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PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.
Tang H, Thomas PD. Tang H, et al. Among authors: thomas pd. Bioinformatics. 2016 Jul 15;32(14):2230-2. doi: 10.1093/bioinformatics/btw222. Epub 2016 May 18. Bioinformatics. 2016. PMID: 27193693
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. Thomas PD, et al. Nucleic Acids Res. 2003 Jan 1;31(1):334-41. doi: 10.1093/nar/gkg115. Nucleic Acids Res. 2003. PMID: 12520017 Free PMC article.
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. Thomas PD, et al. Genome Res. 2003 Sep;13(9):2129-41. doi: 10.1101/gr.772403. Genome Res. 2003. PMID: 12952881 Free PMC article.
Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects.
Thomas PD, Kejariwal A. Thomas PD, et al. Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15398-403. doi: 10.1073/pnas.0404380101. Epub 2004 Oct 18. Proc Natl Acad Sci U S A. 2004. PMID: 15492219 Free PMC article.
On the quality of tree-based protein classification.
Lazareva-Ulitsky B, Diemer K, Thomas PD. Lazareva-Ulitsky B, et al. Among authors: thomas pd. Bioinformatics. 2005 May 1;21(9):1876-90. doi: 10.1093/bioinformatics/bti244. Epub 2005 Jan 12. Bioinformatics. 2005. PMID: 15647305
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. Thomas PD, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W645-50. doi: 10.1093/nar/gkl229. Nucleic Acids Res. 2006. PMID: 16912992 Free PMC article.
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
Mi H, Guo N, Kejariwal A, Thomas PD. Mi H, et al. Among authors: thomas pd. Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. doi: 10.1093/nar/gkl869. Epub 2006 Nov 27. Nucleic Acids Res. 2007. PMID: 17130144 Free PMC article.
PANTHER pathway: an ontology-based pathway database coupled with data analysis tools.
Mi H, Thomas P. Mi H, et al. Among authors: thomas p. Methods Mol Biol. 2009;563:123-40. doi: 10.1007/978-1-60761-175-2_7. Methods Mol Biol. 2009. PMID: 19597783 Free PMC article.
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. Mi H, et al. Among authors: thomas pd. Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16. Nucleic Acids Res. 2010. PMID: 20015972 Free PMC article.
The use of orthologous sequences to predict the impact of amino acid substitutions on protein function.
Marini NJ, Thomas PD, Rine J. Marini NJ, et al. Among authors: thomas pd. PLoS Genet. 2010 May 27;6(5):e1000968. doi: 10.1371/journal.pgen.1000968. PLoS Genet. 2010. PMID: 20523748 Free PMC article.
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