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Ron Shamir

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Ron Shamir
Born(1953-11-29)29 November 1953
Jerusalem, Israel
NationalityIsraeli
Alma materUniversity of California
Known forThe Edmond J. Safra Center for Bioinformatics; the Tel Aviv University B.Sc. program in Bioinformatics; the Expander software;
Scientific career
FieldsBioinformatics
Design and analysis of algorithms
Algorithmic graph theory
InstitutionsTel Aviv University
Blavatnik School of Computer Science
Doctoral advisorRichard M. Karp and Ilan Adler
Doctoral students(students in academia) Haim Kaplan, Itsik Pe’er, Roded Sharan, Irit Gat-Viks, Dekel Tsur, Amos Tanay, Rotem Sorek, Igor Ulitsky, Adi Akavia, Michal Ziv-Ukelson, Mukul Bansal, Reut Shalgi [1]
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 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 highschool championship in shot put.

Shamir started his B.Sc. studies in mathematics and physics at Tel-Aviv University (1973-1975) and completed his degree at the Hebrew University of Jerusalem (1975-1977). He later began M.Sc. studies in operations research at Tel-Aviv University under the supervision of Uri Yechiali, and then joined the PhD program at the IEOR department of UC Berkeley, where he studied in 1981-1984. His PhD thesis was conducted under the supervision of Richard Karp and Ilan Adler.

He is married to Michal Oren-Shamir. They have three sons - Alon, Ittai and Yoav. They live in Rehovot, Israel.

Research

Early Years

Shamir started his research 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.[2] 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.[3]

Algorithmic Graph Theory

In the early 1990s, Shamir turned his focus to algorithmic graph theory. Together with his student at the time Haim Kaplan and Martin Golumbic he studied graph sandwich problems,[4] graph completion problems and a variety of problems related to interval graphs.[5][6] One of his papers on the interval satisfiability problem was later applied to the study of DNA physical mapping;[7] 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.[8] His CAST algorithm, with Zohar Yakhini and Amir Ben-Dor was published in 1999[9] 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[10] with Roded Sharan and the SAMBA algorithm with Amos Tanay and Roded Sharan for biclustering[11] are in broad use.

Shamir broadened his research to include additional aspects of bioinformatics, such as analysis of biological networks,[12][13] genome rearrangements,[14] sequence motif finding,[15][16] and transcriptional regulation.[17][18] Many tools developed in his laboratory are available as a part of the EXPANDER suite[19] 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.

Additional Activities

Shamir was on the founding steering committee of the RECOMB meeting,[20] 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 in 2004-2006. 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.[21] 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"[22] with Pavel A. Pevzner.

Awards and Honors

Selected Publications

  • Ben-Dor, A.; Shamir, R.; Yakhini, Z. (1999), "Clustering gene expression patterns", Journal of Computational Biology - JCB, 6 (3–4): 281–297, doi:10.1089/106652799318274, PMID 10582567.
  • Sharan, R.; Maron-Katz, A.; Shamir, R. (2000), "CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis", Intelligent Systems in Molecular Biology - ISMB, 19 (14): 307–316, doi:10.1093/bioinformatics/btg232.
  • Tanay, A.; Sharan, R.; Shamir, R. (2000), "Discovering statistically significant biclusters in gene expression data", Bioinformatics, 18 (1): S136–S144, doi:10.1093/bioinformatics/18.suppl_1.S136, PMID 12169541.
  • Sharan, R.; Maron-Katz, A.; Shamir, R. (2003), "CLICK and EXPANDER: a system for clustering and visualizing gene expression data", Bioinformatics/computer Applications in the Biosciences -Bioinformatics, 19 (14): 1787–1799, doi:10.1093/bioinformatics/btg232.
  • Ulitsky, Igor; Maron-Katz, Adi; Shavit, Seagull; Sagir, Dorit; Linhart, Chaim; Elkon, Ran; Tanay, Amos; Sharan, Roded; Shiloh, Yosef; Shamir, Ron (2010), "Expander: From expression microarrays to networks and functions", Nature Protocols, 5 (2): 303–22, doi:10.1038/nprot.2009.230, PMID 20134430

References

  1. ^ Ron Shamir at the Mathematics Genealogy Project
  2. ^ Adler, Ilan; Karp, Richard M.; Shamir, Ron (1987), "A simplex variant solving an m × d linear program in O(min(m^2, d^2)) expected number of pivot steps", Journal of Complexity, 3 (4): 372–387, doi:10.1016/0885-064X(87)90007-0
  3. ^ Hochbaum, Dorit S.; Shamir, Ron (1991). "Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem". Operations Research. 39 (4): 648–653. doi:10.1287/opre.39.4.648. ISSN 0030-364X.
  4. ^ Golumbic, Martin Charles; Kaplan, Haim; Shamir, Ron (1995), "Graph Sandwich Problems", Journal of Algorithms, 19 (3): 449–473, doi:10.1006/jagm.1995.1047
  5. ^ Kaplan, Haim; Shamir, Ron (1996), "Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques", SIAM Journal on Computing, 25 (3): 540–561, doi:10.1137/S0097539793258143
  6. ^ Kaplan, Haim; Shamir, Ron; Tarjan, Robert E. (1999), "Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval Graphs", SIAM Journal on Computing, 28 (5): 1906–1922, doi:10.1137/S0097539796303044
  7. ^ Golumbic, M.C.; Kaplan, H.; Shamir, R. (1994), "On the Complexity of DNA Physical Mapping", Advances in Applied Mathematics, 15 (3): 251–261, doi:10.1006/aama.1994.1009
  8. ^ Hartuv, E.; Shamir, R. (2000), "A clustering algorithm based on graph connectivity", Information Processing Letters, 76 (4–6): 175–181, doi:10.1016/S0020-0190(00)00142-3
  9. ^ Ben-Dor, Amir; Shamir, Ron; Yakhini, Zohar (1999), "Clustering Gene Expression Patterns", Journal of Computational Biology, 6 (3–4): 281–97, doi:10.1089/106652799318274, PMID 10582567
  10. ^ Sharan, R.; Shamir, R. (2000), "CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis", Proceedings ISMB ’00, 8: 307–316C
  11. ^ Tanay, A.; Sharan, R.; Shamir, R. (2000), "Discovering statistically significant biclusters in gene expression data", Bioinformatics, 18 (1): S136–S144, doi:10.1093/bioinformatics/18.suppl_1.S136, PMID 12169541
  12. ^ Ulitsky, I.; Shamir, R. (2007), "Identification of functional modules using network topology and high-throughput data", BMC Systems Biology, 1 (8), doi:10.1186/1752-0509-1-8{{citation}}: CS1 maint: unflagged free DOI (link)
  13. ^ Mueller, F.J.; Williams, R.; Kostka, D.; Laurent, L.; Ulitsky, I.; Lu, C.; Rao, M.S.; Shamir, R.; Schwartz, P.H.; Schmidt, N.O.; Loring, J.F. (2008), "Regulatory networks define phenotypic classes of human stem cell lines", Nature, 455: 401–405, doi:10.1038/nature07213
  14. ^ Kaplan, H.; Shamir, R.; Tarjan, R.E. (1999), "A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals", SIAM Journal of Computing, 29 (3): 880–892, doi:10.1137/s0097539798334207
  15. ^ Elkon, R.; Linhart, C.; Sharan, R.; Shamir, R.; Shiloh, Y. (2003), "Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells", Genome Research, 13 (5): 773–780, doi:10.1101/gr.947203
  16. ^ Linhart, C.; Halperin, Y.; Shamir, R. (2008), "Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets", Genome Research, 18 (7): 1180–1189, doi:10.1101/gr.076117.108
  17. ^ Tanay, A.; Regev, A.; Shamir, R. (2005), "Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast", Proceedings of the National Academy of Sciences USA, 122 (20): 7203–7208
  18. ^ Belle, A.; Tanay, A.; Bitincka, L.; Shamir, R.; O'Shea, E.K. (2006), "Quantification of protein half-lives in the budding yeast proteome", Proceedings of the National Academy of Sciences USA, 103 (35): 13004–9, doi:10.1073/pnas.0605420103, PMC 1550773, PMID 16916930
  19. ^ Ulitsky, Igor; Maron-Katz, Adi; Shavit, Seagull; Sagir, Dorit; Linhart, Chaim; Elkon, Ran; Tanay, Amos; Sharan, Roded; Shiloh, Yosef; Shamir, Ron (2010), "Expander: From expression microarrays to networks and functions", Nature Protocols, 5 (2): 303–22, doi:10.1038/nprot.2009.230, PMID 20134430
  20. ^ RECOMB steering committee, including former member Ron Shamir. Accessed January 12, 2014
  21. ^ http://safrabio.cs.tau.ac.il/steering_committee.htm Members of the steering committee of the Edmond J. Safra Center for Bioinformatics
  22. ^ Pevzner, Pavel; Shamir, Ron (2011), Bioinformatics for biologists, Cambridge University Press, ISBN 9781107648876
  23. ^ International Society for Computational Biology fellows
  24. ^ ACM fellow profile, Association for Computing Machinery
  25. ^ RECOMB award winners. Accessed January 12, 2014
  26. ^ Landau Prize Winners for 2010 (Hebrew). Accessed January 12, 2014
  27. ^ The Raymond and Beverly Sackler Chair in Bioinformatics endowed chairs. Accessed January 12, 2014
  28. ^ Intelligent System for Molecular Biology (ISMB) keynote speakers, ISMB. Accessed January 12, 2014.

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