Osnat Penn



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:  penn@post.tau.ac.il



Research interests:
Molecular evolution - evolutionary rate shifts in proteins, modelling protein evolution, positive and purifying selection.
Alignment reliability - confidence scores for multiple sequence alignments.
Evolution of viral genes - especially HIV and SIV.
Immunoinformatics - computational epitope mapping.


Computer programs:
GUIDANCE - Web server for estimating alignment confidence scores.
RASER - Software for inferring evolutionary rate shifts.
Pepitope - Web server for epitope mapping.


Teaching:
Spring 2011: Teaching the course Tools in Bioinformatics.
Alignment workshop 2010 (materials , lecture) .
Fall 2009-2010: Teaching the course Tools in Bioinformatics.
Fall 2008-2009: Teaching assistant in the course Introduction to Bioinformatics.
Spring 2007: Teaching the course Biological Sequences Analysis.
Fall 2006-2007: Teaching assistant in the course Introduction to Bioinformatics.
Fall 2005-2006: Teaching assistant in the course Introduction to Bioinformatics.


Publications:
Gelfman S., Burstein D., Penn O., Schwartz S., Pupko T., Ast G. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Research. accepted.

Turner D., Amit S., Chalom S., Penn O., Pupko T., Katchman E., Matus N., Tellio H., Katzir M., Avidor B. Emergence of an HIV-1 cluster harboring the major protease L90M mutation among treatment-naive patients in Tel-Aviv, Israel. HIV Medicine, accepted.

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

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. *Authors contributed equally.

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

Stern A., Mayrose I., Penn O., Shaul S., Gophna U., Pupko T. 2010. An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes. Systematic Biology 59(2): 212-225.

Blanga-Kanfi S., Miranda H., Penn O., Pupko T., DeBry RW., Huchon D. 2009. Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evolutionary Biology 9:71.

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 Computational Biology 4(11): e1000214. *Authors contributed equally.

Mayrose I., Penn O., Erez E., Rubinstein ND., Shlomi T., Tarnovitski Freund N., Bublil E., Rupin E., Sharan R., Gershoni JM., Martz E., Pupko, T. 2007. Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics 23(23):3244-3246.

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

Useful links:
The ConSurf Server - Server for the identification of functional regions in proteins.
The Selecton Server - Server for the identification of site-specific positive selection & purifying selection.
Algorithm summary: Kimura Two Parameters Model


Collaborators
Prof. Dan Graur and Dr. Giddy Landan, University of Houston.
Sahar Gelfman and Prof. Gil Ast, Sackler Medical School, Tel-Aviv University.
Prof. Jonathan M. Gershoni Cell Research and Immunology Department, Faculty of Life Sciences, Tel-Aviv University.
Dr. Dan Turner and Dr. Boaz Avidor, The Crusaid Kobler AIDS Center, Infectious Diseases Unit, Tel Aviv Sourasky Medical Center.

My lab colleagues (past and present): Dr. Itay Mayrose, Dr. Adi Doron-Faigenboim, Dr. Adi Stern, Dr. Eyal Privman, Nimrod Rubinstein, David Burstein, Ofir Cohen, David Zeevi, Haim Ashkenazy, Yaara Oren, Tal Peled, Diana Alaluf.


Some pictures:
"Group photo"
A picture of me starting my Ph.D.