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 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 from 1981 to 1984. His PhD thesis was conducted under the supervision of Richard Karp and Ilan Adler.
Research
Early years
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]
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's current research focuses on integrative analysis of heterogeneous high-throughput bio-medical data, genome rearrangements in cancer, and gene regulation.
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.
^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
^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, CiteSeerX10.1.1.34.9275, doi:10.1137/S0097539793258143
^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, CiteSeerX10.1.1.12.2803, doi:10.1137/S0097539796303044
^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
^Ulitsky, I.; Shamir, R. (2007), "Identification of functional modules using network topology and high-throughput data", BMC Systems Biology, 1 (8): 8, doi:10.1186/1752-0509-1-8, PMC1839897, PMID17408515
^Kaplan, H.; Shamir, R.; Tarjan, R.E. (1999), "A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals", SIAM Journal on Computing, 29 (3): 880–892, CiteSeerX10.1.1.43.5245, doi:10.1137/s0097539798334207
^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, PMC430898, PMID12727897
^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, PMC2493407, PMID18411406
^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, 102 (20): 7203–7208, Bibcode:2005PNAS..102.7203T, doi:10.1073/pnas.0502521102, PMC1091753, PMID15883364
^Sharan, Roded; Ideker, Trey; Kelley, Brian; Shamir, Ron; Karp, Richard M. (July 2005). "Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data". Journal of Computational Biology. 12 (6): 835–846. CiteSeerX10.1.1.139.231. doi:10.1089/cmb.2005.12.835. ISSN1066-5277. PMID16108720.
