Bateman group Publications

InterPro in 2011: new developments in the family and domain prediction database

Nucleic acids research. Volume 40, Number D1, (2012), p.D343–D350

HUNTER, S., Jones P., Mitchell A., Apweiler R., Attwood T. K., Bateman A., Bernard T., Binns D., Bork P., BURGE S., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D306–D312

Making your database available through Wikipedia: the pros and cons

Finn, R. D., Gardner P. P., and Bateman A.

Nucleic acids research. Volume 40, Number D1, (2012), p.D9–D12

Bioimage informatics: a new category in Bioinformatics

Punta, M., Coggill P. C., Eberhardt R. Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., et al.

Nucleic acids research. Volume 40, Number D1, (2012), p.D290–D301

Peng, H., Bateman A., Valencia A., and Wren J. D.

Bioinformatics. Volume 28, Number 8, (2012), p.1057–1057

Bioinformatics Advance Access published March 6, 2012

Peng, H., Bateman A., Valencia A., and Wren J. D.

(2012),

Biocurators and Biocuration: surveying the 21st century challenges

BURGE, S., Attwood T. K., Bateman A., Berardini T. Z., Cherry M., O'Donovan C., and others

Database: the journal of biological databases and curation. Volume 2012, (2012), doi:

AntiFam: a tool to help identify spurious ORFs in protein annotation

Eberhardt, R. Y., Haft D. H., Punta M., MARTIN M., O'Donovan C., and Bateman A.

Database: The Journal of Biological Databases and Curation. Volume 2012, (2012), doi:

The YARHG Domain: An Extracellular Domain in Search of a Function

Coggill, P., and Bateman A.

PloS one. Volume 7, Number 5, (2012), p.e35575

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks

Buljan, M., Chalancon G., Eustermann S., Wagner G. P., Fuxreiter M., Bateman A., and Babu M. M.

Molecular cell. Volume 46, Number 6, (2012), p.871–883

2011

Asparagine Peptide Lyases

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions

Journal of Biological Chemistry. Volume 286, Number 44, (2011), p.38321–38328

Woodwark, C., and Bateman A.

PloS one. Volume 6, Number 5, (2011), p.e14814

Rfam: Wikipedia, clans and the “decimal” release

Gardner, P. P., Daub J., Tate J., Moore B. L., Osuch I. H., Griffiths-Jones S., Finn R. D., Nawrocki E. P., Kolbe D. L., Eddy S. R., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D141

RNIE: genome-wide prediction of bacterial intrinsic terminators

Gardner, P. P., Barquist L., Bateman A., Nawrocki E. P., and Weinberg Z.

Nucleic acids research. Volume 39, Number 14, (2011), p.5845–5852

Every Spider Web has a Simple Flat Twist Tessellation

Lang, R. J., and Bateman A.

Origami 5: Fifth International Meeting of Origami Science, Mathematics, and Education. (2011), p.455

The rise and fall of supervised machine learning techniques

Jensen, L. J., and Bateman A.

Bioinformatics. Volume 27, Number 24, (2011), p.3331–3332

Towards BioDBcore: a community-defined information specification for biological databases| Macquarie University ResearchOnline

Gaudet, P., Bairoch A., Chisholm R. L., Cochrane G., Cook C. E., Eppig J. T., Galperin M. Y., Gentleman R., Goble C. A., Gojobori T., et al.

(2011),

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

Gaudet, P., Bairoch A., Field D., Sansone S. A., TAYLOR C., Attwood T. K., Bateman A., Blake J. A., Bult C. J., Cherry J. M., et al.

Nucleic acids research. Volume 39, Number suppl 1, (2011), p.D7

RNAcentral: A vision for an international database of RNA sequences

Bateman, A., Agrawal S., Birney E., Bruford E. A., Bujnicki J. M., Cochrane G., Cole J. R., Dinger M. E., Enright A. J., Gardner P. P., et al.

RNA. Volume 17, Number 11, (2011), p.1941–1946 doi:

2010

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Xu, Q., Bateman A., Finn R. D., Abdubek P., Astakhova T., Axelrod H. L., Bakolitsa C., Carlton D., Chen C., Chiu H. J., et al.

Journal of molecular biology. Volume 396, Number 1, (2010), p.31–46

Genome Biology

Buljan, M., Frankish A., and Bateman A.

Genome Biology. Volume 11, (2010), p.R74

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

Finn, R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G., Forslund K., et al.

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D211–D222

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

Cell host & microbe. Volume 8, Number 4, (2010), p.377–387

Curators of the world unite: the International Society of Biocuration

SnoPatrol: how many snoRNA genes are there

Bioinformatics. Volume 26, Number 8, (2010), p.991

Gardner, P. P., Bateman A., Poole A. M., and others

J Biol. Volume 9, Number 4, (2010),

Rfam and Wikipedia: Harnessing people power| SciVee

DUFs: families in search of function

scivee. (2010),

Bateman, A., Coggill P., and Finn R. D.

Acta Crystallographica Section F: Structural Biology and Crystallization Communications. Volume 66, Number 10, (2010), p.1148–1152

Dosage sensitivity shapes the evolution of copy-number varied regions

Schuster-Böckler, B., Conrad D., and Bateman A.

PloS one. Volume 5, Number 3, (2010), p.e9474

Ten simple rules for editing Wikipedia

Logan, D. W., Sandal M., Gardner P. P., Manske M., and Bateman A.

PLoS computational biology. Volume 6, Number 9, (2010), p.e1000941

Time to underpin Wikipedia wisdom

Bateman, A., and Logan D. W.

Nature. Volume 468, Number 7325, (2010), p.765–765

Quantifying the mechanisms of domain gain in animal proteins

Buljan, M., Frankish A., Bateman A., and others

Genome Biol. Volume 11, (2010), p.R74

Tissue-specific rewiring of signalling pathways through alternatively spliced disordered segments

Nucleic acids research. Volume 38, Number suppl 1, (2010), p.D227–D233

Buljan, M., Bateman A., and Babu M. M.

New Biotechnology. Volume 27, (2010), p.S31

2009

Bioinformatics for next generation sequencing

Bateman, A., and QUACKENBUSH J.

Bioinformatics. (2009),

Cloud computing

Bateman, A., and Wood M.

Bioinformatics. Volume 25, Number 12, (2009), p.1475–1475

Pepsin homologues in bacteria

Rawlings, N., and Bateman A.

BMC genomics. Volume 10, Number 1, (2009), p.437

The structure of Jann\_2411 (DUF1470) from Jannaschia sp. at 1.45 A resolution reveals a new fold (the ABATE domain) and suggests its possible role as a transcription regulator

Nucleic Acids Res. Volume 38, (2009), p.D227–233

Bakolitsa, C., Bateman A., Jin K. K., McMullan D., Krishna S. S., Miller M. D., Abdubek P., Acosta C., Astakhova T., Axelrod H. L., et al.

Acta Crystallographica Section F: Structural Biology and Crystallization Communications. Volume 66, Number 10, (2009), p.1198–1204

A home for RNA families at RNA Biology

Gardner, P. P., and Bateman A. G.

RNA Biology. Volume 6, Number 1, (2009), p.2–4

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

Bateman, A., Finn R. D., Sims P. J., Wiedmer T., Biegert A., and Söding J.

Bioinformatics. Volume 25, Number 2, (2009), p.159–162

Rfam: updates to the RNA families database

Gardner, P. P., Daub J., Tate J. G., Nawrocki E. P., Kolbe D. L., Lindgreen S., Wilkinson A. C., Finn R. D., Griffiths-Jones S., Eddy S. R., et al.

Nucleic acids research. Volume 37, Number suppl 1, (2009), p.D136–D140

Broadening Pfam Protein Sequence Annotations

Mistry, J., Cogghill P., Eddy S., Finn R., Tate J., and Bateman A.

(2009),

The structure of pyogenecin immunity protein, a novel bacteriocin-like immunity protein from Streptococcus pyogenes

Chang, C., Coggill P., Bateman A., Finn R., Cymborowski M., Otwinowski Z., Minor W., Volkart L., and Joachimiak A.

BMC structural biology. Volume 9, Number 1, (2009), p.75

DATABASE Editorial Board 2009

Landsman, D., Gentleman R., Kelso J., Ouellette F., Altman R., Attwood T., Bader G., Bairoch A., Bateman A., Baxevanis A. D., et al.

DATABASE. (2009),

The evolution of protein domain families

Buljan, M., Bateman A., and others

Biochem Soc Trans. Volume 37, Number Pt 4, (2009), p.751–755

Ten Simple Rules for Chairing a Scientific Session

Bateman, A., and Bourne P. E.

PLoS Computational Biology. Volume 5, Number 9, (2009), p.e1000517

2008

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

Bushell, K. M., Söllner C., Schuster-Boeckler B., Bateman A., and Wright G. J.

Genome research. Volume 18, Number 4, (2008), p.622–630

A Unified View of Protein Sequence and Structure Using the Distributed Anno-tation System

Prlic, A., Down T., Bateman A., Hubbard T., Orengo C., Dibley M., and Finn R. D.

(2008),

Pfam 10 years on: 10 000 families and still growing

SAMMUT, S. J., Finn R. D., and Bateman A.

Briefings in bioinformatics. Volume 9, Number 3, (2008), p.210–219

The RNA WikiProject: community annotation of RNA families

Daub, J., Gardner P. P., Tate J., Ramsköld D., Manske M., Scott W. G., Weinberg Z., Griffiths-Jones S., and Bateman A.

Rna. Volume 14, Number 12, (2008), p.2462–2464

Databases, data tombs and dust in the wind

Wren, J. D., and Bateman A.

Bioinformatics. Volume 24, Number 19, (2008), p.2127–2128

Protein interactions in human genetic diseases

Identifying protein domains with the Pfam database

Genome biology. Volume 9, Number 1, (2008), p.R9

Coggill, P., Finn R. D., and Bateman A.

Curr Protoc Bioinformatics. Volume 2, Number 2.5, (2008),

Rawlings, N. D., Morton F. R., Kok C. Y., Kong J., and Barrett A. J.

Nucleic Acids Research. Volume 36, Number suppl 1, (2008), p.D320–D325

In the editorial for 2007 Database issue, the name of the editor was spelt incorrectly. The correct name should read

Finn, R. D., Tate J., Mistry J., Coggill P. C., SAMMUT S. J., Hotz H. R., Ceric G., Forslund K., Eddy S. R., Sonnhammer E. L. L., et al.

Nucleic acids research. Volume 36, Number suppl 1, (2008), p.D281–D288

2007

The tify family previously known as ZIM

Nucleic Acids Research. Volume 35, Number 2, (2007),

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

Trends in plant science. Volume 12, Number 6, (2007), p.239–244

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

Bateman, A., and Finn R. D.

Bioinformatics. Volume 23, Number 7, (2007), p.809–814

Predicting active site residue annotations in the Pfam database

Mistry, J., Bateman A., and Finn R.

BMC bioinformatics. Volume 8, Number 1, (2007), p.298

An introduction to hidden Markov models

Reuse of structural domain–domain interactions in protein networks

Current protocols in bioinformatics. (2007),

Structural genomics meets computational biology

BMC bioinformatics. Volume 8, Number 1, (2007), p.259

2006

Bateman, A., and Valencia A.

Bioinformatics. Volume 22, Number 19, (2006), p.2319–2319

Bioinformatics—The new home for protein sequence motifs

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

Bioinformatics. Volume 22, Number 1, (2006), p.2–2

Seitan, V. C., Banks P., Laval S., Majid N. A., Dorsett D., Rana A., Smith J., Bateman A., Krpic S., Hostert A., et al.

PLoS biology. Volume 4, Number 8, (2006), p.e242

miRBase: microRNA sequences, targets and gene nomenclature

Rawlings, N. D., Morton F. R., and Barrett A. J.

Nucleic Acids Research. Volume 34, Number suppl 1, (2006), p.D270–D272

Griffiths-Jones, S., Grocock R. J., Van Dongen S., Bateman A., and Enright A. J.

Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D140–D144 doi:

Pfam: clans, web tools and services

Finn, R. D., Mistry J., Schuster-Böckler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., et al.

Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D247–D251

Software patents in Bioinformatics

Valencia, A., and Bateman A.

Bioinformatics. Volume 22, Number 12, (2006), p.1415–1415

2005

Rfam: annotating non-coding RNAs in complete genomes

Griffiths-Jones, S., Moxon S., Marshall M., Khanna A., Eddy S. R., and Bateman A.

Nucleic acids research. Volume 33, Number suppl 1, (2005), p.D121

Visualizing profile–profile alignment: pairwise HMM logos

InterPro, progress and status in 2005

Bioinformatics. Volume 21, Number 12, (2005), p.2912–2913

Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., et al.

Nucleic Acids Research. Volume 33, Number suppl 1, (2005), p.D201–D205

Gene Families

Bateman, A., and Mifsud W.

(2005),

Increasing the impact of Bioinformatics

Valencia, A., and Bateman A.

Bioinformatics. Volume 21, Number 1, (2005), p.1

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

Bateman, A., Holden M. T. G., and Yeats C.

Bioinformatics. Volume 21, Number 8, (2005), p.1301–1303

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

Finn, R. D., Marshall M., and Bateman A.

Bioinformatics. Volume 21, Number 3, (2005), p.410–412

An update from the Bioinformatics Editors

Bateman, A., and Valencia A.

Bioinformatics. Volume 21, Number 24, (2005), p.4319

Rfam: annotating non-coding rnas in complete genomes

Khanna, A., Eddy S. R., Griffiths-Jones S., Moxon S., Marshall M., and Bateman A.

Nucleic Acids Research. Volume 33, (2005),

2004

New Leadership for Bioinformatics

Bateman, A., and Valencia A.

Bioinformatics. Volume 20, Number 12, (2004), p.1821–1821

Enhanced protein domain discovery using taxonomy

Coin, L., Bateman A., and Durbin R.

BMC bioinformatics. Volume 5, Number 1, (2004), p.56

Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica

Studholme, D. J., Fuerst J. A., and Bateman A.

FEMS microbiology letters. Volume 236, Number 2, (2004), p.333–340

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

Dillon, S., and Bateman A.

BMC bioinformatics. Volume 5, Number 1, (2004), p.109

eFamily: Bridging Sequence and Structure

Bateman, A., Coin L., Durbin R., Finn R. D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E. L. L., et al.

Nucleic acids research. Volume 32, Number suppl 1, (2004), p.D138–D141

Finn, R. D., Prlic A., Das U., McNeil P., Mulder N., VELANKAR S., Andreeva A., Howorth D., Dibley M., Hubbard T., et al.

Proceedings of UK e-Science All Hands Meeting 2004 (AHM04): 31st August–3rd September 2004; Nottingham, UK. (2004), p.1069–1072

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

Yeats, C., Rawlings N. D., and Bateman A.

Trends in biochemical sciences. Volume 29, Number 4, (2004), p.169–172

2003

New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor

Yeats, C., Bentley S., and Bateman A.

BMC microbiology. Volume 3, Number 1, (2003), p.3

A comparison of Pfam and MEROPS: Two databases, one comprehensive, and one specialised.

Studholme, D., Rawlings N., Barrett A., and Bateman A.

BMC bioinformatics. Volume 4, Number 1, (2003), p.17

The InterPro Database, 2003 brings increased coverage and new features

Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Barrell D., Bateman A., Binns D., Biswas M., Bradley P., Bork P., et al.

Nucleic acids research. Volume 31, Number 1, (2003), p.315–318

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

Bateman, A., and Rawlings N. D.

Trends in biochemical sciences. Volume 28, Number 5, (2003), p.234–237

Rfam: an RNA family database

Griffiths-Jones, S., Bateman A., Marshall M., Khanna A., and Eddy S. R.

Nucleic acids research. Volume 31, Number 1, (2003), p.439–441

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

Coin, L., Bateman A., and Durbin R.

Proceedings of the National Academy of Sciences. Volume 100, Number 8, (2003), p.4516

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

Bateman, A., and Kickhoefer V.

BMC bioinformatics. Volume 4, Number 1, (2003), p.49

The BON domain: a putative membrane-binding domain

Yeats, C., and Bateman A.

Trends in biochemical sciences. Volume 28, Number 7, (2003), p.352–355

Identifying protein domains with the Pfam database

Finn, R., Griffiths-Jones S., and Bateman A.

Current Protocols in Bioinformatics. (2003),

2002

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

Bateman, A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. R., Griffiths-Jones S., Howe K. L., Marshall M., and Sonnhammer E. L. L.

Nucleic acids research. Volume 30, Number 1, (2002), p.276–280

Mulder, N. J., Apweiler R., Attwood T. K., Bairoch A., Bateman A., Binns D., Biswas M., Bradley P., Bork P., Bucher P., et al.

Briefings in Bioinformatics. Volume 3, Number 3, (2002), p.225–235

The ENTH domain

De Camilli, P., Chen H., Hyman J., Panepucci E., Bateman A., and Brunger A. T.

FEBS letters. Volume 513, Number 1, (2002), p.11–18

The PASTA domain: a [beta]-lactam-binding domain

Yeats, C., Finn R. D., and Bateman A.

Trends in biochemical sciences. Volume 27, Number 9, (2002), p.438–440

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

Mifsud, W., Bateman A., and others

Genome Biol. Volume 3, Number 1, (2002), p.5

The SGS3 protein involved in PTGS finds a family

HMM-based databases in InterPro

BMC bioinformatics. Volume 3, Number 1, (2002), p.21

Bateman, A., and Haft D. H.

Briefings in bioinformatics. Volume 3, Number 3, (2002), p.236–245

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

Griffiths-Jones, S., and Bateman A.

Bioinformatics. Volume 18, Number 9, (2002), p.1243–1249

QuickTree: building huge Neighbour-Joining trees of protein sequences

Bateman, A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. R., Griffiths-Jones S., Howe K. L., Marshall M., and Sonnhammer E. L. L.

Nucleic acids research. Volume 30, Number 1, (2002), p.276

Howe, K., Bateman A., and Durbin R.

Bioinformatics. Volume 18, Number 11, (2002), p.1546

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

Bentley, S. D., Chater KF, CERDENO-TARRAGA A. M., Challis GL, Thomson N. R., James K. D., Harris DE, Quail M. A., Kieser H., Harper D., et al.

Nature. Volume 417, Number 6885, (2002), p.141–147

2001

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

Murzin, A. G., and Bateman A.

Proteins: Structure, Function, and Bioinformatics. Volume 45, Number S5, (2001), p.76–85

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Apweiler, R., Attwood T. K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. R., et al.

Nucleic Acids Research. Volume 29, Number 1, (2001), p.37–40

Mining the draft human genome

Birney, E., Bateman A., Clamp M. E., and Hubbard T. J.

Nature. Volume 409, Number 6822, (2001), p.827–828

Initial sequencing and analysis of the human genome

Lander, E. S., Linton L. M., Birren B., Nusbaum C., Zody M. C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al.

Nature. Volume 409, Number 6822, (2001), p.860–921

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

de Bakker, P. I. W., Bateman A., Burke D. F., Miguel R. N., Mizuguchi K., Shi J., Shirai H., and Blundell T. L.

Bioinformatics. Volume 17, Number 8, (2001), p.748

2000

The PA domain: A protease-associated domain

Bateman, A., Birney E., Durbin R., Eddy S. R., Howe K. L., and Sonnhammer E. L. L.

Nucleic Acids Research. Volume 28, Number 1, (2000), p.263–266

Mahon, P., and Bateman A.

Protein Science. Volume 9, Number 10, (2000), p.1930–1934

Bateman, A., Birney E., Durbin R., Eddy S. R., Howe K. L., and Sonnhammer E. L. L.

Nucleic acids research. Volume 28, Number 1, (2000), p.263–266

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

Eddy, S. R., Sonnhammer E. L. L., Bateman A., Birney E., Durbin R., and Howe K. L.

Nucleic Acids Research. Volume 28, Number 1, (2000), p.263–266

Cerutti, L., Mian N., Bateman A., and others

Trends in biochemical sciences. Volume 25, Number 10, (2000), p.481

Searching databases to find protein domain organization

Bateman, A., and Birney E.

Advances in protein chemistry. Volume 54, (2000), p.137–157

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

Apweiler, R., Attwood T. K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. R., et al.

Bioinformatics. Volume 16, Number 12, (2000), p.1145

The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD) 1

Bateman, A., and Bycroft M.

Journal of molecular biology. Volume 299, Number 4, (2000), p.1113–1119

Searching Databases to Find Protein Domain Organization-II.-Protein Domains

Bateman, A., and Birney E.

Advances in Protein Chemistry. Volume 54, (2000), p.138–142

1999

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

Bycroft, M., Bateman A., Clarke J., Hamill S. J., Sandford R., Thomas R. L., and Chothia C.

The EMBO journal. Volume 18, Number 2, (1999), p.297–305

The Caenorhabditis elegans genes egl-27 and egr-1 are similar to MTA1, a member of a chromatin regulatory complex, and are redundantly required for embryonic patterning

Solari, F., Bateman A., and Ahringer J.

Development. Volume 126, Number 11, (1999), p.2483–2494

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

Bateman, A., Birney E., Durbin R., Eddy S. R., Finn R. D., and Sonnhammer E. L. L.

Nucleic Acids Research. Volume 27, Number 1, (1999), p.260

The SIS domain: a phosphosugar-binding domain.

Bateman, A., and others

Trends in biochemical sciences. Volume 24, Number 3, (1999), p.94

The PLAT domain: a new piece in the PKD1 puzzle.

Bateman, A., Sandford R., and others

Current biology: CB. Volume 9, Number 16, (1999), p.R588

1998

The DUTT1Gene, 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., et al.

Molecular and Cellular Neuroscience. Volume 11, Number 1-2, (1998), p.29–35

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

Sonnhammer, E. L. L., Eddy S. R., Birney E., Bateman A., and Durbin R.

Nucleic acids research. Volume 26, Number 1, (1998), p.320

Structure and distribution of pentapeptide repeats in bacteria

Bateman, A., Murzin A. G., and Teichmann S. A.

Protein science. Volume 7, Number 6, (1998), p.1477–1480

1997

Distant homology recognition using structural classification of proteins

Murzin, A. G., and Bateman A.

Proteins: Structure, Function, and Bioinformatics. Volume 29, Number S1, (1997), p.105–112

A member of the immunoglobulin superfamily in bacteriophage T4

Bateman, A., Eddy S. R., and Mesyanzhinov V. V.

Virus genes. Volume 14, Number 2, (1997), p.163–165

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