Ron Shamir | |
|---|---|
| רון שמיר | |
 | |
| Born | (1953-11-29)29 November 1953 (age 71) |
| Nationality | Israeli |
| Alma mater | Hebrew University of Jerusalem (BSc) Tel-Aviv University (MSc) University of California, Berkeley (PhD) |
| Awards |
|
| Scientific career | |
| Fields | Bioinformatics Design and analysis of algorithms Algorithmicgraph theory |
| Institutions | Tel Aviv University Blavatnik School of Computer Science |
| Doctoral advisor | Richard M. Karp Ilan Adler[2] |
| Website | www |
Ron Shamir (Hebrew: רון שמיר; born 29 November 1953) is an Israeli professor ofcomputer science known for his work ingraph theory and incomputational biology. He holds the Raymond and Beverly Sackler Chair in Bioinformatics, and is the founder and former head of the Edmond J. Safra Center for Bioinformatics atTel Aviv University.
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Ron Shamir was born in Jerusalem, Israel, in 1953, the eldest son of Varda and Raphael Shamir. His father's Sepharadic family has lived in the old city of Jerusalem formore than 400 years. His mother's parents were pioneers who came from Russia to Israel in theThird Aliyah in the early 1920s. He has two younger sisters, Daphna and Gadit.
Shamir studied inGymnasia Rehavia,Jerusalem, for 12 years. In high school, he was active in the scouts and in athletics; among other accomplishments, he won the Jerusalem high school championship inshot put.
Shamir started his B.Sc. studies in mathematics and physics atTel-Aviv University (1973–1975) and completed his degree at theHebrew University of Jerusalem (1975–1977). He later began M.Sc. studies inoperations research at Tel-Aviv University under the supervision of Uri Yechiali, and then joined the PhD program at the IEOR department ofUC Berkeley, where he studied from 1981 to 1984. His PhD thesis was conducted under the supervision ofRichard Karp and Ilan Adler.
Shamir started his research[3][4][5][6] career in operations research, studying optimization problems related tolinear programming and to thesimplex method. His PhD thesis with Adler and Karp dealt with average case analysis of theSimplex 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 andNimrod Megiddo. He later worked withDorit S. Hochbaum on efficient algorithms for structured optimization problems.[8]
In the early 1990s, Shamir turned his focus to algorithmicgraph theory. Together with his student, Haim Kaplan, andMartin Golumbic, he studied graph sandwich problems,[9] graph completion problems and a variety of problems related tointerval graphs.[10][11]One of his papers on the interval satisfiability problem was later applied to the study ofDNA physical mapping;[12] this marked his introduction to the field ofcomputational biology.
Shamir used his expertise in graph theory to developclustering algorithms for analyzinggene expression problems. His first paper in this area, with Erez Hartuv, introduced theHCS 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 forbiclustering[16] are in broad use.
Shamir broadened his research to include additional aspects of bioinformatics, such as analysis ofbiological networks,[17][18]genome rearrangements,[19]sequence motif finding,[20][21] andtranscriptional 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'scomputational biology group in cooperation with the group of Yosef Shiloh, anIsrael Prize recipient for his research in systems biology, and the group ofKaren Avraham, a leading researcher of humandeafness, all fromTel 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] withPavel A. Pevzner.
Students
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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 areHaim 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,Yaron Orenstein,Adi Maron-Katz andLianrong Pu.
Shamir is married to Michal Oren-Shamir.[when?] They have three sons: Alon, Ittai and Yoav. They live inRehovot, Israel.[citation needed]
