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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: ashkenazy h. Bioinformatics. 2010 Nov 15;26(22):2914-5. doi: 10.1093/bioinformatics/btq549. Epub 2010 Sep 27. Bioinformatics. 2010. PMID: 20876605
Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept.
Kliger Y, Levy O, Oren A, Ashkenazy H, Tiran Z, Novik A, Rosenberg A, Amir A, Wool A, Toporik A, Schreiber E, Eshel D, Levine Z, Cohen Y, Nold-Petry C, Dinarello CA, Borukhov I. Kliger Y, et al. Among authors: ashkenazy h. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13797-801. doi: 10.1073/pnas.0906514106. Epub 2009 Aug 5. Proc Natl Acad Sci U S A. 2009. PMID: 19666568 Free PMC article.
Reducing phylogenetic bias in correlated mutation analysis.
Ashkenazy H, Kliger Y. Ashkenazy H, et al. Protein Eng Des Sel. 2010 May;23(5):321-6. doi: 10.1093/protein/gzp078. Epub 2010 Jan 12. Protein Eng Des Sel. 2010. PMID: 20067922
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. Ashkenazy H, et al. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W529-33. doi: 10.1093/nar/gkq399. Epub 2010 May 16. Nucleic Acids Res. 2010. PMID: 20478830 Free PMC article.
GUIDANCE: a web server for assessing alignment confidence scores.
Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. Penn O, et al. Among authors: ashkenazy h. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W23-8. doi: 10.1093/nar/gkq443. Epub 2010 May 23. Nucleic Acids Res. 2010. PMID: 20497997 Free PMC article.
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N. Wainreb G, et al. Among authors: ashkenazy h. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W523-8. doi: 10.1093/nar/gkq528. Epub 2010 Jun 11. Nucleic Acids Res. 2010. PMID: 20542913 Free PMC article.
Hidden conformations in protein structures.
Ashkenazy H, Unger R, Kliger Y. Ashkenazy H, et al. Bioinformatics. 2011 Jul 15;27(14):1941-7. doi: 10.1093/bioinformatics/btr292. Epub 2011 May 17. Bioinformatics. 2011. PMID: 21586517
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site.
Wainreb G, Wolf L, Ashkenazy H, Dehouck Y, Ben-Tal N. Wainreb G, et al. Among authors: ashkenazy h. Bioinformatics. 2011 Dec 1;27(23):3286-92. doi: 10.1093/bioinformatics/btr576. Epub 2011 Oct 13. Bioinformatics. 2011. PMID: 21998155 Free PMC article.
FastML: a web server for probabilistic reconstruction of ancestral sequences.
Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T. Ashkenazy H, et al. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. doi: 10.1093/nar/gks498. Epub 2012 May 31. Nucleic Acids Res. 2012. PMID: 22661579 Free PMC article.
Uncovering the co-evolutionary network among prokaryotic genes.
Cohen O, Ashkenazy H, Burstein D, Pupko T. Cohen O, et al. Among authors: ashkenazy h. Bioinformatics. 2012 Sep 15;28(18):i389-i394. doi: 10.1093/bioinformatics/bts396. Bioinformatics. 2012. PMID: 22962457 Free PMC article.
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