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106 results
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GLOOME: gain loss mapping engine.
Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T. Cohen O, et al. Among authors: pupko t. Bioinformatics. 2010 Nov 15;26(22):2914-5. doi: 10.1093/bioinformatics/btq549. Epub 2010 Sep 27. Bioinformatics. 2010. PMID: 20876605
A fast algorithm for joint reconstruction of ancestral amino acid sequences.
Pupko T, Pe'er I, Shamir R, Graur D. Pupko T, et al. Mol Biol Evol. 2000 Jun;17(6):890-6. doi: 10.1093/oxfordjournals.molbev.a026369. Mol Biol Evol. 2000. PMID: 10833195
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.
Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. Pupko T, et al. Bioinformatics. 2002;18 Suppl 1:S71-7. doi: 10.1093/bioinformatics/18.suppl_1.s71. Bioinformatics. 2002. PMID: 12169533
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families.
Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N. Pupko T, et al. Bioinformatics. 2002 Aug;18(8):1116-23. doi: 10.1093/bioinformatics/18.8.1116. Bioinformatics. 2002. PMID: 12176835
ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N. Glaser F, et al. Among authors: pupko t. Bioinformatics. 2003 Jan;19(1):163-4. doi: 10.1093/bioinformatics/19.1.163. Bioinformatics. 2003. PMID: 12499312
Detecting excess radical replacements in phylogenetic trees.
Pupko T, Sharan R, Hasegawa M, Shamir R, Graur D. Pupko T, et al. Gene. 2003 Nov 13;319:127-35. doi: 10.1016/s0378-1119(03)00802-3. Gene. 2003. PMID: 14597178
ConSeq: the identification of functionally and structurally important residues in protein sequences.
Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N. Berezin C, et al. Among authors: pupko t. Bioinformatics. 2004 May 22;20(8):1322-4. doi: 10.1093/bioinformatics/bth070. Epub 2004 Feb 10. Bioinformatics. 2004. PMID: 14871869
Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.
Mayrose I, Graur D, Ben-Tal N, Pupko T. Mayrose I, et al. Among authors: pupko t. Mol Biol Evol. 2004 Sep;21(9):1781-91. doi: 10.1093/molbev/msh194. Epub 2004 Jun 16. Mol Biol Evol. 2004. PMID: 15201400
The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.
Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. Glaser F, et al. Among authors: pupko t. Proteins. 2005 Feb 15;58(3):610-7. doi: 10.1002/prot.20305. Proteins. 2005. PMID: 15614759
Selecton: a server for detecting evolutionary forces at a single amino-acid site.
Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T. Doron-Faigenboim A, et al. Among authors: pupko t. Bioinformatics. 2005 May 1;21(9):2101-3. doi: 10.1093/bioinformatics/bti259. Epub 2005 Jan 12. Bioinformatics. 2005. PMID: 15647294
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