Prof. Tal Pupko

מח חקר התא ואימונולוגיה סגל אקדמי בכיר
Prof. Tal Pupko
Phone: 03-6407693
Fax: 03-6422046
Office: Britannia-Porter, 405

Biography

Tal Pupko holds a PhD in computation biology from Tel-Aviv University.  His undergraduate training is both in pure mathematics and in biology, and his research combines mathematical, statistical and computer science concepts with molecular biology and evolution.  He is an associate editor for the journal Molecular Biology and Evolution

Research Interests

 My research interests are concerned with various fields of Molecular Evolution and Bioinformatics:​

  • Molecular evolution- studying the evolutionary selective forces shaping genes and genomes and the in-silico predictions of these forces using probabilistic evolutionary models
  • Phylogenetics- reconstructing evolutionary relationships and ancestral sequences, inferring lateral gene transfer, alignment and alignment reliability.
  • Pathogenomics- developing and applying machine-learning tools for predicting effector proteins in pathogenic bacteria such as Legionella and Coxiella. Predicting hydrogenosomal proteins in Trichomonas vaginalis. Functional and evolutionary analysis of HIV-1 genomes.
  • Immunoformatics- predicting B cell epitopes and developing algorithms for analyzing phage display experiments.

 

Recent Publications

For the full list, please see his website.

 

 

Since 2012:

Molshanski-Mor, S., Yosef, I., Kiro, R., Edgar, R., Manor, M., Gershovits, M., Laserson, M., Pupko, T., and Qimron, U. 2014. Revealing Bacterial Targets of Growth Inhibitors Encoded by Bacteriophage T7. Proc Natl Acad Sci USA. Accepted. 

 

Ashkenazy, H., Cohen, O., Pupko, T., and Huchon D. 2014. Indel reliability in indel-based phylogenetic inference. Genome Biol Evol. In press. 

 

Oren, Y., Smith, M.B., Johns, N.I., Kaplan Zeevi, M., Biran. D., Ron, E.Z., Corander, J., Wang, H.H., Alm. E.J., and Pupko T. 2014. Transfer of noncoding DNA drives regulatory rewiring in bacteria. Proc Natl Acad Sci USA. 111(45):16112-7.  

 

Levy Karin, E., Susko, E., and Pupko, T. 2014. Alignment errors strongly impact likelihood-based tests for comparing topologies. Mol Biol Evol. 31(11):3057-3067.  

 

Lifshitz, Z., Burstein, D., Schwartz, K., Shuman, H.A., Pupko, T., and Segal G. 2014. Identification of novel Coxiella burnetii Icm/Dot effectors and genetic analysis of their involvement in modulating a mitogen-activated protein kinase pathway. Infect Immun. 82(9):3740-3752.  

 

Mayrose, I., Stern, A., Burdelova, E.O., Sabo, Y., Laham-Karam, N., Zamostiano, R., Bacharach, E., and Pupko, T. 2013. Synonymous site conservation in the HIV-1 genome. BMC Evolutionary Biology. 13:164.

 

Yossef, I., Shitrit, D., Goren, M.G., Burstein, D., Pupko, T., and Qimron, U. 2013. DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci USA. 110(35):14396-401.

 

Anisimova, M., Liberles, D.A., Philippe, H., Provan, J., Pupko, T., and von Haeseler, A. 2013. State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evolutionary Biology. 13:161.

 

Cohen, O., Ashkenazy, H., Levy Karin, E., Burstein, D., and Pupko, T. 2013. CoPAP: Co-evolution of Presence-Absence Patterns. Nucleic Acids Research. 41(Web Server issue):W232-W237.  

 

Celniker, G., Nimrod, G., Ashkenazy, H., Glaser, F., Martz, E., Mayrose, I., Pupko, T., and Ben-Tal, N. 2013. ConSurf: using evolutionary data to raise testable hypotheses about protein function. Israel Journal of Chemistry. 53(3-4):199-206.

 

Lifshitza, Z., Burstein, D., Peeri, M., Zusman, T., Schwartz, K., Shuman, H.A., Pupko, T., and Segal, G. 2013. Computational modeling and experimental validation of the Legionella and Coxiella virulence-related Type-IVB secretion signal. Proc Natl Acad Sci USA. 110(8):E707-715.  

 

Cohen, O., Ashkenazy, H., Burstein, D., and Pupko, T. 2012. Uncovering the co-evolutionary network among prokaryotic genes. Bioinformatics. 28 ECCB 2012:i389-i394.  

 

Ryvkin, A., Ashkenazy, H., Smelyanski, L., Kaplan, G., Penn, O., Weiss-Ottolenghi, Y., Privman, E., Ngam, P.B., Woodward, J.E., May, G.D., Bell, C., Pupko, T., and Gershoni, J.M. 2012. Deep panning: steps towards probing the IgOme. PLoS ONE. 7(8): e41469.  

 

Ashkenazy, H., Penn, O., Doron-Faigenboim, A., Cohen, O., Cannarozzi, G., Zomer, O., and Pupko, T. 2012. FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Research. 40(Web Server issue):W580-W584.

 

Liberles, D.A, Teichmann, S.A., Bahar, I., Bastolla, U., Bloom, J., Bornberg-Bauer, E., Colwell, L.J., de Koning, A.P., Dokholyan, N.V., Echave, J., Elofsson, A., Gerloff, D.L., Goldstein, R.A., Grahnen, J.A., Holder, M.T., Lakner, C., Lartillot, N., Lovell, S.C., Naylor, G., Perica, T., Pollock, D.D, Pupko, T., Regan, L., Roger, A., Rubinstein, N., Shakhnovich, E., Sjolander, K., Sunyaev, S., Teufel, A.I., Thorne, J.L., Thornton, J.W., Weinreich, D.M., Whelan, S. 2012. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. 21(6):769-785.

 

Amit, M., Donyo, M., Hollander, D., Goren, Aa., Kim, E., Gelfman, S., Lev-Maor, G., Burstein, D., Schwartz, S., Postolsky, B., Pupko, T., and Ast, G. 2012. Differential GC content between exons and introns establishes distinct strategies of splice-site recognition. Cell Reports. 1(5):543-556.

 

Gelfman, S., Burstein, D., Penn, O., Schwartz, S., Pupko, T., and Ast, G. 2012. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res. 22(1):35-50.

 

Privman, E, Penn, O. and Pupko, T. 2012. Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol. Biol. Evol. 29(1):1-5.

 

Burstein, D., Gould, S.B., Zimorski, V., Klosges, T., Kiosse, F., Major, P., Martin, W., Pupko, T., Dagan, T. 2012. A machine-learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Eukaryotic Cell 11:217-228

 

Turner, D., Amit, S., Chalom, S., Penn, O., Pupko T., Katchman, E., Matus, N., Tellio, H., Katzir, M., Avidor, B. 2012. Emergence of an HIV-1 cluster harboring the major protease L90M mutation among treatment-naive patients in Tel-Aviv, Israel. HIV Medicine 13:202-206.  

 

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