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Items: 1 to 20 of 113

1.

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.

2.

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
3.

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.

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.

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.

6.

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
7.

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.

8.

The TIGRFAMs database of protein families.

Haft DH, Selengut JD, White O.

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

9.

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.

10.

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.

11.

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database.

Gowri VS, Pandit SB, Karthik PS, Srinivasan N, Balaji S.

Nucleic Acids Res. 2003 Jan 1;31(1):486-8.

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.

Subfamily hmms in functional genomics.

Brown D, Krishnamurthy N, Dale JM, Christopher W, Sjölander K.

Pac Symp Biocomput. 2005:322-33.

14.

Accurate domain identification with structure-anchored hidden Markov models, saHMMs.

Tångrot JE, Kågström B, Sauer UH.

Proteins. 2009 Aug 1;76(2):343-52. doi: 10.1002/prot.22349.

PMID:
19173309
15.
17.

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.

18.

PASS2: an automated database of protein alignments organised as structural superfamilies.

Bhaduri A, Pugalenthi G, Sowdhamini R.

BMC Bioinformatics. 2004 Apr 2;5:35.

19.

Automated protein subfamily identification and classification.

Brown DP, Krishnamurthy N, Sjölander K.

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

20.

ProDom: automated clustering of homologous domains.

Servant F, Bru C, Carrère S, Courcelle E, Gouzy J, Peyruc D, Kahn D.

Brief Bioinform. 2002 Sep;3(3):246-51.

PMID:
12230033

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