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Items: 1 to 20 of 89

1.

The PANTHER database of protein families, subfamilies, functions and pathways.

Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D284-8.

2.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.

Mi H, Guo N, Kejariwal A, Thomas PD.

Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. Epub 2006 Nov 27.

3.

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O.

Nucleic Acids Res. 2003 Jan 1;31(1):334-41. Erratum in: Nucleic Acids Res. 2003 Apr 1;31(7):2024.

4.

PANTHER: a library of protein families and subfamilies indexed by function.

Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A.

Genome Res. 2003 Sep;13(9):2129-41.

5.

Large-scale gene function analysis with the PANTHER classification system.

Mi H, Muruganujan A, Casagrande JT, Thomas PD.

Nat Protoc. 2013 Aug;8(8):1551-66. doi: 10.1038/nprot.2013.092. Epub 2013 Jul 18.

PMID:
23868073
6.

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, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

7.

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

Thomas PD, Kejariwal A, Guo N, Mi H, Campbell MJ, Muruganujan A, Lazareva-Ulitsky B.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W645-50.

8.

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.

Mi H, Muruganujan A, Thomas PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D377-86. doi: 10.1093/nar/gks1118. Epub 2012 Nov 27.

9.

Automated protein subfamily identification and classification.

Brown DP, Krishnamurthy N, Sjölander K.

PLoS Comput Biol. 2007 Aug;3(8):e160.

10.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
11.

PANTHER version 10: expanded protein families and functions, and analysis tools.

Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD.

Nucleic Acids Res. 2016 Jan 4;44(D1):D336-42. doi: 10.1093/nar/gkv1194. Epub 2015 Nov 17.

12.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16.

13.

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, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

14.

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, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D201-5.

15.

InterPro protein classification.

McDowall J, Hunter S.

Methods Mol Biol. 2011;694:37-47. doi: 10.1007/978-1-60761-977-2_3.

PMID:
21082426
16.

FunShift: a database of function shift analysis on protein subfamilies.

Abhiman S, Sonnhammer EL.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D197-200.

17.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.

Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, Thomas PD.

Nucleic Acids Res. 2017 Jan 4;45(D1):D183-D189. doi: 10.1093/nar/gkw1138. Epub 2016 Nov 29.

18.

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. 2008 Jan;36(Database issue):D281-8. Epub 2007 Nov 26.

19.

The TIGRFAMs database of protein families.

Haft DH, Selengut JD, White O.

Nucleic Acids Res. 2003 Jan 1;31(1):371-3.

20.

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 Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948. Epub 2011 Nov 16.

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