Ron Shamir (

Hebrew Hebrew (; ; ) is a Northwest Semitic language of the Afroasiatic language family. Historically, it is one of the spoken languages of the Israelites and their longest-surviving descendants, the Jews and Samaritans. It was largely preserved ...

: רון שמיר; born 29 November 1953) is an Israeli professor of

computer science Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to Applied science, practical discipli ...

known for his work in

graph theory In mathematics, graph theory is the study of ''graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of '' vertices'' (also called ''nodes'' or ''points'') which are conne ...

and in

computational biology Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...

. 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 Tel Aviv University (TAU) ( he, אוּנִיבֶרְסִיטַת תֵּל אָבִיב, ''Universitat Tel Aviv'') is a public research university in Tel Aviv, Israel. With over 30,000 students, it is the largest university in the country. Locate ...

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 The Third Aliyah ( he, העלייה השלישית, ''HaAliyah HaShlishit'') refers to the third wave—or aliyah—of modern Jewish immigration to Palestine from Europe. This wave lasted from 1919, just after the end of World War I, until 1923, ...

in the early 1920s. He has two younger sisters, Daphna and Gadit. Shamir studied in

Gymnasia Rehavia Rehavia Gymnasium or the Jerusalem Rehavia Gymnasium, by its Hebrew name Gymnasia Rehavia ( he, גמנסיה רחביה, Gimnazya Rehavya), is a high school in the Rehavia neighborhood in West Jerusalem. History The high school's initial name wa ...

Jerusalem Jerusalem (; he, יְרוּשָׁלַיִם ; ar, القُدس ) (combining the Biblical and common usage Arabic names); grc, Ἱερουσαλήμ/Ἰεροσόλυμα, Hierousalḗm/Hierosóluma; hy, Երուսաղեմ, Erusałēm. i ...

, 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 The shot put is a track and field event involving "putting" (throwing) a heavy spherical ball—the ''shot''—as far as possible. The shot put competition for men has been a part of the modern Olympics since their revival in 1896, and women's ...

. Shamir started his B.Sc. studies in mathematics and physics at

Tel-Aviv University Tel Aviv University (TAU) ( he, אוּנִיבֶרְסִיטַת תֵּל אָבִיב, ''Universitat Tel Aviv'') is a public research university in Tel Aviv, Israel. With over 30,000 students, it is the largest university in the country. Locate ...

(1973–1975) and completed his degree at the

Hebrew University of Jerusalem The Hebrew University of Jerusalem (HUJI; he, הַאוּנִיבֶרְסִיטָה הַעִבְרִית בִּירוּשָׁלַיִם) is a public research university based in Jerusalem, Israel. Co-founded by Albert Einstein and Dr. Chaim Weiz ...

(1975–1977). He later began M.Sc. studies in

operations research Operations research ( en-GB, operational research) (U.S. Air Force Specialty Code: Operations Analysis), often shortened to the initialism OR, is a discipline that deals with the development and application of analytical methods to improve deci ...

at Tel-Aviv University under the supervision of Uri Yechiali, and then joined the PhD program at the IEOR department of

UC Berkeley The University of California, Berkeley (UC Berkeley, Berkeley, Cal, or California) is a public university, public land-grant university, land-grant research university in Berkeley, California. Established in 1868 as the University of Californi ...

, where he studied from 1981 to 1984. His PhD thesis was conducted under the supervision of

Richard Karp Richard Manning Karp (born January 3, 1935) is an American computer scientist and computational theorist at the University of California, Berkeley. He is most notable for his research in the theory of algorithms, for which he received a Turing ...

and Ilan Adler.

Research

Early years

Shamir started his research career in operations research, studying optimization problems related to

linear programming Linear programming (LP), also called linear optimization, is a method to achieve the best outcome (such as maximum profit or lowest cost) in a mathematical model whose requirements are represented by linear function#As a polynomial function, li ...

and to the

simplex method In mathematical optimization, Dantzig's simplex algorithm (or simplex method) is a popular algorithm for linear programming. The name of the algorithm is derived from the concept of a simplex and was suggested by T. S. Motzkin. Simplices are ...

. His PhD thesis with Adler and Karp dealt with average case analysis of the

Simplex Method In mathematical optimization, Dantzig's simplex algorithm (or simplex method) is a popular algorithm for linear programming. The name of the algorithm is derived from the concept of a simplex and was suggested by T. S. Motzkin. Simplices are ...

, and showed that a certain Simplex variant was quadratic under a simple input data model. Similar results were given at the same time by Michael Todd and by Adler and

Nimrod Megiddo , birth_date = , birth_place = , death_date = , death_place = , citizenship = , field = Operations researchAlgorithms ComplexityMachine learning Game theory , workplaces = IBM Research ...

. He later worked with

Dorit S. Hochbaum Dorit S. Hochbaum is a professor of industrial engineering and operations research at the University of California, Berkeley.

Algorithmic Graph Theory

In the early 1990s, Shamir turned his focus to algorithmic

. Together with his student, Haim Kaplan, and Martin Golumbic, he studied graph sandwich problems, graph completion problems and a variety of problems related to

interval graph In graph theory, an interval graph is an undirected graph formed from a set of intervals on the real line, with a vertex for each interval and an edge between vertices whose intervals intersect. It is the intersection graph of the intervals. Int ...

s. One of his papers on the interval satisfiability problem was later applied to the study of DNA physical mapping; this marked his introduction to the field of

Bioinformatics

Shamir used his expertise in graph theory to develop

clustering algorithm Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of ...

s for analyzing

gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. The ...

problems. His first paper in this area, with Erez Hartuv, introduced the

HCS clustering algorithm Th HCS (Highly Connected Subgraphs) clustering algorithm(also known as the HCS algorithm, and other names such as Highly Connected Clusters/Components/Kernels) is an algorithm based on graph connectivity for cluster analysis. It works by represen ...

. His CAST algorithm, with Zohar Yakhini and Amir Ben-Dor was published in 1999 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 with Roded Sharan and the SAMBA algorithm with Amos Tanay and Roded Sharan for

biclustering Biclustering, block clustering, Co-clustering or two-mode clustering is a data mining technique which allows simultaneous clustering of the rows and columns of a matrix. The term was first introduced by Boris Mirkin to name a technique introduce ...

are in broad use. Shamir broadened his research to include additional aspects of bioinformatics, such as analysis of

biological network A biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. In general, networks or graphs are used to capture relationships between entities or objects. A typi ...

genome rearrangement In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

sequence motif In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''As ...

finding, and

transcriptional regulation In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from alt ...

. 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

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated interactions for particular human pathways. SPIKE was developed by Shamir's

group in cooperation with the group of Yosef Shiloh, an

Israel Prize The Israel Prize ( he, פרס ישראל; ''pras israél'') is an award bestowed by the State of Israel, and regarded as the state's highest cultural honor. History The Israel Prize is awarded annually, on Israeli Independence Day, in a state cer ...

recipient for his research in systems biology, and the group of

Karen Avraham Karen B. Avraham is an Israeli-American human geneticist and the first female Dean of the Tel Aviv University's Faculty of Medicine. Born in Canada in 1962, Avraham moved to the US at a young age. Her research focuses on the discovery and chara ...

, a leading researcher of human

deafness Deafness has varying definitions in cultural and medical contexts. In medical contexts, the meaning of deafness is hearing loss that precludes a person from understanding spoken language, an audiological condition. In this context it is written ...

, all from

Additional activities

Shamir was on the founding steering committee of the RECOMB meeting, 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. 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" with Pavel A. Pevzner. Students 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 ar
Haim KaplanDekel TsurDalit NaorItsik Pe'erRoded SharanAmos TanayAdi AkaviaReut ShalgiRani ElkonRotem SorekIrit Gat-ViksMichal Ziv-UkelsonIgor UlitskyMukul Bansal
Meirav Zehavi an
Yaron Orenstein

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" (2016) * Elected

ISCB Fellow ISCB Fellowship is an award granted to scientists that the International Society for Computational Biology (ISCB) judges to have made “outstanding contributions to the fields of computational biology and bioinformatics”. , there are 76 Fellow ...

by the

International Society for Computational Biology The International Society for Computational Biology (ISCB) is a scholarly society for researchers in computational biology and bioinformatics. The society was founded in 1997 to provide a stable financial home for the Intelligent Systems for Mole ...

(2012) * Elected

ACM Fellow ACM or A.C.M. may refer to: Aviation * AGM-129 ACM, 1990–2012 USAF cruise missile * Air chief marshal * Air combat manoeuvring or dogfighting * Air cycle machine * Arica Airport (Colombia) (IATA: ACM), in Arica, Amazonas, Colombia Computing ...

by the

Association for Computing Machinery The Association for Computing Machinery (ACM) is a US-based international learned society for computing. It was founded in 1947 and is the world's largest scientific and educational computing society. The ACM is a non-profit professional member ...

(2012) * RECOMB "Test of Time Award" for his 1999 paper "Clustering gene expression patterns" (2011) * The Michael Landau National Prize in the Sciences in Bioinformatics (2010) * The Raymond and Beverly Sackler Chair in Bioinformatics, Tel Aviv University (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 Israel Academy of Sciences and Humanities, based in Jerusalem, was established in 1961 by the State of Israel to foster contact between Israeli scholars in the sciences and humanities and create a think tank for advising the government on re ...

(1987)

Personal life

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

Rehovot Rehovot ( he, רְחוֹבוֹת ''Rəḥōvōt'', ar, رحوڤوت ''Reḥūfūt'') is a city in the Central District of Israel, about south of Tel Aviv. In it had a population of . Etymology Israel Belkind, founder of the Bilu movement, ...

, Israel.

References

{{DEFAULTSORT:Shamir, Ron 1953 births Living people Israeli Jews Israeli bioinformaticians Tel Aviv University faculty Fellows of the International Society for Computational Biology Fellows of the Association for Computing Machinery Israel Defense Prize recipients