Nimrod Rubinstein

I am a Ph.D. student at The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel , under the supervision of Prof. Tal Pupko. Tel: 972-3-640-9245 Fax: 972-3-642-2046 Email: rubi@post.tau.ac.il

Overview:

My Ph.D. is now kindly funded by the Edmond J. Safra Bioinformatics Program.

The research of Tal Pupko's lab is concerned with various fields of Bioinformatics. Among those, my Research Interests are:

Molecular evolution:

· Selection on synonymous substitutions.

· Evolutionary rate shifts.

Computational immunology:

· Antibody-antigen interactions and the basis of immune recognition.

· Computational approaches to epitope mapping.

These Useful Links illustratethe kind of work we do in the lab:

· Consurf: A server for the Identification of Functional Regions in Proteins

· Conseq: A server for the identification of functionally and structurally important residues in protein sequences

· Selecton: A server for the identification of site-specific positive selection & purifying selection

· Pepitope: A server for epitope mapping using affinity selected peptides

· Epitopia: A server for detection of immunogenic regions in protein structures or sequences

· Principal Components Analysis (PCA) scribe

I am also involved in Teaching of undergraduate courses:

· Fall 2009-2010: Teacher: Tools in Bioinformatics (TAU)

· Falls 2007-2008, 2008-2009: T.A.: Introduction to Bioinformatics (TAU)

· Falls 2007-2008, 2008-2009: T.A.: Molecular Evolution (MTA)

· Springs 2007, 2008: Teacher: Biological Sequences Analysis (MTA)

· Falls 2005-2006, 2006-2007: T.A.: Molecular Evolution (TAU)

These are mypastand present Lab Colleagues:

Adi Doron, Adi Stern, Daiana Alaluf , David Burstein, David Zeevi, Itay Mayrose, Ofir Cohen, Osnat Penn, Tal Peled

So farI have contributed to these Publications:

Rubinstein ND, Zeevi D, Oren Y, Segal G, Pupko T. 2011. The operonic location of auto-trnascriptional repressors is highly conserved in bacteria. Mol. Biol. evol. Accepted (minor revisions).

Rubinstein ND, Doron-Faigenboim A, Mayrose I, Pupko T. 2011. Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection. Mol. Biol. evol. Accepted.

Rubinstein ND , Mayrose I, Martz E, Pupko T. 2009. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics. Sep 14;10:287.

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

Penn O, Stern A, Rubinstein ND, Dutheil J, Bacharach E, Galtier N, Pupko T. 2008. Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol. Nov;4(11):e1000214.

Cohen O, Rubinstein ND, Stern A, Gophna U, Pupko T. 2008. A Bayesian framework to analyze phyletic patterns. Proc. R. Soc. Lond., B. 363:3903-3911.

Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T. 2008. Computational characterization of B-cell epitopes. Mol Immunol. 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):3244-6.

Bublil EM, Tarnovitski N, Mayrose I, Pen O, Rubinstein ND, Roitburd A, Pupko T, Gershoni JM. 2007. Stepwise prediction of conformational discontinuous B-cell epitopes using the mapitope algorithm. Proteins 68(1):293-304.

Mayrose I, Shlomi T, Rubinstein ND, Gershoni J, Ruppin R, Sharan R, Pupko T 2007. Epitope mapping using combinatorial phage-display libraries: A graph-based algorithm. Nucleic Acids Res. 35(1):69-78.