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 2014:

 

Guerrero, IJ, Perez-Montano, F., Mateus da Silva, G., Wagner, N., Shkedy, D., Zhao, M., Pizarro, L.,Bar, M., Walcott, R., Sessa, G., Pupko, T., Burdman, S. 2020. Show me your secret(ed) weapons: a multifaceted approach reveals a wide arsenal of type III-secreted effectors in the cucurbit pathogenic bacterium Acidovorax citrulli and novel effectors in the Acidovorax genus. Molecular Plant Pathology. 21(1):17–37. [pdf] [abs]
 

Sugis, E., Dauvillier, J., Leontjeva, A., Adler, P., Hindie, V., Moncion, T., Collura, V., Daudin, R., Loe-Mie, Y., Herault, Y., Lambert, J.C., Hermjakob, H., Pupko, T., Rain, J.C., Xenarios, I., Vilo, J., Simonneau, M., and Peterson, H. 2019. HENA, Heterogeneous network-based data set for Alzheimer's disease. Scientific Data. 6(1):151. [pdf] [abs]
 

Avram, O., Rapoport, D., Portugez, S., and Pupko, T. 2019. M1CR0B1AL1Z3R - a user-friendly web server for the analysis of large-scale microbial genomics data. Nucleic Acids Research. 47(Web Server issue):W88-W92. [pdf] [abs]
 

Abadi, S., Azouri, D., Pupko, T., and Mayrose, I. 2019. Model selection may not be a mandatory step for phylogeny reconstruction. Nature Communications. 10(1):934. [pdf] [abs]
 

Moshe, A., and Pupko, T. 2019. Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices. Bioinformatics. 35(15):2562-2568. [pdf] [abs]
 

Levy Karin, E., Ashkenazy, H., Jotun, H., and Pupko, T. 2019. A simulation-based approach to statistical alignment. Systematics Biology. 68(2):252-266. [pdf] [abs]
 

Ashkenazy, H., Sela, I., Levy Karin, E., Landan, G., and Pupko, T. 2019. Multiple sequence alignment averaging improves phylogeny reconstruction. Systematics Biology. 68(1):117-130. [pdf] [abs]
 

Davis, E.W., Tabima, J.F., Weisberg, A.J., Lopes, L.C., Wiseman, M.S., Pupko, T., Belcher, M.S., Sechler, A.J., Tancos, M.A., Schroeder, B.K., Murray, T.D., Luster, D.G., Schneider, W.L., Rogers, E.E., Andreote, F.D., Grunwald, N.J., Putnam, M.D., and Chang, J.H. 2018. Evolution of the US biological select agent, Rathayibacter toxicus. mBio. 9:e01280-18. [pdf] [abs]
 

Avram, O., Vaisman-Mentesh A, Yehezkel, D., Ashkenazy, H., Pupko, T., and Wine, Y. 2018. ASAP, a webserver for immunoglobulin-sequencing analysis pipeline. Front. Immunol. 9:1686 [pdf] [abs]
 

Bar, L., Levy Karin, E., Pupko, T., and Hazkani-Covo, E. 2018. The prevalence and evolutionary conservation of inverted repeats in proteobacteria. Genome Biol Evol. 10(3):918-927. [pdf] [abs]
 

Ryvkin, A., Ashkenazy, H., Weiss-Ottolenghi, Y., Piller, C., Pupko, T., and Gershoni, J. 2018. Phage display peptide libraries: deviations from randomness and correctives. Nucleic Acids Research. 46(9):e52. [pdf] [abs]
 

Xue, Y.A., DiPizio, A., Levit, A., Yarnitzky, T., Penn, O., Pupko, T., and Niv, M.Y. 2018. Independent evolution of strychnine recognition by bitter taste receptor subtypes. Frontiers in Molecular Biosciences. 5:9. [pdf] [abs]
 

Danziger, O., Pupko, T., Bacharach, E., and Ehrlich, E. 2018. Interleukin-6 and interferon-alpha signaling via JAK1-STAT differentially regulate oncolytic versus cytoprotective antiviral states. Front. Immunol. 9:94. [pdf] [abs]
 

Nissan, G., Gershovits, M., Morozov, M., Chalupowicz, L., Sessa, G., Manulis-Sasson, S., Barash, I., and Pupko, T. 2018. Revealing the inventory of type III effectors in Pantoea agglomerans gall-forming pathovars by using draft genome sequences and a machine-learning approach. Mol Plant Pathol. 19(2):381-392. [pdf] [abs]
 

Mushegian, A., Levy Karin, E., and Pupko, T. 2018. Sequence analysis of malacoherpesvirus proteins: Pan-herpesvirus capsid module and replication enzymes with an ancient connection to "Megavirales". Virology. 513:114-128. [pdf] [abs]
 

Ashkenazy, H., Levy Karin, E., Mertens, Z., Cartwright, R.A., and Pupko, T. 2017. SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Research. 45(W1):W453-W457. [pdf] [abs]
 

Levy Karin, E., Ashkenazy, H., Wilcke, S., Pupko, T., and Mayrose, I. 2017. TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Research. 45(W1):W260-W264. [pdf] [abs]
 

Levy Karin, E., Shkedy, D., Ashkenazy, H., Cartwright, R.A., and Pupko, T. 2017. Inferring rates and length-distributions of indels using Approximate Bayesian Computation. Genome Biol Evol. 9(5):1280-1294. [pdf] [abs]
 

Levy Karin, E., Wilcke, S., Pupko, T., and Mayrose, I. 2017. An integrated model of phenotypic trait changes and site-specific sequence evolution. Systematics Biology. 66(6):917-933. [pdf] [abs]
 

Preisner, H., Levy Karin, E., Poschmann, G., Stuhler, K., Pupko, T., and Gould SB. 2016. The cytoskeleton of parabasalian parasites comprises proteins that share properties common to intermediate filament proteins. Protist. 167(6):526-543. [pdf] [abs]
 

McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., Vehkala, M., Valimaki, N., Prentice, M.B., Ashour ,A., Avram, O., Pupko, T., Dobrindt, U., Literak, I., Guenther, S., Schaufler, K., Wieler, L.H., Zhiyong, Z., Sheppard, S.K., McInerney, J.O., Corander, J. 2016. Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genet. 12(9):e1006280. [pdf] [abs]
 

Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., and Ben-Tal, N. 2016. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research. 44(Web Server issue):W344-W350. [pdf] [abs]
 

Eckshtain-Levi, N., Shkedy, D., Gershovits, M., Da Silva, G.M., Tamir-Ariel, D., Walcott, R., Pupko, T., and Burdman, S. 2016. Insights from the genome sequence of Acidovorax citrulli M6, a group I strain of the causal agent of bacterial Fruit Blotch of cucurbits. Front Microbiol. 7:430. [pdf] [abs]
 

Burstein, D., Amaro, F., Zusman, T., Lifshitz, Z., Cohen, O., Gilbert, J.A., Pupko, T., Shuman, H.A., and Segal, G. 2016. Genomic analysis of 38 Legionella species reveals large and diverse effector repertoires . Nature Genetics. 48(2):167-75. [pdf] [abs]
 

Teper, D., Burstein, D., Salomon, D., Gershovitz, M., Pupko, T., and Sessa, G. 2016. Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach. Mol Plant Pathol. 17(3):398-411. [pdf] [abs]
 

Faigenbloom, L., Rubinstein, N.D., Kloog, Y., Mayrose, I., Pupko, T., and Stein, R. 2015. Regulation of alternative splicing at the single-cell level . Mol Syst Biol. 11(12):845. [pdf] [abs]
Levy Karin, E., Rabin, A., Ashkenazy, H., Shkedy, D., Avram, O., Cartwright, R.A., and Pupko, T. 2015. Inferring indel parameters using a simulation-based approach . Genome Biol Evol. 7(12):3226-38. [pdf] [abs]
 

Bar-Rogovsky, H., Stern, A., Penn, O., Kobl, I., Pupko, T., and Tawfik, D.S. 2015. Assessing the prediction fidelity of ancestral reconstruction by a library approach. Protein Engineering, Design & Selection. 28(11):507-518. [pdf] [abs]
 

Sela, I., Ashkenazy, H., Kazutaka, K., and Pupko, T. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Research. 43(W1):W7-W14. [pdf] [abs]
 

Burstein, D., Satanower, S., Simovitch, M., Belnik ,Y., Zehavi, M., Yerushalmi, G., Ben-Aroya, S., Pupko, T., and Banin, E. 2015. Novel type III effectors in Pseudomonas aeruginosa. mBio. 6(2):e00161-15. [pdf] [abs]
 

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. 111(52):18715-18720. [pdf] [abs]
 

Ashkenazy, H., Cohen, O., Pupko, T., and Huchon, D. 2014. Indel reliability in indel-based phylogenetic inference. Genome Biol Evol.6(12):3199-3209. [pdf] [abs]
 

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):16112-16117. [pdf] [abs]
 

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. [pdf] [abs]
 

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. [pdf] [abs]

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