Hi, I conducted my PhD studies under the supervision of Prof. Tal Pupko (title: "Reliability of multiple sequence alignments: applications in molecular evolution"; earned 6/2016).

Now I'm a post-doctoral fellow
at The Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University

I was a fellow of the Edmond J. Safra Bioinformatics Center.

Download my CV

                                                   E-mail: haimash@tau.ac.il

                                                   Tel.: (972-3) 6409245
                                                   Fax.: (972-3) 6422046

                                                   Address: Haim Ashkenazy,
                                                                 Dept. of Cell Research and Immunology,
                                                                 George S. Wise Faculty of Life Sciences,
                                                                 Tel-Aviv University 69978, Israel.


  1. Ashkenazy H., Sela I., Levy Karin E., Landan G., and Pupko T.
    Multiple sequence alignment averaging improves phylogeny reconstruction.

    Under revision for Systematic Biology
  2. Ryvkin A.*, Ashkenazy H.*, Weiss-Ottolenghi Y., Piller C., Pupko T., and Gershoni MJ.
    Phage display peptide libraries: deviations from randomness and correctives.

    Nucleic Acids Res. In press. [ABS],[PDF]
    *Authors contributed equally.
  3. Ashkenazy H.*, Levy Karin E.*, Mertens Z., Cartwright RA., and Pupko T.
    SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm.
    Nucleic Acids Res. 2017, 45 (W1):W453–W457. [ABS],[PDF]
    *Authors contributed equally.
  4. Levy Karin E.*, Ashkenazy H.*, Wicke S., Pupko T., and Mayrose I.
    TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites.
    Nucleic Acids Res. 2017, 45 (W1):W260–W264. [ABS],[PDF]
    *Authors contributed equally.
  5. Levy Karin E.*, Shkedy D.*, Ashkenazy H., Cartwright RA., and Pupko T.
    Inferring rates and length-distributions of indels using approximate Bayesian computation.
    Genome Biol Evol. 2017 May 1;9(5):1280-1294. [ABS],[PDF]
    *Authors contributed equally.
  6. Ashkenazy H., Abadi S., Martz E., Chay O., Mayrose I, Pupko T, and Ben-Tal N.
    ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
    Nucleic Acids Res. 2016, 44(W1):W344-350. [ABS],[PDF]
  7. Levy Karin E.*, Rabin A.*, Ashkenazy H., Shkedy D., Avram O., Cartwright R.A., and Pupko T.
    Inferring indel parameters using a simulation-based approach
    Genome Biol Evol. 2015, 7 (12): 3226-3238. [ABS],[PDF]
    *Authors contributed equally.
  8. Narunsky A., Nepomnyachiy S., Ashkenazy H., Kolodny R., and Ben-Tal N.
    ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure.
    Structure. 2015 Nov 3;23(11):2162-70. [ABS],[PDF]
  9. Sela I.*, Ashkenazy H.*, Katoh K. and Pupko T.
    GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
    Nucleic Acids Res. 2015 Jul 1;43(W1):W7-W14. [ABS],[PDF]
    *Authors contributed equally.
  10. Narunsky A., Ashkenazy H., Kolodny R., and Ben-Tal N.
    Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations
    BMC Bioinformatics. 2015, 16 (Suppl 3), A3. [ABS],[PDF]
  11. Ashkenazy H., Cohen O., Pupko T. and Huchon D.
    Indel reliability in indel-based phylogenetic inference.
    Genome Biol Evol. 2014, 6(12):3199-3209. [ABS],[PDF]
  12. Yachdav G., Kloppmann E., Kajan L., Hecht M., Goldberg T., Hamp T., Hönigschmid P., Schafferhans A., Roos M., Bernhofer M., Richter L., Ashkenazy H., Punta M., Schlessinger A., Bromberg Y., Schneider R., Vriend G., Sander C., Ben-Tal N., and Rost B.
    PredictProtein--an open resource for online prediction of protein structural and functional features.
    Nucleic Acids Res. 2014, Jul;42(Web Server issue):W337-43. [ABS],[PDF]
  13. Cohen O., Ashkenazy H., Levy Karin E., Burstein D. and Pupko T.
    CoPAP: Co-evolution of Presence-Absence Patterns.
    Nucleic Acids Res. 2013, Jul;41(Web Server issue):W232-7. [ABS],[PDF]
  14. Celniker G., Nimrod G., Ashkenazy H., Glaser F., Martz E., Mayrose I., Pupko T. and Ben-Tal N.
    ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function.
    Isr. J. Chem., 2013, 53(3-4):199-206. [ABS],[PDF]
  15. Cohen O., Ashkenazy H., Burstein D. and Pupko T.
    Uncovering the co-evolutionary network among prokaryotic genes.
    Bioinformatics. 2012 Sep 15;28(18):i389-i394. [ABS],[PDF]
  16. Ryvkin A.*, Ashkenazy H.*, Smelyanski L., Kaplan G., Penn O., Weiss-Ottolenghi Y., Privman E., Ngam PB., Woodward JE., May GD., Bell C., Pupko T. and Gershoni JM.
    Deep Panning: steps towards probing the IgOme.
    PLoS One. 2012;7(8):e41469. [ABS],[PDF]
    *Authors contributed equally.
  17. Ashkenazy H.*, Penn O.*, Doron-Faigenboim A., Cohen O., Cannarozzi G., Zomer O. and Pupko T.
    FastML: a web server for probabilistic reconstruction of ancestral sequences
    Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. [ABS],[PDF]
    *Authors contributed equally.
  18. Wainreb G., Wolf L., Ashkenazy H., Dehouck Y. and Ben-Tal N.
    Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site.
    Bioinformatics. 2011 Dec 1;27(23):3286-92. [ABS],[PDF]
  19. Ashkenazy H., Unger R. and Kliger Y.
    Hidden conformations in protein structures.
    Bioinformatics. 2011 Jul 15;27(14):1941-7. [ABS],[PDF]
  20. Cohen O., Ashkenazy H., Belinky F., Huchon D. and Pupko T.
    GLOOME: Gain Loss Mapping Engine.
    Bioinformatics. 2010 Nov 15;26(22):2914-5. [ABS],[PDF]
  21. Wainreb G., Ashkenazy H., Bromberg Y., Starovolsky-Shitrit A, Haliloglu T, Ruppin E. Avraham K. Rost B. and Ben-Tal N.
    MuD: an interactive web-server for the prediction of non-neutral substitutions using protein structural data.
    Nucleic Acids Res. 2010 Jul 1;38 Suppl:W523-8. [ABS],[PDF]
  22. Penn O., Privman E., Ashkenazy H., Landan G., Graur D. and Pupko T.
    GUIDANCE: a web server for assessing alignment confidence scores.
    Nucleic Acids Res. 2010 Jul 1;38 Suppl:W23-8. [ABS],[PDF]
  23. Ashkenazy H.*, Erez E.*, Martz E., Pupko T. and Ben-Tal N.
    ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids.
    Nucleic Acids Res. 2010 Jul 1;38 Suppl:W529-33. [ABS],[PDF]
    *Authors contributed equally.
  24. Ashkenazy H. and Kliger Y.
    Reducing phylogenetic bias in correlated mutation analysis.
    Protein Eng Des Sel. 2010 May;23(5):321-6. [ABS],[PDF]
    (Selected for cover illustration)
  25. 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 C.A. and Borukhov I.
    Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept.
    Proc Natl Acad Sci U.S.A. 2009 Aug 18;106(33):13797-801. [ABS],[PDF]
  26. Ashkenazy H., Unger R. and Kliger Y.
    Optimal data collection for correlated mutation analysis.

    Proteins 2009 Feb 15;74(3):545-55. [ABS],[PDF]
    (Selected by Faculty of 1000 Biology)