Ron Shamir

Shamir started his research[3][4][5][6] career in operations research, studying optimization problems related to linear programming and to the simplex method. His PhD thesis with Adler and Karp dealt with average case analysis of the Simplex Method, and showed that a certain Simplex variant was quadratic under a simple input data model.[7] Similar results were given at the same time by Michael Todd and by Adler and Nimrod Megiddo. He later worked with Dorit S. Hochbaum on efficient algorithms for structured optimization problems.[8]

In the early 1990s, Shamir turned his focus to algorithmic graph theory. Together with his student, Haim Kaplan, and Martin Golumbic, he studied graph sandwich problems,[9] graph completion problems and a variety of problems related to interval graphs.[10][11] One of his papers on the interval satisfiability problem was later applied to the study of DNA physical mapping;[12] this marked his introduction to the field of computational biology.

Shamir used his expertise in graph theory to develop clustering algorithms for analyzing gene expression problems. His first paper in this area, with Erez Hartuv, introduced the HCS clustering algorithm.[13] His CAST algorithm, with Zohar Yakhini and Amir Ben-Dor was published in 1999[14] and drew a lot of attention from the bioinformatics community; the techniques described in the paper became popular for analyzing genomic data. The CLICK clustering algorithm[15] with Roded Sharan and the SAMBA algorithm with Amos Tanay and Roded Sharan for biclustering[16] are in broad use.

Shamir broadened his research to include additional aspects of bioinformatics, such as analysis of biological networks,[17][18] genome rearrangements,[19] sequence motif finding,[20][21] and transcriptional regulation.[22][23] Many tools developed in his laboratory are available as a part of the EXPANDER suite,[6] which provides an integrated environment for analyzing high-throughput biological data.

Shamir's current research focuses on integrative analysis of heterogeneous high-throughput bio-medical data, genome rearrangements in cancer, and gene regulation.

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated interactions for particular human pathways.[24] SPIKE was developed by Shamir's computational biology group in cooperation with the group of Yosef Shiloh, an Israel Prize recipient for his research in systems biology, and the group of Karen Avraham, a leading researcher of human deafness, all from Tel Aviv University.

Shamir was on the founding steering committee of the RECOMB meeting,[25] the premier theoretical conference in bioinformatics, and served on it for thirteen years. He co-founded the Israeli Society of Bioinformatics and Computational Biology, and was society president from 2004 to 2006. He is the head of the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University and holds the Raymond and Beverly Sackler Chair in Bioinformatics.[26] Shamir also devotes time to bioinformatics education. He developed extensive lecture notes which are in broad use on Computational Genomics (Algorithms for Molecular Biology) and on Analysis of Gene Expression, DNA Chips and Gene Networks. He established the joint Life Sciences / Computer Science undergraduate degree program in bioinformatics at Tel Aviv University; he teaches the program's core courses and has supervised many M.Sc. and Ph.D. students. He also co-edited the book "Bioinformatics for Biologists"[27] with Pavel A. Pevzner.

Students

Shamir has mentored more than 80 graduate students and postdocs, many of whom developed impressive careers in academia and the industry. Among his students in academia are Haim Kaplan, Dekel Tsur, Dalit Naor, Itsik Pe'er, Roded Sharan, Amos Tanay, Adi Akavia, Reut Shalgi, Rani Elkon, Rotem Sorek, Irit Gat-Viks, Michal Ziv-Ukelson, Igor Ulitsky, Mukul Bansal, Meirav Zehavi and Yaron Orenstein.