CURRICULUM VITAE –ULITSKY IGOR, PHD
Department of Biological Regulation, Weizmann Institute of Science
Date of birth: Aug 26, 1980 (St. Petersburg, Russia)
Citizenship: Israeli
Email: igor.ulitsky@weizmann.ac.il
Homepage: http://www.weizmann.ac.il/~igoru/
Education / Positions held
8/2013-Present
Senior Scientist, Department of Biological Regulation, Weizmann
Institute of Science, Rehovot, Israel
9/2009-8/2013
Postdoctoral Fellow at the lab of Prof. David Bartel, Whitehead
Institute for Biomedical Research, Cambridge MA
7/2004-7/2009
(awarded
10/6/2010)
Ph.D. (direct track) in Computer Science, Tel Aviv University,
Advisor: Prof. Ron Shamir.
2001 – 2004
B.Sc. in Computer Science (Summa Cum Laude) and Life Sciences
(Summa Cum Laude), Tel Aviv University, combined program with an
emphasis on Bioinformatics (double major).
Thesis: Network-based algorithms for Analysis of Heterogeneous
Biomedical Data.
Fellowships and Awards
2010-2011
EMBO long term postdoctoral fellowship
2009
Legacy Heritage Fund stem cells research fellowship
2008
Wolf prize for outstanding PhD students (a nation-wide prize)
2005-2009
Fellow, Edmond J. Safra Program in bioinformatics, Tel Aviv University
2004-2005
President and Rector's M.Sc fellowship
2005
Special excellence award, Knesset education committee and university
directors committee (a nation-wide prize)
2004
B.Sc. summa cum laude
Teaching Experience
Teacher at MIT Advanced undergraduate seminar on Biological networks 2010/2011, 2011/2012,
2012/2013
Teaching assistant at Tel-Aviv University (Lectured in recitations, created assignments and final
projects, designed and graded exams):
Computational Genomics 2006/2007, 2007/2008, 2008/2009
Analysis of Gene Expression Data, DNA Chips and Gene Networks 2006/2007
Course instructor (Solely responsible for the course from design to grading):
Tools in Bioinformatics 2006/2007, 2007/2008, 2008/2009
Professional Activities
Program Committee: ISMB 2012, ISMB 2013
Journal reviewing: Nature, Science, Cell, Nature Genetics, Genome Research, PNAS, Genome
Biology, Nucleic Acids Research, RNA, PLoS Computational Biology, PLoS One, Bioinformatics,
BMC Genomics, BMC Bioinformatics, BMC Systems Biology, Journal of Metabolic Engineering,
IEEE Transactions on Computational Biology and Bioinformatics
Reviewing for Conferences: RECOMB (2005, 2006, 2007, 2008), ISMB (2006, 2007, 2008,
2009), ECCB (2006), PSB (2008), RECOMB Satellite on Systems Biology (2008).
Industry Experience
2012-2013
2009,2011
2004-2005
Consulting services to Kailos Genetics, Huntsville AL
Consulting services to NextBio, Cupertino CA
Computational biologist in Biolog Technologies - developing an algorithmic
framework for studying protein sequence and structure in the pharmaceutical
industry
Publications
Scientific journals
[1] I. Ulitsky and D.P. Bartel. “lincRNAs: Genomics, Evolution, and Mechanisms”. Cell. 154(1):26-46
(2013). Peer-reviewed review.
[2] V. Ayeung, I. Ulitsky, S.E. McGeary and D.P. Bartel. “Beyond secondary structure: primarysequence determinants license pri-miRNA hairpins for processing”. Cell. 152(4):844-58 (2013)
[3] I. Ulitsky, A. Shkumatava, C. Jan, A.O. Subtelny, D. Koppstein, H. Sive and D.P. Bartel. “Extensive
alternative polyadenylation during zebrafish development”. Genome Research 22:2054-2066 (2012)
[4] I. Ulitsky*, A. Shkumatava*, C. Jan, H. Sive and D.P. Bartel. “Conserved Function of lincRNAs in
Vertebrate Embryonic Development despite Rapid Sequence Evolution”. Cell 147(7):1537-50 (2011).
Highlighted in Nature Reviews Genetics and Faculty of 1000. (* - equal contribution)
[5] L.C. Laurent, I. Ulitsky, I. Slavin, H. Tran, A. Schork, R. Morey, C. Lynch, J.V. Harness, S. Lee, M.J.
Barrero, S. Ku, M. Martynova, R. Semechkin, V. Galat, J. Gottesfeld, J.C. Izpisua Belmonte, C. Murry,
H.S. Keirstead, H.S. Park, U. Schmidt, A.L. Laslett, F.J. Muller, C.M. Nievergelt, R. Shamir and J.F.
Loring. “Dynamic changes in the copy number of pluripotency and cell proliferation genes in human
ESCs and iPSCs during reprogramming and time in culture”. Cell Stem Cell 3(1) 106-118 (2011)
[6] L. Marom, I. Ulitsky, Y. Cabilly, R. Shamir and O. Elroy-Stein. “A point mutation in translation
initiation factor eIF2B leads to function- and time-specific changes in brain gene expression”. PLoS One
6(10):e26992 (2011)
[7] T.Elkan-Miller, I. Ulitsky, R. Hertzano, A. Rudnicki, A.A. Dror, D.R. Lenz, R. Elkon, M. Irmler, J.
Beckers, R. Shamir and K.B. Avraham. “Integration of Proteomics, Transcriptomics and MicroRNA
Analysis Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear”. PLoS One
6(4):e18195 (2011)
[8] I. Ulitsky, L.C. Laurent and R. Shamir. “Towards computational prediction of microRNA function
and activity”. Nucleic Acids Research 38(15):e160 (2010)
[9] I. Ulitsky, A. Krishnamurthy, R.M. Karp and R. Shamir. “DEGAS: de novo discovery of
dysregulated pathways in human diseases”. PLoS One 5(10):e13367 (2010)
[10] P.S. Aguilar, F. Fröhlich, M. Rehman, M. Shales, I. Ulitsky, A. Olivera-Couto, H. Braberg, R.
Shamir, P. Walter, M. Mann, C.S. Ejsing, N.J. Krogan, T.C. Walther. “A Plasma Membrane E-MAP
Reveals Links Between the Eisosome, Sphingolipid Metabolism and Endosomal Trafficking”. Nature
Structural and Molecular Biology 17(7):901-8 (2010)
[11] I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh
and R. Shamir. “Expander: From Expression Microarrays to Networks and Functions”. Nature Protocols
5:303-322 (2010)
[12] S. Abraham, S.D. Sheridan, L.C. Laurent, K. Albert, C. Stubban, I. Ulitsky, B. Miller, J.F. Loring,
R.R. Rao. “Propagation of human embryonic and induced pluripotent stem cells in an indirect co-culture
system”. Biochemical and Biophysical Research Communications 393:211-216 (2010)
[13] G.H. Romano, Y. Gurevich, O. Lavi, I. Ulitsky, R. Shamir and M. Kupiec. “Dissection of the
Complex Genetic Network Determining Natural Genetic Variability”. Molecular System Biology 6:346
(2010)
[14] I. Ulitsky, N.J. Krogan and R. Shamir. “Towards accurate imputation of quantitative genetic
interactions”. Genome Biology 10:R140 (2009)
[15] I. Ulitsky and R. Shamir. “Identifying functional modules using expression profiles and confidencescored protein interactions”. Bioinformatics 25:1158-1164 (2009)
[16] Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir. "Discovering transcriptional modules by
combined analysis of expression profiles and regulatory sequences". Nucleic Acids Research 37:15661579 (2009)
[17] F.J. Mueller, D. Kostka, L. Laurent, I. Ulitsky, R. Williams, C. Lu, I.H. Park, M.S. Rao, R. Shamir,
P.H. Schwartz, N.O. Schmidt and J.F. Loring. “Regulatory networks define phenotypic classes of human
stem cell lines”. Nature 455:401-405 (2008)
[18] L.C. Laurent, J. Chen, I. Ulitsky, F.J Mueller, C. Lu, R. Shamir, J.B. Fan and J.F. Loring.
“Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated
by a single seed sequence”. Stem Cells 26:1506-1518 (2008)
[19] I. Ulitsky, T. Shlomi, M. Kupiec and R. Shamir "From E-MAPs to module maps: dissecting
quantitative genetic interactions using physical interactions". Molecular Systems Biology 4:209 (2008)
[20] R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, N. Orlev, G. Sternberg, R. Blekhman, J.
Assa, Y. Shiloh and R. Shamir. “SPIKE: A database, visualization and analysis tool of cellular signaling
pathways”. BMC Bioinformatics 9:110 (2008)
[21] I. Ulitsky*, I. Gat-Viks* and R. Shamir. “MetaReg: a platform for modeling, analysis and
visualization of biological systems using large-scale experimental data”. Genome Biology 9:R1 (2008) (*
- equal contribution)
[22] I. Ulitsky and R. Shamir. “Pathway redundancy and protein essentiality revealed in the S. cerevisiae
interaction networks”. Molecular Systems Biology 3:104 (2007)
[23] R. Sharan*, I. Ulitsky* and R. Shamir. “Network-based prediction of protein function”. Molecular
Systems Biology 3:88 (2007) (* - equal contribution). Peer-reviewed review.
[24] I. Ulitsky and R. Shamir. “Identification of functional modules using network topology and high-
throughput data”. BMC Systems Biology 1:8 (2007)
[25] I. Ulitsky*, D. Burstein*, T. Tuller and B. Chor. “The average common substring approach to
phylogenomic reconstruction.” Journal of Computational Biology 13:336-350 (2006) (* - equal
contribution)
Peer-reviewed conferences
[26] I. Ulitsky and R. Shamir. "Detecting pathways transcriptionally correlated with clinical parameters".
Proceedings of CSB 2008 249-258, Imperial College Press, London, UK (2008)
[27] I. Ulitsky, R.M. Karp and R. Shamir. "Detecting disease-specific dysregulated pathways via analysis
of clinical expression profiles". Proceedings of RECOMB 2008. Lecture Notes in Computer Science Vol.
4205, pp. 87-98
[28] D. Burstein, I. Ulitsky, T. Tuller and B. Chor. “Information Theoretic Approaches to Whole Genome
Phylogenomics”. Proceedings of RECOMB 2005. Lecture Notes in Computer Science Vol. 3500, pp.
283-295
Oral presentations
“A link between long intervening noncoding RNAs and microRNA regulation.” Gordon Conference on
the Biology of Post-Transcriptional Regulation, July 2012.
“Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence
evolution.” Cold Spring Harbor Laboratory meeting on Eukaryotic mRNA Processing, August 2011.
“Towards computational prediction of microRNA function and activity.” RECOMB Satellite on
Regulatory Genomics, Cambridge MA, December 2009.
“Regulatory networks define phenotypic classes of human stem cell lines”. ISMB/ECCB 2009,
Stockholm July 2009.
“Regulatory networks define phenotypic classes of human stem cell lines”. International Stem Cell
Conference, Tel Aviv, June 2009.
"Integrated analysis of concurrent microRNA and gene expression in the context of protein interactions".
3rd Cold Spring Harbor Laboratory/Wellcome Trust conference on Interactome Networks, Hinxton UK,
August 2007.
“Pathway Redundancy and Protein Essentiality Revealed in the S. cerevisiae Interaction Networks”
RECOMB satellite meeting on Systems Biology, San Diego, December 2006.