Adi Doron-Faigenboim





I am now a post-doctoral fellow in the lab of
Dr. Uri Gophna,
in the Department of Molecular Microbiology and Biotechnology ,
Tel Aviv University

Tel: 972-3-6409245
e-mail:  doronadi@post.tau.ac.il



My Research Interests:
Molecular sequence evolution, in particular:
The development of codon-based evolutionary models.
Inference of positive and purifying selection via computation of the Ka/Ks ratio.


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 Stern (PhD 2009)
Tal Peled (MSc 2009)

Links:
Selecton Server - a server for the identification of site-specific selection (positive and purifying selection)
Consurf Server - a server for the identification of functional regions in proteins

Algorithm Summaries:
Neighbour Joining Algorithm (Saitou and Nei)
Jukes and Cantor one parameter model
F81 (Felsenstein 1981) model
Best Branch Lengths using Expectation Maximization (EM-BBL)

Converting Empirical Amino-Acid Replacement Matrices into Codon-Based Substitution Matrices

Teaching:
Fall 2007-2008: Introduction to bioinformatics
Fall 2006-2007: Introduction to bioinformatics
Fall 2005-2006: Introduction to bioinformatics


Publications:


Refereed journals:

5. Lev-Maor, G., Goren, A., Sela, A., Kim, E., Keren, H., Doron-Faigenboim, A., Leibman-Barak, S., Pupko, T., and Ast, G. 2007. The "alternative" choice of constitutive exons through evolution. Plos Genetics. 3(11):e203. [pdf] [abs]

4. Mayrose, I.*, Doron-Faigenboim, A.*, Bacharach, E., and Pupko, T. 2007. Towards realistic codon models: among site variability and dependency of synonymous and nonsynonymous rates. Bioinformatics. 23:i319-i327. *Authors contributed equally. [pdf] [abs]

3. Stern, A.*, Doron-Faigenboim, A.*, Bacharach, E., and Pupko, T. 2007. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Research. 35:W506-W511. *Authors contributed equally. [pdf] [abs]

2. Doron-Faigenboim, A., and Pupko, T. 2007. A combined empirical and mechanistic codon model. Mol. Biol. Evol. 24(2):388-97. [pdf] [abs]

1. Doron-Faigenboim, A., Stern, A., Mayrose, I., Bacharach, E., and Pupko, T. 2005. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9): 2101-2103. [pdf] [abs]


Book chapter:

1. Pupko, T., Doron-Faigenboim, A., Liberles, DA., and Cannarozzi, GM. 2007. Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences. In Liberles DA (Editor). Ancestral sequence reconsruction. Oxford University Press.