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    CV E. Privman

    Eyal
    Privman

    Address: The
    Department of Evolutionary and Environmental Biology,

    University of Haifa,

    Abba Hushi 199

    Haifa
    3498838

    Israel

    Phone: Office +972
    (0)4-8280707

    Mobile +972 (0)54-5224888

    E-mail / homepage: This email address is being protected from spambots. You need JavaScript enabled to view it. / http://www.unil.ch/dee/page82898_en.html

    Personal status: Married+2

    Education:

    2004-2010 Tel Aviv University. Edmond J. Safra Ph.D. fellowship at the
    Faculty of Life Sciences. Computational research of molecular evolution under
    the supervision of Prof. Tal Pupko,
    including co-evolution of homing endonucleases with their hosts and development
    of hybrid algorithms for phylogeny reconstruction and multiple sequence
    alignment.

    2000-2003 Tel Aviv University. B.Sc. studies
    in Computer Science and Life Sciences in the Bioinformatics Program.

    Positions held:

    2013- to date University of Haifa. Lecturer in the
    Dept. of Evolutionary and Environmental Biology. Affiliated to the Institute of
    Evolution.

    2011-2013 University of Lausanne. Post-doctoral
    research fellowship in the laboratory of Prof.
    Laurent Keller, Dept. of Ecology and
    Evolution.

    "Embedded bioinformatician" associated with Prof. Marc Robinson-Rechavi, the Swiss Institute of Bioinformatics.

    2010 Gename Ltd. Bioinformatics consultant.

    Candidate gene list preparation for a genome-wide association study.

    2009,2012 AVA Biodefender Ltd. Bioinformatics consultant.

    Identifying conserved elements in the influenza genome.

    2002-2004 Compugen Ltd., Biological Data Assessment Team.

    Part of the group developing the LEADS platform
    for eukaryotic transcriptome modeling, based on alignments of ESTs to the
    genome. I developed a software package
    for evaluating the biological correctness of the output of LEADS. I worked with the Algorithms Team on fine-tuning
    LEADS to the biological phenomena it models.

    Teaching:

    2014- to date University of Haifa. Lecturer in a Perl programming course at the Faculty of Natural
    Sciences.

    2011-2012 University of Lausanne. Supervisor of a master student. Thesis topic:
    evolution of the sex determination locus in bees.

    2011-2012 University of Lausanne. Supervisor of undergraduate bioinformatics
    programming projects in the School of Biology.

    2012 Lecturer in the summer school
    of the SIB (Swiss Institute of Bioinformatics) PhD Training Network: Bioinformatics
    and Population Genomics.

    2010 Lecturerin an alignment reliability workshop at the COST Training School, Hebrew University of Jerusalem.

    2009-2010 Tel Aviv Academic College. Lecturerin the sequence analysis course in the
    bioinformatics undergraduate program.

    2008-2010 Tel Aviv University. Supervisor of an undergraduate student who
    participated in the development of a computational pipeline for identification
    of homing endonucleases and prediction of their targets.

    2007-2009 Tel Aviv University, the Bioinformatics Unit. Lecturer in Perl programming workshops
    for biologists.

    2005-2009 Tel Aviv University, the Bioinformatics Unit. Lecturer in the Perl programming coursegiven to graduate students at the Faculty of Life
    Sciences. I initiated the course and prepared all teaching materials including
    presentations, hands-on classes, exercises, and exams. I developed this course
    from 7 students in 2005 to 35 in 2009.

    Peer-reviewed publications:

    1) Roux J., Privman E., Moretti
    S., Daub J.T., Robinson-Rechavi M., Keller L. In review. Patterns
    of positive selection in seven ant genomes. arXiv:1311.4706.

    2) Privman E., Wurm Y., Keller L. 2013. Duplication and concerted
    evolution in a master sex determiner under balancing selection. Proceedings
    of the Royal Society B, 280:
    20122968.

    3) Simola D. F., Wissler L., Donahue
    L., Waterhouse R.M., Helmkampf M., Roux J., Nygaard S., Glastad K.M., Hagen D.,
    Viljakainen L., Reese J.T., Hunt. B.G., Graur D., Elhaik E., Krivenseva E.V.,
    Wen J., Parker B.J., Cash E., Privman E., Childer C.P., Munoz-Torres
    M.C., Boomsma J.J., Bornberg-Bauer E., Currie C., Elsik C.G., Suen G., Goodisman
    M.A.D., Keller L., Liebig J., Rawls A., Reinberg D., Smith C.D., Smith C.R.,
    Tsutsui N., Wurm Y., Zdobnov E.M., Berger S.L., & Gadau J. 2013. Social
    insect genomes exhibit dramatic evolution in gene composition and regulation
    while preserving regulatory features linked to sociality. Genome Research, doi: 10.1101/gr.155408.113.

    4) 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., Gershoni J.M. 2012. Deep
    Panning: Steps towards probing the IgOme. PLoS One, 7: e41469, doi: 10.1371/journal.pone.0041469.

    5) Privman E.*, Penn O.*, and Pupko T. 2011. Improving the
    performance of positive selection inference by filtering unreliable alignment
    regions. Molecular
    Biology and Evolution, 29: 1-5, doi:
    10.1093/molbev/msr177.

    6) Barzel A.*, Privman E.*, Pe'eri
    M., Burstein D., Gophna U., Pupko T., Kupiec M. 2011. Native homing
    endonucleases can target conserved genes in humans and in animal models. Nucleic Acids
    Research,
    39: 6646-6659, doi: 10.1093/nar/gkr242.

    7) Barzel A., Naor A., Privman E.,
    Kupiec M., Gophna U. 2011. Homing endonucleases residing within inteins:
    evolutionary puzzles awaiting genetic solutions. Biochemical
    Society transactions, 39:
    169-173, doi: 10.1042/BST0390169.

    8) Penn O.*, Privman E.*,
    Ashkenazy H., Landan G., Graur D., Pupko T. 2010. GUIDANCE: a web server for
    assessing alignment confidence scores. Nucleic Acids Research, 38: W23-W28, doi: 10.1093/nar/gkq443.

    ** A chapter reviewing GUIDANCE appeared in Hall B. G. (2011) Phylogenetic Trees Made Easy: A How-To Manual (Sinauer, Sunderland,
    MA).

    9) Penn O.*, Privman E.*,
    Landan G., Graur D., Pupko T. 2010. An alignment confidence score capturing
    robustness to guide-tree uncertainty. Molecular Biology and Evolution, 27: 1759-1767, doi: 10.1093/molbev/msq066.

    10) Ninio M.*, Privman E.*, Pupko
    T., Friedman N. 2007. Phylogeny reconstruction: increasing the accuracy of
    pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics, 23: e136-e141, doi: 10.1093/bioinformatics/btl304.

    11) Stern
    A., Privman E., Rasis M., Lavi S., Pupko T. 2007. Evolution of the metazoan protein phosphatase 2C
    superfamily. Journal of Molecular Evolution, 64: 61-70, doi: 10.1007/s00239-006-0033-y.

    * These authors contributed equally

    Book chapters:

    1) Privman E. 2014. Bioinformatic identification of homing
    endonucleases and their target sites. In Homing Endonucleases (ed Edgell,
    D). Methods
    in Molecular Biology 1123:
    Ch. 2, 27-35.

    Patents:

    2) Barzel A., Privman E.,
    Michael P., Pupko T., Kupiec M. 2009. Homing endonuclease genes and their
    targets. Patent application no. US 2011/0064717 A1.

    3) Barzel A., Privman E.,
    Burstein D., Gophna U., Pupko T., Kupiec M. 2009. Method for searching for
    homing endonucleases, their genes and their targets. Patent applicationno. US 2010/0317724 A1.

    4) Akiva P., Dlber A., Pollock S.,
    Levine Z., Nemzer S., Grebinskiy V., Meloon B., Olson A., Rosenberg A., Haviv A.,
    Zevin S., Zekhari T., Shaged Z., Olshansky M., Farkash A., Privman E.,
    Novik A., Keren N., Cojocaru G., Cohen Y., Shemesh R., Sella-Tavor O., Mintz L.,
    Xie H., Dahary D., Levanon E., Freilich S., Beck N., Zhu W., Wasserman A.,
    Chermesh C., Azar I., Sorek R., Bernstein J.
    2006. Novel calcium channel
    variants and methods of use thereof. Patent application no. US 2006/0147946 A1.

    5) Diber A., Pollock S., Levine Z.,
    Nemzer S., Grebinskiy V., Meloon B., Olson A., Rosenberg A., Haviv A., Zevin S.,
    Zekharia T., Shaked Z., Olshansky M., Farkash A., Privman E., Novik A.,
    Keren N., Cojocaru G., Akiva P., Cohen Y., Shemesh R., Sella-Tavor O., Mintz L.,
    Xie H., Dahary D., Levanon E., Freilich S., Beck N., Zhu W., Wasserman A.,
    Chermesh C., Azar I., Sorek R., Bernstein J.
    2006. Methods and systems for
    annotating biomolecular sequences. Patent application no. US 2006/0068405 A1.

    Oral presentations:

    1) Privman E. (invited speaker) 2013. Filtering multiple alignments
    in phylogenomic pipelines. Phylogenomics workshop in the Annual Meeting of the Swiss Institute of Bioinformatics (SIB),
    Biel/Bienne, Switzerland.

    2) Privman E. (invited speaker), Penn O., Ashkenazy H., Pupko
    T. 2012. Filtering multiple sequence alignments to avoid artifacts in
    downstream analyses. Annual Meeting of the Society for Molecular Biology
    and Evolution (SMBE), Dublin, Ireland.

    3) Privman E. (speaker), Wurm Y., Riba-Grognuz O., Roux J., Keller
    L. 2012. Looking for adaptation in ant genomics. Annual Meeting of the Swiss Institute of Bioinformatics (SIB),
    Biel/Bienne, Switzerland.

    4) Privman, E. (speaker)* and Penn, O. (speaker)*. 2010. Alignment
    and alignment reliability workshop. The COST Training School – Advances in
    Symbiosis Research, Hebrew University of Jerusalem, Israel.

    5) Barzel A. (speaker)*, Privman
    E.*, Pupko T., Kupiec M. 2008. Gene targeting via homing endonucleases. Annual
    Congress of the European Society of Gene
    and Cell Therapy (ESGCT), Bruges, Belgium.

    6) Privman E. (speaker), Dutheil J., Ninio M., Friedman N., Galtier
    N., Pupko T. 2007. A hybrid distance/Bayesian phylogeny reconstruction method
    with models of rate variation among sites and lineages: application to
    bacterial rRNA. Annual Meeting of the Society
    for Molecular Biology and Evolution
    (SMBE), Halifax, Canada.

    7)
    Privman
    E. (speaker)*, Ninio M.*, Pupko T.,
    Friedman N. 2006. Phylogeny reconstruction: increasing the accuracy of pairwise
    distance estimation using Bayesian inference of evolutionary rates. European Conference of Computational
    Biology (ECCB), Eilat, Israel.

    * These authors
    contributed equally

    Awards and Scholarships:

    2006-2010 Edmond J. Safra Bioinformatics Ph.D.
    Scholarship.

    2009 Prize for excellence in teaching
    from the Faculty of Life Sciences.

    2008 Constantiner Travel Fellowship to
    the Annual Congress of the European Society of Gene and Cell Therapy
    (ESGCT).

    2008 Edmond J. Safra Travel Fellowship
    to the Annual Meeting of the Society for Molecular Biology and Evolution
    (SMBE).

    2007 Anat Krauskopf Travel Fellowship to
    the Annual Meeting of the Society for Molecular Biology and Evolution
    (SMBE).

    2006 Prize for excellence in teaching
    from the Faculty of Life Sciences.

    2004 Best software project award at the
    School of Computer Science. The project
    dealt with gene prediction in bacteria.

    2001 Excellence award from the Dean of
    the Faculty of Exact Sciences

    Reviewed articles for:

    Molecular Biology and Evolution, PLoS Genetics, Genome
    Research, Genome Biology, Nucleic Acids Research, Bioinformatics, Journal of Molecular
    Evolution, Annual Meeting of the Society for Molecular Biology and Evolution
    (SMBE), Intelligent Systems for Molecular Biology (ISMB), European Conference
    of Computational Biology (ECCB), Annual International Conference on Research in
    Computational Molecular Biology (RECOMB), Trends in Microbiology, PLoS One.

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