Ron Shamir

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Ron Shamir
Tel-Aviv University
Hebrew University of Jerusalem
University of California
Known forThe Edmond J. Safra Center for Bioinformatics
Tel Aviv University B.Sc. program in Bioinformatics
Expander software[citation needed]
Awards
Scientific career
Fields
Design and analysis of algorithms
Algorithmic graph theory
InstitutionsTel Aviv University
Blavatnik School of Computer Science
Doctoral advisorRichard M. Karp
Ilan Adler[2]
Websitewww.cs.tau.ac.il/~rshamir/

Ron Shamir (

Hebrew: רון שמיר; born 29 November 1953) is an Israeli professor of computer science known for his work in graph theory and in computational 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 at Tel Aviv University
.

Biography

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 for over 400 years. His mother's parents were pioneers who came from Russia to Israel in the Third Aliyah in the early 1920s. He has two younger sisters, Daphna and Gadit.

Shamir studied in

Gymnasia 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 in shot put
.

Shamir started his B.Sc. studies in mathematics and physics at

Richard Karp
and Ilan Adler.

Research

Early years

Shamir started his research

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]

Algorithmic Graph Theory

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
.

Bioinformatics

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

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
.

Additional activities

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, Yaron Orenstein and Lianrong Pu.

Awards and honors

Personal life

Shamir is married to Michal Oren-Shamir.[when?] They have three sons: Alon, Ittai and Yoav. They live in Rehovot, Israel.[citation needed]

References

  1. ^ a b Anon (2017). "ISCB Fellows". iscb.org. International Society for Computational Biology. Archived from the original on 2017-03-20.
  2. ^ Ron Shamir at the Mathematics Genealogy Project
  3. PMID 10582567
  4. PMID 14512350
    .
  5. PMID 14512350
  6. ^
    S2CID 3504270
  7. doi:10.1016/0885-064X(87)90007-0
  8. ISSN 0030-364X
    .
  9. doi:10.1006/jagm.1995.1047
  10. doi:10.1137/S0097539793258143
  11. doi:10.1137/S0097539796303044
  12. doi:10.1006/aama.1994.1009
  13. doi:10.1016/S0020-0190(00)00142-3
  14. PMID 10582567
  15. PMID 10977092
  16. PMID 12169541
  17. PMID 17408515
  18. PMID 18724358
  19. doi:10.1137/s0097539798334207
  20. PMID 12727897
  21. PMID 18411406
  22. PMID 15883364
  23. PMID 16916930
  24. PMID 21097778
    .
  25. ^ RECOMB steering committee, including former member Ron Shamir. Accessed January 12, 2014
  26. ^ http://safrabio.cs.tau.ac.il/steering_committee.htm Members of the steering committee of the Edmond J. Safra Center for Bioinformatics
  27. ISBN 9781107648876
  28. PMID 35758791
    . Retrieved 2023-06-04.
  29. PMID 16108720
    .
  30. ^ ACM fellow profile, Association for Computing Machinery
  31. ^ RECOMB award winners. Accessed January 12, 2014
  32. ^ Landau Prize Winners for 2010 Archived 2011-10-08 at the Wayback Machine (Hebrew). Accessed January 12, 2014
  33. ^ The Raymond and Beverly Sackler Chair in Bioinformatics endowed chairs. Accessed January 12, 2014
  34. ^ Intelligent System for Molecular Biology (ISMB) keynote speakers, ISMB. Accessed January 12, 2014.
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