Ron Shamir

Israeli professor of computer science (born 1953)

Ron Shamir

רון שמיר
Born|  (1953-11-29) 29 November 1953 (age 71)

Jerusalem, Israel

Nationality| Israeli
Alma mater| Hebrew University of Jerusalem (BSc)
Tel-Aviv University (MSc)
University of California, Berkeley (PhD)
Awards|

* Michael Landau Prize in Bioinformatics (2011)
* ISCB Fellow (2012)[1]
* ACM Fellow (2012)

Scientific career
Fields| Bioinformatics
Design and analysis of algorithms
Algorithmic graph theory
Institutions| Tel Aviv University
Blavatnik School of Computer Science
Doctoral advisor| Richard M. Karp
Ilan Adler[2]
Website| www.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

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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 for more than 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

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### Early years

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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

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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

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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

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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

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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

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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 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, Adi Maron-Katz and Lianrong Pu.

## Awards and honors

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* Accomplishments by a Senior Scientist Award, the International Society for Computational Biology[28] (2022)
* Kadar Family Prize for outstanding research, Tel Aviv University (2017)
* RECOMB "Test of Time Award" for the 2004 paper ""Identification of protein complexes"[29] (2016)
* Elected ISCB Fellow by the International Society for Computational Biology[1] (2012)
* Elected ACM Fellow by the Association for Computing Machinery[30] (2012)
* RECOMB "Test of Time Award" for his 1999 paper "Clustering gene expression patterns"[31] (2011)
* The Michael Landau National Prize in the Sciences in Bioinformatics[32] (2010)
* The Raymond and Beverly Sackler Chair in Bioinformatics, Tel Aviv University[33] (2003)
* ISMB Best Paper Award for his paper "Spectrum Alignment"[34] (2000)
* Alon Fellowship from the Israel Academy of Sciences and Humanities (1987)

## Personal life

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

## References

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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. ^ Ben-Dor, A.; Shamir, R.; Yakhini, Z. (1999), "Clustering gene expression patterns", Journal of Computational Biology, 6 (3–4): 281–297, CiteSeerX 10.1.1.34.5341, doi:10.1089/106652799318274, PMID 105825673–4&rft.pages=281-297&rft.date=1999&rft_id=https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.34.5341#id-name=CiteSeerX&rft_id=info:pmid/10582567&rft_id=info:doi/10.1089/106652799318274&rft.aulast=Ben-Dor&rft.aufirst=A.&rft.au=Shamir,+R.&rft.au=Yakhini,+Z.&rfr_id=info:sid/en.wikipedia.org:Ron+Shamir" class="Z3988">
4. ^ Sharan, R.; Maron-Katz, A.; Shamir, R. (2000), "CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis", Intelligent Systems in Molecular Biology, 19 (14): 307–316, CiteSeerX 10.1.1.126.8500, doi:10.1093/bioinformatics/btg232, PMID 14512350.
* 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
5. ^ Sharan, R.; Maron-Katz, A.; Shamir, R. (2003), "CLICK and EXPANDER: a system for clustering and visualizing gene expression data", Bioinformatics, 19 (14): 1787–1799, CiteSeerX 10.1.1.126.8500, doi:10.1093/bioinformatics/btg232, PMID 14512350
6. ^ a b 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, S2CID 3504270
7. ^ 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
8. ^ 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.
9. ^ Golumbic, Martin Charles; Kaplan, Haim; Shamir, Ron (1995), "Graph Sandwich Problems", Journal of Algorithms, 19 (3): 449–473, CiteSeerX 10.1.1.12.8158, doi:10.1006/jagm.1995.1047
10. ^ 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, CiteSeerX 10.1.1.34.9275, doi:10.1137/S0097539793258143
11. ^ 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, CiteSeerX 10.1.1.12.2803, doi:10.1137/S0097539796303044
12. ^ 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
13. ^ Hartuv, E.; Shamir, R. (2000), "A clustering algorithm based on graph connectivity", Information Processing Letters, 76 (4–6): 175–181, CiteSeerX 10.1.1.17.1450, doi:10.1016/S0020-0190(00)00142-34–6&rft.pages=175-181&rft.date=2000&rft_id=https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.17.1450#id-name=CiteSeerX&rft_id=info:doi/10.1016/S0020-0190(00)00142-3&rft.aulast=Hartuv&rft.aufirst=E.&rft.au=Shamir,+R.&rfr_id=info:sid/en.wikipedia.org:Ron+Shamir" class="Z3988">
14. ^ Ben-Dor, Amir; Shamir, Ron; Yakhini, Zohar (1999), "Clustering Gene Expression Patterns", Journal of Computational Biology, 6 (3–4): 281–97, CiteSeerX 10.1.1.34.5341, doi:10.1089/106652799318274, PMID 105825673–4&rft.pages=281-97&rft.date=1999&rft_id=https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.34.5341#id-name=CiteSeerX&rft_id=info:pmid/10582567&rft_id=info:doi/10.1089/106652799318274&rft.aulast=Ben-Dor&rft.aufirst=Amir&rft.au=Shamir,+Ron&rft.au=Yakhini,+Zohar&rfr_id=info:sid/en.wikipedia.org:Ron+Shamir" class="Z3988">
15. ^ Sharan, R.; Shamir, R. (2000), "CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis", Proceedings ISMB '00, 8: 307–316C, PMID 10977092
16. ^ 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
17. ^ 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, PMC 1839897, PMID 17408515
18. ^ 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 (7211): 401–405, Bibcode:2008Natur.455..401M, doi:10.1038/nature07213, PMC 2637443, PMID 18724358
19. ^ 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, CiteSeerX 10.1.1.43.5245, doi:10.1137/s0097539798334207
20. ^ 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, PMC 430898, PMID 12727897
21. ^ 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, PMC 2493407, PMID 18411406
22. ^ 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, PMC 1091753, PMID 15883364
23. ^ 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, Bibcode:2006PNAS..10313004B, doi:10.1073/pnas.0605420103, PMC 1550773, PMID 16916930
24. ^ Paz, Arnon; Brownstein Zippora; Ber Yaara; Bialik Shani; David Eyal; Sagir Dorit; Ulitsky Igor; Elkon Ran; Kimchi Adi; Avraham Karen B; Shiloh Yosef; Shamir Ron (Jan 2011). "SPIKE: a database of highly curated human signaling pathways". Nucleic Acids Res. 39 (Database issue). England: D793-9. doi:10.1093/nar/gkq1167. PMC 3014840. 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. ^ Pevzner, Pavel; Shamir, Ron (2011), Bioinformatics for biologists, Cambridge University Press, ISBN 9781107648876
28. ^ Fogg, Christina (2022). "2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir". Bioinformatics. 38 (Suppl 1): i1 – i2. doi:10.1093/bioinformatics/btac339. PMC 9236576. PMID 35758791. Retrieved 2023-06-04.
29. ^ 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\. CiteSeerX 10.1.1.139.231. doi:10.1089/cmb.2005.12.835. ISSN 1066-5277. 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.

* v
* t
* e

Fellows of the International Society for Computational Biology by year of election

2009|

* David Haussler
* David Lipman
* Webb Miller
* David Sankoff
* Temple Smith
* Janet Thornton
* Michael Waterman

2010|

* Russ Altman
* Lawrence Hunter
* Eugene Myers
* Chris Sander
* Gary Stormo
* Alfonso Valencia

2011|

* Michael Ashburner
* Phil Bourne
* Søren Brunak
* Richard Durbin

2012|

* Bonnie Berger
* Peter Karp
* Jill Mesirov
* Pavel Pevzner
* Ron Shamir
* Martin Vingron
* Gunnar von Heijne

2013|

* Pierre Baldi
* David Eisenberg
* Minoru Kanehisa
* Satoru Miyano
* Ruth Nussinov
* Steven Salzberg

2014|

* Amos Bairoch
* Ewan Birney
* Nir Friedman
* Robert Gentleman
* Andrej Šali

2015|

* Rolf Apweiler
* Cyrus Chothia
* Julio Collado-Vides
* Mark Gerstein
* Des Higgins
* Thomas Lengauer
* Michael Levitt
* Burkhard Rost

2016|

* Helen M. Berman
* Steven Brenner
* Dan Gusfield
* Barry Honig
* Janet Kelso
* Michal Linial
* Christine Orengo
* Aviv Regev
* Lincoln Stein
* Sarah Teichmann
* Anna Tramontano
* Shoshana Wodak
* Haim Wolfson

2017|

* Alex Bateman
* Andrea Califano
* Daphne Koller
* Anders Krogh
* William Stafford Noble
* Lior Pachter
* Olga Troyanskaya
* Tandy Warnow

2018|

* Patricia Babbitt
* Terry Gaasterland
* Hanah Margalit
* Yves Moreau
* Bernard Moret
* William Pearson
* Mona Singh
* Mike Steel

2019|

* Vineet Bafna
* Eleazar Eskin
* Xiaole Shirley Liu
* Marie-France Sagot

2020|

* Serafim Batzoglou
* Judith Blake
* Mark Borodovsky
* Rita Casadio
* Paul Flicek
* Osamu Gotoh
* Rafael Irizarry
* Laxmi Parida
* Katherine Pollard
* Ben Raphael
* Zhiping Weng
* Xuegong Zhang

2021|

* Atul Butte
* A. Keith Dunker
* Eran Halperin
* Wolfgang Huber
* Sorin Istrail
* Christina Leslie
* Ming Li
* Núria López Bigas
* Dana Pe'er
* Teresa Przytycka
* Eytan Ruppin
* Gustavo Stolovitzky

2022|

* Barbara Bryant
* Sean Eddy
* Mikhail Gelfand
* Takashi Gojobori
* Trey Ideker
* David Jones
* Fran Lewitter
* Jun Liu
* Debora Marks
* Mihai Pop
* Reinhard Schneider

Authority control databases

International|

* VIAF
* WorldCat

National|

* Germany
* United States
* Netherlands
* Israel

Academics|

* ORCID
* Mathematics Genealogy Project
* Association for Computing Machinery
* zbMATH
* Google Scholar
* DBLP
* MathSciNet

Other|

* Yale LUX

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