Ron Shamir

Born|  (1953-11-29) 29 November 1953 (age 72)

Jerusalem, Israel

Nationality| Israeli
Alma mater| Tel-Aviv University
Hebrew University of Jerusalem
University of California
Known for| The Edmond J. Safra Center for Bioinformatics
Tel Aviv University B.Sc. program in Bioinformatics
Expander software[citation needed]
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 head of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.

## Contents

* 1 Biography
* 2 Research
* 2.1 Early years
* 2.2 Bioinformatics
* 2.3 Additional Activities
* 3 Awards and honors
* 4 Personal life
* 5 References

## 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 1981–1984. 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.Cite error: Closing `</ref>` missing for `<ref>` tag graph completion problems and a variety of problems related to interval graphs.[7][8] One of his papers on the interval satisfiability problem was later applied to the study of DNA physical mapping;[9] 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.[10] His CAST algorithm, with Zohar Yakhini and Amir Ben-Dor was published in 1999[11] 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[12] with Roded Sharan and the SAMBA algorithm with Amos Tanay and Roded Sharan for biclustering[13] are in broad use.

Shamir broadened his research to include additional aspects of bioinformatics, such as analysis of biological networks,[14][15] genome rearrangements,[16] sequence motif finding,[17][18] and transcriptional regulation.[19][20] 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.

### Additional Activities

Shamir was on the founding steering committee of the RECOMB meeting,[21] 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.[22] 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"[23] with Pavel A. Pevzner.

## Awards and honors

* Kadar Family Prize for outstanding research, Tel Aviv University (2017)
* RECOMB "Test of Time Award" for the 2004 paper ""Identification of protein complexes"[24] (2016)
* Elected ISCB Fellow by the International Society for Computational Biology[1] (2012)
* Elected ACM Fellow by the Association for Computing Machinery[25] (2012)
* RECOMB "Test of Time Award" for his 1999 paper "Clustering gene expression patterns"[26] (2011)
* The Michael Landau National Prize in the Sciences in Bioinformatics[27] (2010)
* The Raymond and Beverly Sackler Chair in Bioinformatics, Tel Aviv University[28] (2003)
* ISMB Best Paper Award for his paper "Spectrum Alignment"[29] (2000)
* Alon Fellowship from the Israel Academy of Sciences and Humanities (1987)

## 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. ↑ 1.0 1.1 Anon (2017). "ISCB Fellows". International Society for Computational Biology. Archived from the original on 2017-03-20. https://web.archive.org/web/20170320114530/https://www.iscb.org/iscb-fellows.
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, doi:10.1089/106652799318274, PMID 10582567
4. ↑ 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, 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, doi:10.1093/bioinformatics/btg232, PMID 14512350
6. ↑ 6.0 6.1 Ulitsky, Igor; Maron-Katz, Adi; Shavit, Seagull; Sagir, Dorit; Linhart, Chaim; Elkon, Ran; Tanay, Amos; Sharan, Roded et al. (2010), "Expander: From expression microarrays to networks and functions", Nature Protocols 5 (2): 303–22, doi:10.1038/nprot.2009.230, PMID 20134430, https://zenodo.org/record/3426102
7. ↑ 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
8. ↑ 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
9. ↑ 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
10. ↑ 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
11. ↑ 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
12. ↑ Sharan, R.; Shamir, R. (2000), "CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis", Proceedings ISMB '00 8: 307–316C
13. ↑ 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
14. ↑ 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, PMID 17408515
15. ↑ Mueller, F.J.; Williams, R.; Kostka, D.; Laurent, L.; Ulitsky, I.; Lu, C.; Rao, M.S.; Shamir, R. et al. (2008), "Regulatory networks define phenotypic classes of human stem cell lines", Nature 455 (7211): 401–405, doi:10.1038/nature07213, PMID 18724358, Bibcode: 2008Natur.455..401M
16. ↑ 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, doi:10.1137/s0097539798334207
17. ↑ 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, PMID 12727897
18. ↑ 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, PMID 18411406
19. ↑ 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, doi:10.1073/pnas.0502521102, PMID 15883364, Bibcode: 2005PNAS..102.7203T
20. ↑ 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, PMID 16916930, Bibcode: 2006PNAS..10313004B
21. ↑ RECOMB steering committee, including former member Ron Shamir. Accessed January 12, 2014
22. ↑ http://safrabio.cs.tau.ac.il/steering_committee.htm Members of the steering committee of the Edmond J. Safra Center for Bioinformatics
23. ↑ Pevzner, Pavel; Shamir, Ron (2011), Bioinformatics for biologists, Cambridge University Press, ISBN 9781107648876
24. ↑ 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. doi:10.1089/cmb.2005.12.835. ISSN 1066-5277. PMID 16108720.
25. ↑ ACM fellow profile, Association for Computing Machinery
26. ↑ RECOMB award winners. Accessed January 12, 2014
27. ↑ Landau Prize Winners for 2010 (Hebrew). Accessed January 12, 2014
28. ↑ The Raymond and Beverly Sackler Chair in Bioinformatics endowed chairs. Accessed January 12, 2014
29. ↑ Intelligent System for Molecular Biology (ISMB) keynote speakers, ISMB. Accessed January 12, 2014.

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Fellows of the International Society for Computational Biology by List of Fellows of the International Society for Computational Biology

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 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

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