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Items: 1 to 20 of 100

1.

MIPS bacterial genomes functional annotation benchmark dataset.

Tetko IV, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Fobo G, Ruepp A, Antonov AV, Surmeli D, Mewes HW.

Bioinformatics. 2005 May 15;21(10):2520-1. Epub 2005 Mar 15.

PMID:
15769832
2.

Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information.

Tetko IV, Rodchenkov IV, Walter MC, Rattei T, Mewes HW.

Bioinformatics. 2008 Mar 1;24(5):621-8. doi: 10.1093/bioinformatics/btm633. Epub 2008 Jan 3.

PMID:
18174184
3.

MIPS: analysis and annotation of genome information in 2007.

Mewes HW, Dietmann S, Frishman D, Gregory R, Mannhaupt G, Mayer KF, Münsterkötter M, Ruepp A, Spannagl M, Stümpflen V, Rattei T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D196-201. Epub 2007 Dec 23.

4.

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.

Klee K, Ernst R, Spannagl M, Mayer KF.

BMC Bioinformatics. 2007 Aug 30;8:320.

5.

The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context.

Ruepp A, Doudieu ON, van den Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Skornia C, Wanka S, Rattei T, Pagel P, Riley L, Frishman D, Surmeli D, Tetko IV, Oesterheld M, Stümpflen V, Mewes HW.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D568-71.

6.

FunCat functional inference with belief propagation and feature integration.

Surmeli D, Ratmann O, Mewes HW, Tetko IV.

Comput Biol Chem. 2008 Oct;32(5):375-7. doi: 10.1016/j.compbiolchem.2008.06.004. Epub 2008 Jul 3.

PMID:
18684672
7.

Benchmarking PSI-BLAST in genome annotation.

Müller A, MacCallum RM, Sternberg MJ.

J Mol Biol. 1999 Nov 12;293(5):1257-71.

PMID:
10547299
8.

BacTregulators: a database of transcriptional regulators in bacteria and archaea.

Martínez-Bueno M, Molina-Henares AJ, Pareja E, Ramos JL, Tobes R.

Bioinformatics. 2004 Nov 1;20(16):2787-91. Epub 2004 May 27.

PMID:
15166024
9.

KAAS: an automatic genome annotation and pathway reconstruction server.

Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5. Epub 2007 May 25.

10.

Evaluation of annotation strategies using an entire genome sequence.

Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA.

Bioinformatics. 2003 Apr 12;19(6):717-26.

PMID:
12691983
11.

annot8r: GO, EC and KEGG annotation of EST datasets.

Schmid R, Blaxter ML.

BMC Bioinformatics. 2008 Apr 9;9:180. doi: 10.1186/1471-2105-9-180.

12.

Exploring microbial genome sequences to identify protein families on the grid.

Sun Y, Wipat A, Pocock M, Lee PA, Flanagan K, Worthington JT.

IEEE Trans Inf Technol Biomed. 2007 Jul;11(4):435-42.

PMID:
17674626
13.

SIMAP--the similarity matrix of proteins.

Arnold R, Rattei T, Tischler P, Truong MD, Stümpflen V, Mewes W.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii42-6.

PMID:
16204123
14.

MIPS: a database for genomes and protein sequences.

Mewes HW, Heumann K, Kaps A, Mayer K, Pfeiffer F, Stocker S, Frishman D.

Nucleic Acids Res. 1999 Jan 1;27(1):44-8.

15.

Automated annotation of microbial proteomes in SWISS-PROT.

Gattiker A, Michoud K, Rivoire C, Auchincloss AH, Coudert E, Lima T, Kersey P, Pagni M, Sigrist CJ, Lachaize C, Veuthey AL, Gasteiger E, Bairoch A.

Comput Biol Chem. 2003 Feb;27(1):49-58.

PMID:
12798039
16.

Mining sequence annotation databanks for association patterns.

Artamonova II, Frishman G, Gelfand MS, Frishman D.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii49-57.

PMID:
16306393
17.

MIPS: a database for protein sequences, homology data and yeast genome information.

Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F.

Nucleic Acids Res. 1997 Jan 1;25(1):28-30.

18.

ProtRepeatsDB: a database of amino acid repeats in genomes.

Kalita MK, Ramasamy G, Duraisamy S, Chauhan VS, Gupta D.

BMC Bioinformatics. 2006 Jul 7;7:336.

19.

Automated annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques.

Bazzan AL, Engel PM, Schroeder LF, da Silva SC.

Bioinformatics. 2002;18 Suppl 2:S35-43.

PMID:
12385981
20.

MPact: the MIPS protein interaction resource on yeast.

Güldener U, Münsterkötter M, Oesterheld M, Pagel P, Ruepp A, Mewes HW, Stümpflen V.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D436-41.

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