Itay Mayrose Home Page:
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Welcome!
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Mayrose I, Barker MS, Otto SP. 2009.
Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy. Systematic Biology.
Rubinstein ND, Mayrose I, Martz E, Pupko T. 2009.
Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics. 10:287.
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. Nature's Research Highlight IU Press Release
Stern A, Mayrose I, Shaul S, Gophna U, Pupko T.
On the evolution of thymidine synthesis: a tale of two enzymes and a virus. Systematic Biology (accepted pending revisions).
Pupko T and Mayrose I. 2009.
Probabilistic methods and rate heterogeneity.
In Lodhi H and Muggleton S. (editors). Element of Computational Systems Biology, Wiley book series on Bioinformatics: Computational Techniques and Engineering.
John Wiley and Sons Inc.
Rubinstein ND, Mayrose I, Pupko T. 2009.
A machine learning approach for predicting B-cell epitopes. Molecular Immunology. 46(5):840-847.
[pdf] [abs]
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.
[pdf]
[abs]
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.
[pdf]
[abs]
Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007.
Towards realistic codon models: among site variability and dependency of
synonymous and nonsynonymous rates. ECCB/ISMB 2007. Bioinformatics. 23:i319-i327.
[pdf]
[abs]. Selected for Faculty of 1000.
Bublil EM, Tarnovitski N, Mayrose I, Penn O, Roitburd A, Pupko T, Gershoni JM. 2007.
Stepwise prediction of conformational discontinuous B-cell epitopes using the
Mapitope algorithm. Proteins. 10;68(1):294-304 [pdf]
[abs]
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(1): 69-78.
[pdf] [abs]
Mayrose I, Fridman N, Pupko T. 2005.
A Gamma mixture model better accounts for among site rate heterogeneity. ECCB 2005. Bioinformatics. 21: Suppl 2:ii151-ii158.
[pdf][abs] 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. 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(9): 2101-2103. [pdf] [abs] Mayrose I, Mitchell A, Pupko T. 2005.
Site-specific evolutionary rate inference: taking phylogenetic uncertainty into
account. J Mol Evol. 60(3): 345-353. [pdf]
[abs]
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. [pdf]
[abs]
Probabilistic algorithms for predicting functional regions in protein-coding genes.
[pdf]
Towards realistic codon models: among site variability and dependency of synonymous and nonsynonymous rates (Oral presentation).
15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). Vienna, austria. July 2007.
[ppt]
Inferring protein-protein interaction sites using combinatorial phage display libraries (Oral presentation).
Prediction function from protein structure symposium. Technion, Israel. April 2007.
Epitope mapping using combinatorial phage-display libraries: a graph-based
algorithm (Poster presentation). Conference on Computational Biology (ECCB).
Eilat, Israel. January 2007
Improving Among Site Rate Variation Models (Oral presentation). Annual meeting
for the Society for Molecular Biology and Evolution. Tempe, Arizona. May 2006.
A Gamma Mixture Model Better Accounts for Among Site Rate Heterogeneity (Oral
presentation). 13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, Michigan.
June 2005.
McRate: Site-Specific Evolutionary Rate Inference over the Whole Tree Space
(Poster presentation). Mathematics of Evolution and Phylogeny Conference,
Paris, France. June 2005.
[jpg]
Site-specific evolutionary rate inference: a simulation study (Poster
presentation). The 6th Israeli Bioinformatics Symposium. Haifa, Israel. May
2003.[jpg]
My research interests:
I am interested in studying the evolutionary selection forces that shaped genes and genomes,
and in devising methods that would help to transform the abundant genome data into meaningful biological knowledge.
In particular, I am interested in the use of probabilistic models of sequence evolution as a means to infer functional regions in protein-coding regions.
I am also interested in understanding the impact of chromosomal changes on speciation and diversification, especially in plants evolution.
I am currently devising probabilistic models of chromosome number evolution to infer the
number and location of polyploidy and dysploidy events along a phylogeny, and the impact of these events on diversification rates.
In the past I was also involved in the newly developed field of Immunoinformatics.
I developed computational methodologies for epitope mapping using combinatorial libraries,
and took part in devising methods for the characterization and prediction of B-cell epitopes.
CURRICULUM VITAE
Past and current mentors, colleagues, and lab members:
Tal Pupko,
Dan Graur,
Adi Doron,
Adi Stern,
David Burstein,
Eyal Privman,
Ofir Cohen,
Nimrod Rubinstein,
Osnat Penn,
Tal Peled,
Tal Dagan,
Einat Hazkani-Covo,
Amir Mitchell
Computer programs:
Rate4Site
McRate
ConSurf
Pepitope
chromEvol
Weiss S, Gottfried I, Mayrose I, Khare SL, Xiang M, Dawson SJ, Avraham KB. 2003.
The DFNA15 deafness mutation affects POU4F3 protein stability, localization,
and transcriptional activity. Mol Cell Biol. 23(22):7957-64.
[pdf]
[abs]
Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. 2002. Rate4Site: an
algorithmic tool for the identification of functional regions on proteins by
surface mapping of Evolutionary Determinants within their Homologues.
Bioinformatics. 18 Suppl: S71-S77.
[pdf] [abs]
PhD thesis:
Abstracts and Presentations:
![[jpg]](posters/mcRate.jpg){kind=link}
![[jpg]](posters/bayesML.jpg){kind=link}