Prof. Tal Pupko:


The Department of Cell Research and Immunology,

George S. Wise Faculty of Life Sciences,

Tel Aviv University, Tel Aviv 69978, Israel

Tel: 972-3-640-7693
Fax: 972-3-642-2046
Contact:


[Research-interests] [Publications] [Lab members] [Collaborations][Computer programs, web servers and supplementary information for some papers][Teaching][Bioinformatics at Tel-Aviv University] [Non academic links]

My research interests are concerned with various fields of Bioinformatics:
Functional genomics: Studying the evolutionary selection forces shaping genes and genomes and the in-silico predictions of these forces.
Molecular evolution and phylogeny: inferring evolutionary relationships and evolutionary dynamics: biological, statistical and computational aspects. Developing probabilistic evolutionary models.
Computational virology and immunology: inference of functional sites in HIV and predicting anti-viral drug resistance sites, epitope binding-site prediction.

Lab members:
Eyal Privman (a PhD student)
Nimrod Rubinstein (a PhD student)
Ofir Cohen (a PhD student)
Osnat Penn (a PhD student)
David Burstein (a PhD student)
Daiana Alaluf (an MSc student)
David Zeevi (an MSc student)

Past lab members:
Itay Mayrose (PhD 2008)
Adi Doron-Faigenboim (PhD 2008)
Adi Stern (PhD 2009)
Tal Peled (MSc 2009)

Computer programs and web servers:
Phylogeny and functional genomics:
1. FASTML (version 2.02) a program for ancestral sequence reconstruction. The new version of the program includes both the dynamic programming and the branch and bound algorithms.
2. RATE4SITE (version 2.01) a program for computing the evolutionary rate at each amino acid
3. The COMBINE program and supplementary information for the "Combining Multiple Sequences" paper
4. Consurf - a web server for the identification of functional regions in proteins with known 3D structure
5. Conseq - a web server for The identification of functionally and structurally important residues in protein sequences
6. Selecton - a web server for the identification of site-specific selection (positive and purifying selection)
7. SEMPHY - a program for maximum-likelihood based phylogenetic tree reconstruction
8. Source code for computing the likelihood of a tree and site-specific rate using a gamma mixture model

Immunology:
8. Pepitope - a web server for epitope mapping using affinity-selected peptides
9. Epitopia - a web server for detecting immunogenic regions in protein structures or sequences
Teaching 2009-2010:
Introduction to bioinformatics (with Dr. Eran Halperin, Dr. Iftach Nachman) Semester A, Sunday 1800-2000
Tools to bioinformatics Semester A, Sunday 1600-1800 or Monday 1200-1400 or Monday 1400-1600
Molecular Evolution (with Dr. Dorothee Huchon) Semester A, Tuesday 1000-1200 and Wednesday 0800-1000

Bioinformatics at Tel-Aviv university:
The Edmond J. Safra Bioinformatics Program at Tel-Aviv University
Tel-Aviv University Bioinformatics Support Unit

Non academic links:
A picture of Nathan Pupko, my son (born 5.2002)
A picture of Emilie Pupko, my daughter (born 10.2003)
A picture of Arielle Pupko, my daughter (born 7.2008)