Quantifying the mechanisms of domain gain in animal proteins.

Buljan M, Frankish A, Bateman A

Genome Biol, 11(7):R74, 15 Jul 2010

Cited by: 85 articles | PMID: 20633280 | PMCID: PMC2926785

When will RNA get its AlphaFold moment?

Schneider B, Sweeney BA, Bateman A, Cerny J, Zok T, Szachniuk M

Nucleic Acids Res, 51(18):9522-9532, 01 Oct 2023

Cited by: 84 articles | PMID: 37702120 | PMCID: PMC10570031

Pfam 10 years on: 10,000 families and still growing.

Sammut SJ, Finn RD, Bateman A

Brief Bioinform, 9(3):210-219, 15 Mar 2008

Cited by: 84 articles | PMID: 18344544

Review

Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance.

Seitan VC, Banks P, Laval S, Majid NA, Dorsett D, Rana A, Smith J, Bateman A, Krpic S, Hostert A, Rollins RA, Erdjument-Bromage H, Tempst P, Benard CY, Hekimi S, Newbury SF, Strachan T

PLoS Biol, 4(8):e242, 01 Jul 2006

Cited by: 84 articles | PMID: 16802858 | PMCID: PMC1484498

The PA domain: a protease-associated domain.

Mahon P, Bateman A

Protein Sci, 9(10):1930-1934, 01 Oct 2000

Cited by: 79 articles | PMID: 11106166 | PMCID: PMC2144460

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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

Nat Struct Mol Biol, 28(2):210-219, 08 Feb 2021

Cited by: 77 articles | PMID: 33558764 | PMCID: PMC7610652

Dosage sensitivity shapes the evolution of copy-number varied regions.

Schuster-Böckler B, Conrad D, Bateman A

PLoS One, 5(3):e9474, 10 Mar 2010

Cited by: 75 articles | PMID: 20224824 | PMCID: PMC2835737

The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.

Bateman A, Holden MT, Yeats C

Bioinformatics, 21(8):1301-1303, 14 Dec 2004

Cited by: 73 articles | PMID: 15598841

The BON domain: a putative membrane-binding domain.

Yeats C, Bateman A

Trends Biochem Sci, 28(7):352-355, 01 Jul 2003

Cited by: 73 articles | PMID: 12878000

Rfam 15: RNA families database in 2025.

Ontiveros-Palacios N, Cooke E, Nawrocki EP, Triebel S, Marz M, Rivas E, Griffiths-Jones S, Petrov AI, Bateman A, Sweeney B

Nucleic Acids Res, 53(d1):D258-D267, 01 Jan 2025

Cited by: 72 articles | PMID: 39526405 | PMCID: PMC11701678

The SIS domain: a phosphosugar-binding domain.

Bateman A

Trends Biochem Sci, 24(3):94-95, 01 Mar 1999

Cited by: 72 articles | PMID: 10203754

The PepSY domain: a regulator of peptidase activity in the microbial environment?

Yeats C, Rawlings ND, Bateman A

Trends Biochem Sci, 29(4):169-172, 01 Apr 2004

Cited by: 71 articles | PMID: 15124630

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z

Nucleic Acids Res, 39(14):5845-5852, 07 Apr 2011

Cited by: 70 articles | PMID: 21478170 | PMCID: PMC3152330

How to use the MEROPS database and website to help understand peptidase specificity.

Rawlings ND, Bateman A

Protein Sci, 30(1):83-92, 03 Oct 2020

Cited by: 61 articles | PMID: 32920969 | PMCID: PMC7737757

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, [...] Zwieb C

RNA, 17(11):1941-1946, 22 Sep 2011

Cited by: 60 articles | PMID: 21940779 | PMCID: PMC3198587

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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, 14:327, 19 Nov 2013

Cited by: 57 articles | PMID: 24246060 | PMCID: PMC3924330

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors.

Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J

Bioinformatics, 25(2):159-162, 13 Nov 2008

Cited by: 55 articles | PMID: 19010806 | PMCID: PMC2639001

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, [...] UniProt Consortium

Bioinformatics, 36(17):4643-4648, 01 Nov 2020

Cited by: 54 articles | PMID: 32399560 | PMCID: PMC7750954

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, 36(8):2636-2642, 01 Apr 2020

Cited by: 52 articles | PMID: 31950984 | PMCID: PMC7446027

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium

Nucleic Acids Res, 47(d1):D1250-D1251, 01 Jan 2019

Cited by: 52 articles | PMID: 30535383 | PMCID: PMC6323998

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, [...] Smith KG

J Exp Med, 214(4):1111-1128, 28 Mar 2017

Cited by: 51 articles | PMID: 28351984 | PMCID: PMC5379978

The DUTT1 gene, a novel NCAM family member is expressed in developing murine neural tissues and has an unusually broad pattern of expression.

Sundaresan V, Roberts I, Bateman A, Bankier A, Sheppard M, Hobbs C, Xiong J, Minna J, Latif F, Lerman M, Rabbitts P

Mol Cell Neurosci, 11(1-2):29-35, 01 May 1998

Cited by: 51 articles | PMID: 9608531

The European Bioinformatics Institute (EMBL-EBI) in 2021.

Cantelli G, Bateman A, Brooksbank C, Petrov AI, Malik-Sheriff RS, Ide-Smith M, Hermjakob H, Flicek P, Apweiler R, Birney E, McEntyre J

Nucleic Acids Res, 50(d1):D11-D19, 01 Jan 2022

Cited by: 50 articles | PMID: 34850134 | PMCID: PMC8690175

Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes.

Smyshlyaev G, Bateman A, Barabas O

Mol Syst Biol, 17(5):e9880, 01 May 2021

Cited by: 50 articles | PMID: 34018328 | PMCID: PMC8138268

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, 23(5):696-711, 13 Feb 2017

Cited by: 50 articles | PMID: 28193673 | PMCID: PMC5393179

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 (Oxford), 2012:bar059, 20 Mar 2012

Cited by: 47 articles | PMID: 22434828 | PMCID: PMC3308150

Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes.

Rawlings ND, Barrett AJ, Bateman A

J Biol Chem, 286(44):38321-38328, 08 Aug 2011

Cited by: 47 articles | PMID: 21832066 | PMCID: PMC3207474

Identifying protein domains with the Pfam database.

Coggill P, Finn RD, Bateman A

Curr Protoc Bioinformatics, Chapter 2:2.5.1-2.5.17, 01 Sep 2008

Cited by: 45 articles | PMID: 18819075

Database Commons: A Catalog of Worldwide Biological Databases.

Ma L, Zou D, Liu L, Shireen H, Abbasi AA, Bateman A, Xiao J, Zhao W, Bao Y, Zhang Z

Genomics Proteomics Bioinformatics, 21(5):1054-1058, 23 Dec 2022

Cited by: 44 articles | PMID: 36572336 | PMCID: PMC10928426

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 (Oxford), 2014:bau016, 12 Mar 2014

Cited by: 44 articles | PMID: 24622611 | PMCID: PMC3950660

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, [...] Kasif S

PLoS Biol, 11(8):e1001638, 27 Aug 2013

Cited by: 44 articles | PMID: 24013487 | PMCID: PMC3754883

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 (Oxford), 2012:bas003, 20 Mar 2012

Cited by: 44 articles | PMID: 22434837 | PMCID: PMC3308159

The RNA WikiProject: community annotation of RNA families.

Daub J, Gardner PP, Tate J, Ramsköld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A

RNA, 14(12):2462-2464, 22 Oct 2008

Cited by: 43 articles | PMID: 18945806 | PMCID: PMC2590952

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GREENER principles for environmentally sustainable computational science.

Lannelongue L, Aronson HG, Bateman A, Birney E, Caplan T, Juckes M, McEntyre J, Morris AD, Reilly G, Inouye M

Nat Comput Sci, 3(6):514-521, 26 Jun 2023

Cited by: 37 articles | PMID: 38177425

Review

Folding the unfoldable: using AlphaFold to explore spurious proteins.

Monzon V, Haft DH, Bateman A

Bioinform Adv, 2(1):vbab043, 09 Jan 2022

Cited by: 37 articles | PMID: 36699409 | PMCID: PMC9710616

A roadmap for the functional annotation of protein families: a community perspective.

de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, [...] Xu J

Database (Oxford), 2022:baac062, 01 Aug 2022

Cited by: 36 articles | PMID: 35961013 | PMCID: PMC9374478

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, 32(15):2264-2271, 07 Mar 2016

Cited by: 36 articles | PMID: 27153729 | PMCID: PMC4965628

SnoPatrol: how many snoRNA genes are there?

Gardner PP, Bateman A, Poole AM

J Biol, 9(1):4, 25 Jan 2010

Cited by: 35 articles | PMID: 20122292 | PMCID: PMC2871523

Review

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, McEntyre J

Nucleic Acids Res, 51(d1):D9-D17, 01 Jan 2023

Cited by: 34 articles | PMID: 36477213 | PMCID: PMC9825486

Using the MEROPS Database for Proteolytic Enzymes and Their Inhibitors and Substrates.

Rawlings ND, Barrett AJ, Bateman A

Curr Protoc Bioinformatics, 48:1.25.1-1.25.33, 12 Dec 2014

Cited by: 34 articles | PMID: 25501939

Reuse of structural domain-domain interactions in protein networks.

Schuster-Böckler B, Bateman A

BMC Bioinformatics, 8:259, 18 Jul 2007

Cited by: 34 articles | PMID: 17640363 | PMCID: PMC1940023

Enhanced protein domain discovery by using language modeling techniques from speech recognition.

Coin L, Bateman A, Durbin R

Proc Natl Acad Sci U S A, 100(8):4516-4520, 31 Mar 2003

Cited by: 34 articles | PMID: 12668763 | PMCID: PMC404693

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Data management: A global coalition to sustain core data.

Anderson WP, Global Life Science Data Resources Working Group

Nature, 543(7644):179, 01 Mar 2017

Cited by: 33 articles | PMID: 28277502

Tandem domain swapping: determinants of multidomain protein misfolding.

Lafita A, Tian P, Best RB, Bateman A

Curr Opin Struct Biol, 58:97-104, 28 Jun 2019

Cited by: 32 articles | PMID: 31260947 | PMCID: PMC6863430

Review

SCOOP: a simple method for identification of novel protein superfamily relationships.

Bateman A, Finn RD

Bioinformatics, 23(7):809-814, 03 Feb 2007

Cited by: 32 articles | PMID: 17277330 | PMCID: PMC2603044

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Visualizing profile-profile alignment: pairwise HMM logos.

Schuster-Böckler B, Bateman A

Bioinformatics, 21(12):2912-2913, 12 Apr 2005

Cited by: 32 articles | PMID: 15827079

Origins of peptidases.

Rawlings ND, Bateman A

Biochimie, 166:4-18, 01 Aug 2019

Cited by: 30 articles | PMID: 31377195 | PMCID: PMC7117030

Curators of the world unite: the International Society of Biocuration.

Bateman A

Bioinformatics, 26(8):991, 19 Mar 2010

Cited by: 30 articles | PMID: 20305270

An introduction to hidden Markov models.

Schuster-Böckler B, Bateman A

Curr Protoc Bioinformatics, Appendix 3:Appendix 3A, 01 Jun 2007

Cited by: 30 articles | PMID: 18428778

Review

Mining the draft human genome.

Birney E, Bateman A, Clamp ME, Hubbard TJ

Nature, 409(6822):827-828, 01 Feb 2001

Cited by: 30 articles | PMID: 11236999 | PMCID: PMC2658632

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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, 11(4):e01364-20, 25 Aug 2020

Cited by: 29 articles | PMID: 32843546 | PMCID: PMC7448272

Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.

Xu Q, Bateman A, Finn RD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Carlton D, Chen C, Chiu HJ, Chiu M, Clayton T, Das D, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, [...] Wilson IA

J Mol Biol, 396(1):31-46, 10 Nov 2009

Cited by: 28 articles | PMID: 19913036 | PMCID: PMC2817789

Pepsin homologues in bacteria.

Rawlings ND, Bateman A

BMC Genomics, 10:437, 16 Sep 2009

Cited by: 28 articles | PMID: 19758436 | PMCID: PMC2761423

Databases, data tombs and dust in the wind.

Wren JD, Bateman A

Bioinformatics, 24(19):2127-2128, 01 Oct 2008

Cited by: 27 articles | PMID: 18819940

A member of the immunoglobulin superfamily in bacteriophage T4.

Bateman A, Eddy SR, Mesyanzhinov VV

Virus Genes, 14(2):163-165, 01 Jan 1997

Cited by: 27 articles | PMID: 9237357

The Importance of Biological Databases in Biological Discovery.

Baxevanis AD, Bateman A

Curr Protoc Bioinformatics, 50:1.1.1-1.1.8, 19 Jun 2015

Cited by: 26 articles | PMID: 26094768

Reciprocal best structure hits: using AlphaFold models to discover distant homologues.

Monzon V, Paysan-Lafosse T, Wood V, Bateman A

Bioinform Adv, 2(1):vbac072, 06 Oct 2022

Cited by: 25 articles | PMID: 36408459 | PMCID: PMC9666668

Towards BioDBcore: a community-defined information specification for biological databases.

Gaudet P, Bairoch A, Field D, Sansone SA, Taylor C, Attwood TK, Bateman A, Blake JA, Bult CJ, Cherry JM, Chisholm RL, Cochrane G, Cook CE, Eppig JT, Galperin MY, Gentleman R, Goble CA, Gojobori T, Hancock JM, [...] BioDBCore Working Group

Nucleic Acids Res, 39(database issue):D7-10, 18 Nov 2010

Cited by: 25 articles | PMID: 21097465 | PMCID: PMC3013734

Cloud computing.

Bateman A, Wood M

Bioinformatics, 25(12):1475, 12 May 2009

Cited by: 24 articles | PMID: 19435745

The SGS3 protein involved in PTGS finds a family.

Bateman A

BMC Bioinformatics, 3:21, 05 Aug 2002

Cited by: 24 articles | PMID: 12162795 | PMCID: PMC119857

Ten simple rules to make your computing more environmentally sustainable.

Lannelongue L, Grealey J, Bateman A, Inouye M

PLoS Comput Biol, 17(9):e1009324, 20 Sep 2021

Cited by: 23 articles | PMID: 34543272 | PMCID: PMC8452068

Domain atrophy creates rare cases of functional partial protein domains.

Prakash A, Bateman A

Genome Biol, 16:88, 30 Apr 2015

Cited by: 22 articles | PMID: 25924720 | PMCID: PMC4432964

Ten simple rules for editing Wikipedia.

Logan DW, Sandal M, Gardner PP, Manske M, Bateman A

PLoS Comput Biol, 6(9):e1000941, 30 Sep 2010

Cited by: 22 articles | PMID: 20941386 | PMCID: PMC2947980

The TROVE module: a common element in Telomerase, Ro and Vault ribonucleoproteins.

Bateman A, Kickhoefer V

BMC Bioinformatics, 4:49, 16 Oct 2003

Cited by: 22 articles | PMID: 14563212 | PMCID: PMC270063

Making your database available through Wikipedia: the pros and cons.

Finn RD, Gardner PP, Bateman A

Nucleic Acids Res, 40(database issue):D9-12, 05 Dec 2011

Cited by: 21 articles | PMID: 22144683 | PMCID: PMC3245093

The rise and fall of supervised machine learning techniques.

Jensen LJ, Bateman A

Bioinformatics, 27(24):3331-3332, 17 Nov 2011

Cited by: 21 articles | PMID: 22101152 | PMCID: PMC3232371

The characterisation of three types of genes that overlie copy number variable regions.

Woodwark C, Bateman A

PLoS One, 6(5):e14814, 26 May 2011

Cited by: 21 articles | PMID: 21637334 | PMCID: PMC3102654

HMM-based databases in InterPro.

Bateman A, Haft DH

Brief Bioinform, 3(3):236-245, 01 Sep 2002

Cited by: 21 articles | PMID: 12230032

Identifying protein domains with the Pfam database.

Finn R, Griffiths-Jones S, Bateman A

Curr Protoc Bioinformatics, Chapter 2:Unit 2.5, 01 May 2003

Cited by: 20 articles | PMID: 18428696

Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica.

Studholme DJ, Fuerst JA, Bateman A

FEMS Microbiol Lett, 236(2):333-340, 01 Jul 2004

Cited by: 20 articles | PMID: 15251216

ECOD: integrating classifications of protein domains from experimental and predicted structures.

Schaeffer RD, Medvedev KE, Andreeva A, Chuguransky SR, Pinto BL, Zhang J, Cong Q, Bateman A, Grishin NV

Nucleic Acids Res, 53(d1):D411-D418, 01 Jan 2025

Cited by: 19 articles | PMID: 39565196 | PMCID: PMC11701565

Periscope Proteins are variable-length regulators of bacterial cell surface interactions.

Whelan F, Lafita A, Gilburt J, Dégut C, Griffiths SC, Jenkins HT, St John AN, Paci E, Moir JWB, Plevin MJ, Baumann CG, Bateman A, Potts JR

Proc Natl Acad Sci U S A, 118(23):e2101349118, 01 Jun 2021

Cited by: 19 articles | PMID: 34074781 | PMCID: PMC8201768

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

Nat Commun, 10(1):5612, 09 Dec 2019

Cited by: 19 articles | PMID: 31819058 | PMCID: PMC6901522

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 (Oxford), 2013:bat023, 19 Apr 2013

Cited by: 18 articles | PMID: 23603847 | PMCID: PMC3630804

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

Proc Natl Acad Sci U S A, 116(52):26540-26548, 09 Dec 2019

Cited by: 17 articles | PMID: 31818940 | PMCID: PMC6936399

Bioimage informatics: a new category in Bioinformatics.

Peng H, Bateman A, Valencia A, Wren JD

Bioinformatics, 28(8):1057, 06 Mar 2012

Cited by: 17 articles | PMID: 22399678 | PMCID: PMC3324521

CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4.

Murzin AG, Bateman A

Proteins, Suppl 5:76-85, 01 Jan 2001

Cited by: 17 articles | PMID: 11835484

The yeast noncoding RNA interaction network.

Panni S, Prakash A, Bateman A, Orchard S

RNA, 23(10):1479-1492, 12 Jul 2017

Cited by: 16 articles | PMID: 28701522 | PMCID: PMC5602107

Characterization of the nodulation plasmid encoded chemoreceptor gene mcpG from Rhizobium leguminosarum.

Yost CK, Clark KT, Del Bel KL, Hynes MF

BMC Microbiol, 3:1, 28 Jan 2003

Cited by: 16 articles | PMID: 12553885 | PMCID: PMC149452

The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.

Griffiths-Jones S, Bateman A

Bioinformatics, 18(9):1243-1249, 01 Sep 2002

Cited by: 16 articles | PMID: 12217916

Discovery of fibrillar adhesins across bacterial species.

Monzon V, Lafita A, Bateman A

BMC Genomics, 22(1):550, 18 Jul 2021

Cited by: 15 articles | PMID: 34275445 | PMCID: PMC8286594

Bioinformatics for next generation sequencing.

Bateman A, Quackenbush J

Bioinformatics, 25(4):429, 08 Feb 2009

Cited by: 14 articles | PMID: 19202193

Enhanced protein domain discovery using taxonomy.

Coin L, Bateman A, Durbin R

BMC Bioinformatics, 5:56, 11 May 2004

Cited by: 13 articles | PMID: 15137915 | PMCID: PMC434490

FAIR adoption, assessment and challenges at UniProt.

Garcia L, Bolleman J, Gehant S, Redaschi N, Martin M, UniProt Consortium

Sci Data, 6(1):175, 20 Sep 2019

Cited by: 12 articles | PMID: 31541106 | PMCID: PMC6754384

A subgroup of light-driven sodium pumps with an additional Schiff base counterion.

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