Algorithms in Computational Genomics at Tau (ACGT), Tel Aviv, Israel

Description of organization


Tel Aviv University (TAU) is the largest research university in Israel, containing the broadest spectrum of research disciplines in the country. It has a medical school to which the leading research hospitals in Israel are affiliated, strong life science and engineering faculties and a leading computer science school, ranked 28 worldwide in the 2011 Shanghai ranking. It has a thriving bioinformatics community that integrates research and education activities across campus, spanning computer science, medicine, life sciences, statistics, physics and more. The Edmond J. Safra Bioinformatics Program, now in its seventh year, is the uniting platform for the community, providing research infrastructure and fellowships to graduate and post graduate students. Prof. Ron Shamir leads the Computational Genomics group at the Blavatnik School of Computer Science at TAU. He is the head of the Edmond J. Safra Bioinformatics Program at TAU and holds the Raymond and Beverly Sackler Chair in Bioinformatics.


Previous experience

Prof. Shamir received a BSc in Mathematics and Physics from the Hebrew University in 1977, and a PhD in Operations Research from UC Berkeley in 1984. He is on the faculty of TAU since 1987. He has published over 220 scientific works, including 15 books and edited volumes, and supervised 45 graduate students to date. His most recent book, co-edited with Prof. Pavel Pevzner, is the undergraduate textbook "Bioinformatics for Biologists" (Cambridge University Press). He is on the editorial board of eleven scientific journals and series, and was a founding member of the RECOMB Conference series steering committee for thirteen years. He co-founded the Israeli Society of Bioinformatics and Computational Biology, and was society president in 2004-2006. He is a recipient of the 2011 Landau Prize in Bioinformatics. Shamir participated in several EU projects, including APO-SYS, TRIREME, GENEPARK.


Profile of staff members

Prof. Shamir's group focuses on developing novel algorithmic methods in Bioinformatics and Systems Biology. The group's research interests include gene expression analysis, modeling and dissection of molecular networks, gene regulation and cancer genomics. Methods and software tools developed by Shamir's group are in use by numerous laboratories around the world. Prof. Shamir will develop methods for large scale integrated analysis of disease related omics data, combining modeling and machine learning techniques for prognostic and diagnostic dissection of patient data.



Algorithms in Computational Genomics at Tau


Five recent publications relevant to the project

M. Ozery-Flato, C. Linhart, L. Trakhtenbrot , S. Izraeli, R. Shamir. "Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy". Genome Biology , 29;12(6):R61 (2011).


A. Paz, Z. Brownstein, Y. Ber, S. Bialik, E. David, D. Sagir, I. Ulitsky, R. Elkon, A. Kimchi, K. B. Avraham, Y. Shiloh, R. Shamir Spike: A database of highly curated human signaling pathways" Nucleic Acids Research doi: 10.1093/nar/gkq1167 (2011).


G. Karlebach, R. Shamir. "Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case". BMC Systems Biology 4:15 (2010).


I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh, R. Shamir. "Expander: From microarrays to networks and functions". Nature Protocols 5, 303–322 (2010).


F.-J. Mueller, R. Williams, D. Kostka, L. Laurent, I. Ulitsky, C. Lu, M. S. Rao, R. Shamir, P. H. Schwartz, N. O. Schmidt, J. F. Loring. "Regulatory networks define phenotypic classes of human stem cell lines". Nature 455, 401–6 (2008).