CURRICULUM VITAE - Irit Gat-Viks
September 2010
A. Personal Data
Irit Gat-Viks, PhD
igatviks@broadinstitute.org
Tel: 617-714-7753
B. Education
October 2008 – present: Postdoctoral fellow
Aviv Regev’s lab, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Research title: Deciphering the genetic and regulatory mechanisms underlying the response
of mammalian cells to pathogens.
EMBO Fellow (2009), HFSP Fellow (2010)
May 2007- August 2008: Postdoctoral fellow
Martin Vingron’s lab, Computational Molecular Biology Department, Max Planck Institute
for Molecular Genetics, Berlin, Germany.
Research title: Histone H3 turnover and epigenetic gene regulation in yeast.
Nov 2001 - Jan 2007: Ph.D.
Advisor: Prof. Ron Shamir, Computer Science, Computational Genomics Laboratory, Tel
Aviv University, Israel.
Thesis title: Biological Regulatory Networks: Modeling and Reconstruction.
Colton Fellow
1999-2001: M.Sc (Summa Cum Laude)
Advisor: Prof. Dan Graur, Life Science, Laboratory of Information Biology & Molecular
Evolution, Tel Aviv University, Israel.
Thesis title: Prediction of amino acid contacts in proteins by using evolutionary and
statistical principles
1998-1999: B.Sc. (Summa Cum Laude)
Computer Science, Tel Aviv University, Israel.
1995-1997: B.Sc. (Magna Cum Laude)
Life Science, Tel Aviv University, Israel.
Studies at the program for the Fostering of Excellence at Tel Aviv University.
C. Honors & Awards
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Human Frontier Science program (HFSP) cross-disciplinary postdoctoral fellowship (2010)
EMBO fellowship (2009)
Colton fellowship for Ph.D, October 2000 - September 2004.
Dean’s Award for Ph.D – Faculty of Computer Science, Tel Aviv University (2001).
Dean’s Award for M.Sc – Faculty of Life Science, Tel Aviv University (2000).
Dean’s Award for B.Sc – Faculty of Computer Science, Tel Aviv University (1999).
Rector’s Scholarship – Tel Aviv University (1998).
Special excellence award, Israel's parliament education committee (1998).
Dean’s Award for B.Sc - Faculty of Life Science, Tel Aviv University (1996,1997,1998).
D. Refereed Publications (* -- co-first author)
1. S Shapira*, I Gat-Viks*, B Shum, A Dricot, M de Grace, PB Gupta, T Hao, SJ Silver, DE
Root, DE Hill, A Regev, N Hacohen (2009). A physical and regulatory map of host-influenza
interactions reveals pathways in H1N1 infection. Cell 139:1255-1267.
2. I Gat-Viks, R Meller, M Kupiec, R Shamir (2009). Understanding gene sequence variation in
the context of transcription regulation in yeast. PLoS Genetics, In Press.
3. AJ Bass, H Watanabe, S Yu, CH Mermel, S Perner, RG Verhaak, SY Kim, L Wardwell, P
Tamayo, I Gat-Viks et al (2009). SOX2 is an amplified lineage-survival oncogene in lung and
esophageal squamous cell carcinomas. Nature Genetics 41:1238-1242.
4. E Szczurek, I Gat-Viks, J Tiuryn and M Vingron (2009). Elucidating regulatory mechanisms
downstream of a signaling pathway using informative experiments. Nature Molecular Systems
Biology 5:287.
5. I Gat-Viks and M Vingron (2009). Evidence for gene-specific rather than transcription ratedependent histone H3 exchange in yeast coding regions. PLoS Computational Biology
5(2):e1000282.
6. M Ziv-Ukelson*, I Gat-Viks*, Y Wexler* and R Shamir (2008). A non-heuristic speedup of the
Sankoff-85 algorithm. Lecture Notes in Bioinformatics 5251, Springer, Berlin.
7. I Ulitsky*, I Gat-Viks* and R Shamir (2008). MetaReg: a platform for modeling, analysis and
visualization of biological systems using large-scale experimental data. Genome Biology 2:
9(1):R1.
8. I Gat-Viks and R Shamir (2007). Refinement and expansion of signaling pathways: the
osmotic response network in yeast. Genome Research 17(3): 358-67.
9. I Gat-Viks, R Shamir, RM Karp and R Sharan (2006). Reconstructing chain functions in
genetic networks. SIAM Journal of Discrete Mathematics 20: 727-740.
10. I Gat-Viks, A Tanay, D Raijman and R Shamir (2005). A probabilistic methodology for
integrating knowledge and experiments on biological networks. Journal of Computational
Biology 13(2): 165-81.
11. I Gat-Viks, A Tanay, D Raijman and R Shamir (2005). Factor graph network models for
biological systems. Proc. RECOMB 2005, Boston, NY pp. 31-47, Lecture Notes in
Bioinformatics 3500, Springer, Berlin.
12. I Gat-Viks, A Tanay and R Shamir (2004). Biological networks involving metabolic pathways
and gene regulation: modeling and inference. The first RECOMB satellite meeting on
regulatory genomics, University of California, San Diego, March 26-27, 2004. E. Eskin, C.
Workman (Eds.): RECOMB 2004 workshop on Regulatory Genomics, LNBI 3318, pp. 98–113,
2005. Springer-Verlag Berlin Heidelberg.
13. I Gat-Viks, A Tanay and R Shamir (2004). Modeling and analysis of heterogeneous regulation
in biological network. Journal of Computational Biology 11(6): 1034-49.
14. I Gat-Viks, R Shamir, RM Karp and R Sharan (2004). Reconstructing chain functions in
genetic networks. Proc. Pacific Symposium on Biocomputing (PSB 04) pp. 498-509.
15. A Tanay*, I Gat-Viks* and R Shamir (2004). A global view of the selection forces in the
evolution of yeast cis-regulation. Genome Research 14: 829-834.
16. I Gat-Viks and Ron Shamir (2003). Chain functions and scoring functions in genetic networks.
Proc. 11th International Conference on Intelligent Systems for Molecular Biology (ISMB 03),
Brisbane, Australia, July 2003. Bioinformatics S19: i108--i117.
17. I Gat-Viks, R Sharan and R Shamir (2003). Scoring clustering solutions by their biological
relevance. Bioinformatics 19: 2381-2389.
E. Invited talks:
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Refinement and expansion of signaling pathways: the osmotic response network in yeast.
ISMB 07, January 2007.
A computational methodology for improving the knowledge on biological systems using
heterogeneous data. Genopole, Evry, France, January 28, 2005.
Modeling and analysis of heterogeneous regulation in biological networks. Weizmann
bioinformatics workshop on Computational Analysis of Biological Networks, June 24 2004.
Reverse engineering of gene regulatory networks. Fourteenth Seminar on Algorithmics and
Combinatorics in Biology, April 2-4, 2003, Lyon, France.
Computational reconstruction of gene networks and regulatory signals. Tel Aviv University
Bioinformatics Symposium 2003, 30 Sept. 2003.
Inference of genetic regulatory networks: problems and algorithms. ESF workshop on
Microarray data: untapped powers and hidden weaknesses, Leuven, Belguim, September 8-9
2003.
Analysis of genetic networks. Dagstuhl seminar on Computational Biology, Schloss
Dagstuhl, Germany, 18 November 2002.