Ron Shamir

{{BLP unreferenced section|date=April 2025}}

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.

Shamir started his research{{citation| last1=Ben-Dor | first1=A. | last2=Shamir | first2=R. | last3=Yakhini | first3=Z. | year=1999 | title=Clustering gene expression patterns | journal=Journal of Computational Biology | volume=6 | pages=281–297| doi=10.1089/106652799318274| issue=3–4 | pmid=10582567| citeseerx=10.1.1.34.5341 }}{{citation| last1=Sharan | first1=R. | last2=Maron-Katz | first2=A. | last3=Shamir| first3=R. | year=2000 | title=CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis | journal=Intelligent Systems in Molecular Biology | pages=307–316 | doi=10.1093/bioinformatics/btg232| pmid=14512350 | volume=19| issue=14 | citeseerx=10.1.1.126.8500 }}.

• {{Citation | doi=10.1093/bioinformatics/18.suppl_1.S136 | title= Discovering statistically significant biclusters in gene expression data | year=2000 | last1=Tanay | first1=A. | last2=Sharan | first2=R. | last3=Shamir | first3=R. |journal=Bioinformatics| volume=18 | issue=1 | pages=S136–S144 | pmid=12169541| doi-access=free }}{{citation| last1=Sharan | first1= R. | last2=Maron-Katz | first2=A. | last3=Shamir | first3=R. | year=2003 | title=CLICK and EXPANDER: a system for clustering and visualizing gene expression data | journal= Bioinformatics| volume=19 | pages=1787–1799| doi=10.1093/bioinformatics/btg232| pmid= 14512350 | issue=14 | citeseerx= 10.1.1.126.8500 }}{{Citation | doi=10.1038/nprot.2009.230 | title=Expander: From expression microarrays to networks and functions | year=2010 | last1=Ulitsky | first1=Igor | last2=Maron-Katz | first2=Adi | last3=Shavit | first3=Seagull | last4=Sagir | first4=Dorit | last5=Linhart | first5=Chaim | last6=Elkon | first6=Ran | last7=Tanay | first7=Amos | last8=Sharan | first8=Roded | last9=Shiloh | first9=Yosef | last10=Shamir | first10=Ron | journal=Nature Protocols | volume=5 | issue=2 | pages=303–22 | pmid=20134430| s2cid=3504270 | url=https://zenodo.org/record/3426102 }} 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.{{Citation

| title = A simplex variant solving an m × d linear program in O(min(m^2, d^2)) expected number of pivot steps

| year = 1987

| journal = Journal of Complexity

| pages = 372–387

| volume = 3

| issue = 4

| doi = 10.1016/0885-064X(87)90007-0

| last1 = Adler | first1 = Ilan

| last2 = Karp | first2 = Richard M.

| last3 = Shamir | first3 = Ron| doi-access =

}} 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.{{cite journal|last1=Hochbaum|first1=Dorit S.|author1-link= Dorit S. Hochbaum |last2=Shamir|first2=Ron|title=Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem|journal=Operations Research|volume=39|issue=4|year=1991|pages=648–653|issn=0030-364X|doi=10.1287/opre.39.4.648}}

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,{{Citation

| title = Graph Sandwich Problems

| year = 1995

| journal = Journal of Algorithms

| pages = 449–473

| volume = 19

| issue = 3

| doi = 10.1006/jagm.1995.1047

| last1 = Golumbic | first1 = Martin Charles

| last2 = Kaplan | first2 = Haim

| last3 = Shamir | first3 = Ron

| citeseerx = 10.1.1.12.8158

}} graph completion problems and a variety of problems related to interval graphs.{{Citation | doi=10.1137/S0097539793258143 | title=Pathwidth, Bandwidth, and Completion Problems to Proper Interval Graphs with Small Cliques | year=1996 | last1=Kaplan | first1=Haim | last2=Shamir | first2=Ron | journal=SIAM Journal on Computing | volume=25 | issue=3 | pages=540–561| citeseerx=10.1.1.34.9275 }}{{Citation | doi=10.1137/S0097539796303044 | title=Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal, and Proper Interval Graphs | year=1999 | last1=Kaplan | first1=Haim | last2=Shamir | first2=Ron | last3=Tarjan | first3=Robert E. | journal=SIAM Journal on Computing | volume=28 | issue=5 | pages=1906–1922| citeseerx=10.1.1.12.2803 }}

One of his papers on the interval satisfiability problem was later applied to the study of DNA physical mapping;{{Citation | doi=10.1006/aama.1994.1009 | title=On the Complexity of DNA Physical Mapping | year=1994 | last1=Golumbic | first1=M.C. | last2=Kaplan | first2=H. | last3=Shamir | first3=R. | journal=Advances in Applied Mathematics | volume=15 | issue=3 | pages=251–261| doi-access=free }} this marked his introduction to the field of computational biology.

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.{{Citation | doi=10.1016/S0020-0190(00)00142-3| title=A clustering algorithm based on graph connectivity | year=2000 | last1=Hartuv | first1=E. | last2=Shamir | first2=R. | journal=Information Processing Letters| volume=76 | issue=4–6 | pages=175–181| citeseerx=10.1.1.17.1450 }} His CAST algorithm, with Zohar Yakhini and Amir Ben-Dor was published in 1999{{Citation | doi=10.1089/106652799318274 | title=Clustering Gene Expression Patterns | year=1999 | last1=Ben-Dor | first1=Amir | last2=Shamir | first2=Ron | last3=Yakhini | first3=Zohar | journal=Journal of Computational Biology | volume=6 | issue=3–4 | pages=281–97 | pmid=10582567| citeseerx=10.1.1.34.5341 }} 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{{Citation | title=CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis | year=2000 | last1=Sharan | first1=R. | last2=Shamir | first2=R. | journal=Proceedings ISMB '00| volume=8 | pages=307–316C| pmid=10977092 }} with Roded Sharan and the SAMBA algorithm with Amos Tanay and Roded Sharan for biclustering{{Citation | doi=10.1093/bioinformatics/18.suppl_1.S136 | title= Discovering statistically significant biclusters in gene expression data | year=2000 | last1=Tanay | first1=A. | last2=Sharan | first2=R. | last3=Shamir | first3=R. |journal=Bioinformatics| volume=18 | issue=1 | pages=S136–S144 | pmid=12169541| doi-access=free }} are in broad use.

Shamir broadened his research to include additional aspects of bioinformatics, such as analysis of biological networks,{{Citation | doi=10.1186/1752-0509-1-8| pmid= 17408515 | pmc= 1839897 | title= Identification of functional modules using network topology and high-throughput data | year=2007 | last1=Ulitsky | first1=I. | last2=Shamir | first2=R. |journal=BMC Systems Biology| volume=1 | issue=8 | pages= 8 | doi-access= free }}{{Citation | doi=10.1038/nature07213| title= Regulatory networks define phenotypic classes of human stem cell lines| year=2008 | last1=Mueller | first1=F.J. | last2=Williams | first2=R. | last3=Kostka | first3=D.|last4=Laurent|first4=L.|last5=Ulitsky|first5=I.|last6=Lu|first6=C.| last7=Rao |first7=M.S.|last8=Shamir | first8=R.| last9=Schwartz | first9=P.H.|last10=Schmidt| first10=N.O.| last11=Loring| first11=J.F.| volume=455 | issue= 7211| pages=401–405 | journal=Nature | pmid=18724358 | pmc=2637443| bibcode= 2008Natur.455..401M}} genome rearrangements,{{Citation | title= A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals | year=1999 | last1=Kaplan | first1=H. | last2=Shamir | first2=R. |last3=Tarjan| first3=R.E.| journal=SIAM Journal on Computing| volume=29 | issue=3 | pages=880–892 | doi=10.1137/s0097539798334207| citeseerx=10.1.1.43.5245 }} sequence motif finding,{{Citation | doi=10.1101/gr.947203| title= Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells | year=2003 | last1=Elkon | first1=R. | last2=Linhart | first2=C. |last3=Sharan| first3=R.| last4=Shamir| first4=R.| last5=Shiloh| first5=Y.| journal=Genome Research| volume=13 | issue=5 | pages=773–780 | pmid=12727897 | pmc=430898}}{{Citation | doi=10.1101/gr.076117.108 | title= Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets| year=2008 | last1=Linhart | first1=C. |last2=Halperin| first2=Y.| last3=Shamir| first3=R.| journal=Genome Research| volume=18 | issue=7 | pages=1180–1189 | pmid=18411406 | pmc=2493407

}} and transcriptional regulation.{{Citation | title= Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast| year=2005 | last1=Tanay | first1=A. |last2=Regev| first2=A.| last3=Shamir| first3=R.| journal=Proceedings of the National Academy of Sciences USA | volume=102 | issue=20 | pages=7203–7208 |doi=10.1073/pnas.0502521102

| pmid=15883364 | pmc=1091753| bibcode=2005PNAS..102.7203T | doi-access=free }}{{Citation |doi=10.1073/pnas.0605420103| title= Quantification of protein half-lives in the budding yeast proteome| year=2006 | last1=Belle | first1=A. |last2=Tanay| first2=A.| last3=Bitincka | first3=L.|last4=Shamir| first4=R.| last5=O'Shea| first5=E.K.| journal=Proceedings of the National Academy of Sciences USA | volume=103 | issue=35 | pages=13004–9 | pmid=16916930 | pmc=1550773

| bibcode= 2006PNAS..10313004B| doi-access= free}}

Many tools developed in his laboratory are available as a part of the EXPANDER suite, 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 (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated interactions for particular human pathways.{{cite journal |last=Paz|first=Arnon |author2=Brownstein Zippora |author3=Ber Yaara |author4=Bialik Shani |author5=David Eyal |author6=Sagir Dorit |author7=Ulitsky Igor |author8=Elkon Ran |author9=Kimchi Adi |author10=Avraham Karen B |author11=Shiloh Yosef |author12=Shamir Ron |date=Jan 2011|title=SPIKE: a database of highly curated human signaling pathways|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D793-9|location = England| pmid = 21097778|doi = 10.1093/nar/gkq1167| pmc =3014840 }} 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.

Shamir was on the founding steering committee of the RECOMB meeting,[http://www.recomb.org/Steering-Committee RECOMB steering committee], including former member Ron Shamir. Accessed January 12, 2014 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.http://safrabio.cs.tau.ac.il/steering_committee.htm Members of the steering committee of the Edmond J. Safra Center for Bioinformatics 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"{{Citation | title=Bioinformatics for biologists | last1=Pevzner | first1=Pavel | last2=Shamir | first2=Ron | year=2011 | publisher=Cambridge University Press | isbn=9781107648876}} with Pavel A. Pevzner.

Students

{{External links|section|date=March 2025}}

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 [http://www.cs.tau.ac.il/~haimk/ Haim Kaplan], [https://www.cs.bgu.ac.il/~dekelts/ Dekel Tsur], [https://www.int.mta.ac.il/faculty-members/Dr.-Dalit-Naor Dalit Naor], [https://www.engineering.columbia.edu/faculty/itsik-peer Itsik Pe'er], [https://www.cs.tau.ac.il/~roded/ Roded Sharan], [http://compgenomics.weizmann.ac.il/tanay/ Amos Tanay], [https://www2.mta.ac.il/~akavia/ Adi Akavia], [https://reuts4.wixsite.com/reutshalgi Reut Shalgi], [http://www.cs.tau.ac.il/~ranel/ Rani Elkon], [https://www.weizmann.ac.il/molgen/Sorek/ Rotem Sorek], [https://gatvikslab.com/ Irit Gat-Viks], [https://www.cs.bgu.ac.il/~negevcb/Michal/ Michal Ziv-Ukelson], [http://www.weizmann.ac.il/Biological_Regulation/IgorUlitsky/home Igor Ulitsky], [https://mukul-bansal.uconn.edu/ Mukul Bansal], [https://sites.google.com/site/zehavimeirav/ Meirav Zehavi], [https://wwwee.ee.bgu.ac.il/~cb/index.html Yaron Orenstein], [https://www.researchgate.net/profile/Adi-Maron-Katz Adi Maron-Katz] and [https://sdquest.github.io/ Lianrong Pu].

• Accomplishments by a Senior Scientist Award, the International Society for Computational Biology{{Cite journal |last=Fogg |first=Christina |title=2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir |url=https://academic.oup.com/bioinformatics/article/38/Supplement_1/i1/6617502 |access-date=2023-06-04 |journal=Bioinformatics|date=2022 |volume=38 |issue=Suppl 1 |pages=i1–i2 |doi=10.1093/bioinformatics/btac339 |pmid=35758791 |pmc=9236576 }} (2022)
• [https://english.tau.ac.il/kadar_prizewinner_video_gallery/?itemID=4945 Kadar Family Prize] for outstanding research, Tel Aviv University (2017)
• RECOMB "Test of Time Award" for the 2004 paper ""Identification of protein complexes"{{Cite journal|last1=Sharan|first1=Roded|last2=Ideker|first2=Trey|last3=Kelley|first3=Brian|last4=Shamir|first4=Ron|last5=Karp|first5=Richard M.|date=July 2005|title=Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data|journal=Journal of Computational Biology|volume=12|issue=6|pages=835–846|doi=10.1089/cmb.2005.12.835|issn=1066-5277|pmid=16108720|citeseerx=10.1.1.139.231}} (2016)
• Elected ISCB Fellow by the International Society for Computational Biology (2012)
• Elected ACM Fellow by the Association for Computing Machinery[http://awards.acm.org/award_winners/shamir_3130614.cfm ACM fellow profile], Association for Computing Machinery (2012)
• RECOMB "Test of Time Award" for his 1999 paper "Clustering gene expression patterns"[http://www.recomb.org/22470/RECOMB-Awards RECOMB award winners]. Accessed January 12, 2014 (2011)
• The Michael Landau National Prize in the Sciences in Bioinformatics[http://www.pais.co.il/Foundations/Landau/Pages/AwardOfScienceAndResearch-2010.aspx Landau Prize Winners for 2010] {{webarchive|url=https://web.archive.org/web/20111008085802/http://www.pais.co.il/Foundations/Landau/Pages/AwardOfScienceAndResearch-2010.aspx |date=2011-10-08 }} (Hebrew). Accessed January 12, 2014 (2010)
• The Raymond and Beverly Sackler Chair in Bioinformatics, Tel Aviv University[http://www.cs.tau.ac.il/endowedchairs.htm The Raymond and Beverly Sackler Chair in Bioinformatics endowed chairs]. Accessed January 12, 2014 (2003)
• ISMB Best Paper Award for his paper "Spectrum Alignment"Intelligent System for Molecular Biology (ISMB) keynote speakers, ISMB. Accessed January 12, 2014. (2000)
• Alon Fellowship from the Israel Academy of Sciences and Humanities (1987)

Shamir is married to Michal Oren-Shamir.{{when|date=March 2017}} They have three sons: Alon, Ittai and Yoav. They live in Rehovot, Israel.{{citation needed|date=March 2017}}

{{Reflist|30em}}

{{ISCB Fellows}}

{{Authority control}}

{{DEFAULTSORT:Shamir, Ron}}

Category:1953 births

Category:Living people

Category:Israeli Jews

Category:Israeli bioinformaticians

Category:Academic staff of Tel Aviv University

Category:Fellows of the International Society for Computational Biology

Category:2012 fellows of the Association for Computing Machinery

Category:Israel Defense Prize recipients