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InterPro References

Hunter, S., Jones, P., et al. (2012)
InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res. 40 (Database issue), D306-12.

Hunter, C., et al. (2011) The EBI metagenomics archive, integration and analysis resource. In: Frans J. de Bruijn, Ed, Handbook of Molecular Microbial Ecology I: Metagenomics and complementary approaches. Wiley-Blackwell.
Jones, P., Binns, D., et al. (2011)
The InterPro BioMart: federated query and web service access to the InterPro Resource.
Database (Oxford) 2011, bar033.

McDowall, J. and Hunter, S. (2011)
InterPro Protein Classification.
Methods Mol. Biol. 694, 37-47.

Jones, P. and Martens, L. (2010)
Using the PRIDE proteomics identifications database for knowledge discovery and data analysis.
Methods Mol. Biol. 604, 297-307.

Schneider, M.V., et al. (2010)
Bioinformatics training: a review of challenges, actions and support requirements.
Brief. Bioinform. 11, 544-551.

Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Das U., Daugherty L., Duquenne L., Finn R.D., Gough J., Haft D., Hulo N., Kahn D., Kelly E., Laugraud A., Letunic I., Lonsdale D., Lopez R., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J., Mitchell A., Mulder N., Natale D., Orengo C., Quinn A.F., Selengut J.D., Sigrist C.J., Thimma M., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C. (2009)
InterPro: the integrative protein signature database.
Nucleic Acids Research 37: D211-D215.
abstract full-text PDF


Mulder N.J., Apweiler R., Attwood T.K., 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., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., MaslenJ., McAnulla C., McDowall J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Sigrist C.J.A., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C. (2007)
New developments in the InterPro database.
Nucleic Acids Research 35: D224-D228.
abstract full-text PDF

Mulder N.J., Apweiler R. (2006)
Function Prediction with Protein Signatures and InterPro
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 25-36, Nova Science Publishers, Inc, New York (2006).
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Mulder N.J., Apweiler R. (2006)
Genomics and the Genome Era.
In: In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins. Mulder N., and Apweiler R. (eds); pp 3-9, Nova Science Publishers, Inc, New York (2006).
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Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. (2005)
InterProScan: protein domains identifier.
Nucleic Acids Research 33: W116-W120.
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Mulder N.J. (2005)
InterPro.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 2435-2439, John Wiley & Sons, Inc (2005).
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Mulder N.J. (2005)
Getting the most out of protein family classification resources.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics,
Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 2492-2499,
John Wiley & Sons, Inc (2005).
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Mulder N.J., Apweiler R. (2005)
Classification of proteins into families.
In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Jorde L.B., Little P.F.R., Dunn M.J., Subramanian S. (eds.), pp 2351-2358, John Wiley & Sons, Inc (2005).
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Mulder N.J., Apweiler R., Attwood T.K., 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., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya A.N., Orchard S., Pagni M., Ponting C.P., Quevillon E., Selengut J., Sigrist C.J., Silventoinen V., Studholme D.J., Vaughan R., Wu C.H. (2005)
InterPro, progress and status in 2005.
Nucleic Acids Research 33: D201-D205.
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Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bordoli L., Bucher P., Courcelle E., Das U., Durbin R., Flegel V., Fleischmann W., Griffiths-Jones S., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Maslen J., McDowall J., Mulder N., Nikolskaya A.N., Orchard S., Quevillon E., Servant F., Sigrist C.J.A., Silventoinen V., Studholme D.J., Wu C.H. (2004)
InterPro -prediction of protein families, domains and functional sites.
In: Focus on Genome Research. Williams C.R. (ed), Nova Science Publishers Inc., New York, pg 169-204 (2004).
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Mulder N. J., Apweiler R., Attwood T. K., Bairoch A., Barrell D., Bateman A., Binns D., Biswas M., Bradley P., Bork P., Bucher P., Copley R. R., Courcelle E., Das U., Durbin R., Falquet L., Fleischmann W., Griffiths-Jones S., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lopez R., Letunic I., Lonsdale D., Silventoinen V., Orchard S. E., Pagni M., Peyruc D., Ponting C. P., Selengut J. D, Servant F., Sigrist C. J. A., Vaughan R. , and Zdobnov E. M. (2003)
The InterPro Database, 2003 brings increased coverage and new features.
Nucleic Acids Research 31: 315-318.
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Apweiler R. (2002)
Editorial: Focus on InterPro.
Briefings in Bioinformatics 3(3): 221-223.
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Biswas M., O'Rourke J.F., Camon E., Fraser G., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E., Mittard V., Mulder N., Phan I., Servant F., Apweiler R. (2002)
Applications of InterPro in protein annotation and genome analysis.
Briefings in Bioinformatics 3(3): 285-295.
abstract full-text PDF

Mulder N.J., Apweiler R., Attwood T.K., 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., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lopez R., Letunic I., Orchard S., Pagni M., Peyruc D., Ponting C.P., Servant F., Sigrist C.J.A. (2002)
InterPro: An integrated documentation resource for protein families, domains and functional sites.
Briefings in Bioinformatics 3(3): 225-235.
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Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J., Zdobnov E.M. (2001)
The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Nucleic Acids Research 29(1): 37-40.
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Apweiler R., Biswas M., Fleischmann W., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E.V., Mittard V., Mulder N., Phan I., Zdobnov E. (2001)
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
Nucleic Acids Research 29(1): 44-48.
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Biswas M., Kanapin A., Apweiler R. (2001)
Application of InterPro for the functional classification of the proteins of fish origin in Swiss-Prot and TrEMBL.
Journal of Bioscience 26(2): 277-284.
abstract

Mulder N.J., Apweiler R. (2001)
Tools and resources for identifying protein families, domains and motifs.
Genome Biology 3(1): reviews2001.1-2001.8.
abstract full-text PDF

Zdobnov E.M., Apweiler R. (2001)
InterProScan - an integration platform for the signature-recognition methods in InterPro
Bioinformatics 17: 847-848.
abstract full-text PDF

Zdobnov E.M., Hermjakob H., Apweiler R. (2001)
InterProScan - an integration tool for the signature-recognition methods in InterPro.
In: RECOMB 2001 : Annual Conference on Research in Computational Molecular Biology, El-Mabrouk N., Lengauer T., and Sankoff D. (eds), Montreal: CRM. pp. 41-42 (2001).

Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M.D.R., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N.J., Oinn T.M., Pagni M., Servant F., Sigrist C.J.A., Zdobnov E.M. (2000)
InterPro - an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics 16(12): 1145-1150.
full-text PDF

Apweiler R., Attwood T.K., Bairoch A., Bateman A., Birney E., Bucher P., Codani J.-J., Corpet F., Croning M.D.R., Durbin R., Etzold T., Fleischmann W., Gouzy J., Hermjakob H., Jonassen I., Kahn D., Kanapin A., Schneider R., Servant F., Zdobnov E. (2000)
InterPro - An integrated documentation resource for protein families, domains and functional sites.
CCP11 Newsletter Issue 10.
full-text PDF

Apweiler R., Biswas M., Fleischmann W., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E., Mittard V., Mulder N., Oinn T., Phan I., Zdobnov E. (2000)
Proteome analysis: application of InterPro and CluSTr for the functional classification of proteins in whole genomes.
In: Proceedings of the German Conference on Bioinformatics (GCB'00), Bornberg-Bauer E., Rost U., Stoye J., Vingron M. (eds.), pp. 149-157, LogosVerlag, Berlin, Germany (2000).
abstract

Apweiler R., Attwood T. K., Bairoch A., Bateman A., Birney E., Biswas M., Bucher P., Cerutti L., Corpet F., Croning M. D. R., Durbin R., Falquet L., Fleischmann W., Gouzy J., Hermjakob H., Hulo N., Jonassen I., Kahn D., Kanapin A., Karavidopoulou Y., Lopez R., Marx B., Mulder N. J., Oinn T.M., Pagni M., Servant F., Sigrist C. J. A., Zdobnov E. M. (2000)
InterPro - an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics 16(12): 1145-1150.
abstract full-text PDF

Mulder N.J., Fleischmann W., Apweiler R. (2000)
InterPro as a new tool for whole genome analysis. A comparitive analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study.
Regulation and Structure. Vol 2. pp. 35-37.
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Rubin G.M., Yandell M.D., Wortman J.R., Miklos G.L.G., Nelson C.R., Hariharan I.K., Fortini M.E., Li P.W, Apweiler R., Fleischmann W., Cherry J.M., Henikoff S., Skupski M.P., Misra S., Ashburner M., Birney E., Boguski M.S., Brody T., Brokstein P., Celniker S.E., Chervitz S.A,. Coates D., Cravchik A., Gabrielian A., Galle R.F., Gelbart W.M., George R.A., Goldstein L.S.B., Gong F., Guan P., Harris N.L., Hay B.A., Hoskins R.A., Li J., Li Z., Hynes R.O., Jones S.J.M., Kuehl P.M., Lemaitre B., Littleton J.T., Morrison D.K., Mungall C., O'Farrell P.H., Pickeral O.K., Shue C., Vosshall L.B., Zhang J., Zhao Q., Zheng X.H., Zhong F., Zhong W., Gibbs R., Venter J.G., Adams M.D., Lewis S. (2000)
Comparative Genomics of the Eukaryotes.
Science 287: 2204-2215.
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