CURRICULUM VITAE

Personal Information

Name: Itay Mayrose

Address: Beaty Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.

E-mail and homepage: itaymay@gmail.com http://www.zoology.ubc.ca/~mayrose

Languages: Hebrew, English

Education

2008- Post-doctoral fellow at the lab of Prof. Sarah Otto, The Biodiversity Research Centre, University of British Columbia, Canada.

2004-2008 Ph.D. - performed under the supervision of Prof. Tal Pupko, the Department of Cell Research and Immunology, Tel-Aviv University.

· Title of Ph.D. thesis: Probabilistic algorithms for predicting functional regions in protein-coding genes.

· Ph.D. awarded with distinction.

2002-2004 M.Sc. – performed under the supervision of Prof. Dan Graur, Zoology Department, Tel-Aviv University.

§ Title of M.Sc. thesis: Bayesian algorithms for inferring conserved regions in proteins.

§ M.Sc. graduated with summa cum laude.

1997-2001 B.Sc. – the multidisciplinary program in Computer Science and Biology, Tel-Aviv University.

§ B.Sc. was graduated with summa cum laude in Biology and magna cum laude in Computer Science.

Teaching

2002-2007 Teacher assistance in the course Introduction to Bioinformatics given to graduate students in the Life Sciences Faculty, Tel-Aviv University.

2004-2007 Guest lecturer in the course Molecular Evolution given to undergraduate students in the Life Sciences Faculty, Tel-Aviv University.

Prizes and Awards

2008- Killam Postdoctoral Fellowship, University of British Columbia, Canada

2004-2008 A scholarship for outstanding Ph.D. students awarded by the president of Tel-Aviv University

2007 Best poster award, Safra bioinformatics retreat, Sea of Galilea, Israel

2007 The Trotzki Foundation Prize for outstanding graduate students

2007 Travel Award from the Ela Kodesz Institute for Cancer Research

2006 The Anat Krauskopf Fund Travel Award

2007 ISCB Student Travel Award

2005 Award for excellent Ph.D. students for teaching and academic achievements

2005 The Constantiner Institute for Molecular Genetics Travel Scholarship

2005 Katzir-Katchalsky Student Travel Fellowship

2005 ISCB Student Travel Award

2003 The Wolf Foundation Prize for M.Sc. students

2000 The Wolf Foundation Prize for undergraduate students

2000 Award of Excellence for B.Sc students in memory of Rotenberg David

1999 Award of Excellence for B.Sc students in memory of Moshe Avishar

1998-2000 The dean honour list (both Biology and Computer Science), Tel Aviv University

Reviewer

§ Reviewer for the journals Molecular Biology and Evolution, Bioinformatics, BMC Evolutionary Biology, Journal of Molecular Evolution, Protein Engineering Design and Selection, American Naturalist, and Journal of Heredity.

§ Co-reviewer for ECCB 2006 and ISMB 2007 conferences.

Publications

§ Zhan SH, Mayrose I, Barker MS. Low polyploidization rate coupled with high retention rate of individual chromosomes characterizes ferns evolution. In preparation.

§ Mayrose M, Kane N, Mayrose I, Rieseberg L. Increased vigor in invasive and domesticated sunflower correlates with impaired response to biotic and a-biotic stress. In preparation.

§ Mayrose I, Otto SP. A likelihood method for detecting trait-dependent shifts in the rate of molecular evolution. Mol Biol Evol. Under revision.

§ Mayrose I, Barker MS, Otto SP. 2010. Probabilistic models of chromosome number evolution and the inference of polyploidy. Systematic Biology. 59(2):132-144.

§ Stern A, Mayrose I, Shaul S, Gophna U, Pupko T. 2010. On the evolution of thymidine synthesis: a tale of two enzymes and a virus. Systematic Biology. 59(2):212-225.

§ Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PE, Rieseberg LH. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences. U.S.A. 106:13875–13879

§ Rubinstein ND, Mayrose I, Martz E, Pupko T. 2009. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics. 10:287.

§ Rubinstein ND, Mayrose I, Pupko T. 2009. A machine learning approach for predicting B-cell epitopes. Molecular Immunology. 46(5):840-847.

§ Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T. 2008. Computational characterization of B-cell epitopes. Molecular Immunology. 45(12):3477-89.

§ Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Tarnovitski-Freund N, Bublil EM, Ruppin E, Sharan R, Gershoni JM, Martz E, Pupko T. 2007. Pepitope: Inferring epitopes based on affinity-selected peptides. Bioinformatics. 23(23): 3244-3246.

§ Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007. Towards realistic codon models: among site variability and dependency of synonymous and nonsynonymous rates. Bioinformatics (ISMB 2007). 23: i319-i327.

*Selected for Faculty of 1000 Biology.

§ Bublil EM, Tarnovitski N, Mayrose I, Pen O, Roitburd A, Pupko T, Gershoni JM. 2007. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 10: 294-304.

§ Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T. 2007. A graph-based algorithm for epitope mapping using combinatorial phage-display libraries. Nucleic Acid Research. 35: 69-78.

§ Landau M, Mayrose I, Pupko T, Ben-Tal N. 2005. ConSurf 2005: Presenting the evolutionary rate of amino acid sites on protein structures. Nucleic Acid Research. 33: W299-W302.

§ Mayrose I, Fridman N, Pupko T. 2005. A Gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (ECCB 2005). 21: Suppl 2:ii151-ii158.

§ Faigenboim DA, Stern A, Mayrose I, Bacharach E, Pupko T. 2005. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21: 2101-2103.

§ Mayrose I, Mitchell A, Pupko T. 2005. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol. 60: 345-353.

§ Mayrose I, Graur D, Ben-Tal N, Pupko T. 2004. Comparison of site-specific rate-inference methods for protein sequences: Bayesian methods are superior. Mol Biol Evol. 21: 1781-1791.

§ Weiss S, Gottfried I, Mayrose I, Xiang M, Dawson SJ, Avraham KB. 2003. Mislocalization of the POU4F3 transcription factor is a major mechanism for DFNA15 hearing loss. Mol. Cell. Biol. 23: 7957-64.

§ Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. 2002. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics (ISMB 2002). 18 Suppl: S71-S77.

Book Chapters

§ Pupko T, Mayrose I. 2009. Probabilistic methods and rate heterogeneity. Element of Computational Systems Biology, Wiley book series on Bioinformatics: Computational Techniques and Engineering. Lodhi H and Muggleton S. (editors). John Wiley and Sons Inc.

Abstracts

§ Mayrose I, Otto SP. Modeling Trait-Dependent Shifts in the Rate of Molecular Evolution. Evolution 2010, Portland, OR. Oral presentation.

§ Shing ZH, Mayrose I, Otto SP, Rieseberg Loren, Barker MS. Insights into fern evolution from probabilistic phylogenetic modeling of chromosome numbers. Evolution 2010, Portland, OR. Poster presentation.

§ Mayrose M, Kane N, Mayrose I, Rieseberg L. Increased vigor in invasive and domesticated sunflower correlates with impaired response to biotic and a-biotic stress. Evolution 2010, Portland, OR. Poster presentation.

§ Mayrose I, Barker MS, Otto SP. Chromosome number evolution: likelihood models and polyploidy inference. 74th Symposium: Evolution - The Molecular Landscape. Cold Spring Harbor Laboratory, NY. May 2009. Poster presentation.

§ Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. Towards realistic codon models: among site variability and dependency of synonymous and nonsynonymous rates. Intelligent Systems for Molecular Biology (ISMB). Vienna, Austria. July 2007. Oral presentation.

§ Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. European Conference on Computational Biology (ECCB). Eilat, Israel. January 2007. Poster presentation.

§ Mayrose I. Inferring protein-protein interaction sites using combinatorial phage display libraries. Predicting Function from Protein Structure Symposium. Technion, Israel. April 2007. Oral presentation.

§ Mayrose I, Pupko T. Improving among site rate variation models. Annual Meeting for the Society for Molecular Biology and Evolution (SMBE). Tempe, Arizona. May 2006. Oral presentation.

§ Mayrose I, Fridman N, Pupko T. A Gamma mixture model better accounts for among site rate heterogeneity. Intelligent Systems for Molecular Biology (ISMB), Detroit, Michigan, June 2005. Oral presentation.

§ Mayrose I, Pupko T. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. Mathematics of Evolution and Phylogeny Workshop, Paris, France, June 2005. Poster presentation.

Software Development

§ Rate4Site: A program for detecting conserved amino-acid sites. http://www.zoology.ubc.ca/~mayrose/cp/rate4site.html

§ ConSurf: A web server for the identification of functional regions in proteins. http://consurf.tau.ac.il/

§ Pepitope: A web server for epitope mapping using affinity-selected peptides.
http://pepitope.tau.ac.il/

§ ChromEvol: A program for analyzing changes in chromosome-number along a phylogeny. http://www.zoology.ubc.ca/~mayrose/cp/chromEvol/

§ Epitopia: A web server for the detection of immunogenic regions in protein structures or sequences. http://epitopia.tau.ac.il/