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Igor Ulitsky – CV September 2016

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Igor Ulitsky – CV September 2016 Igor Ulitsky – CV September 2016 Date of birth: Aug 26, 1980 (St. Petersburg, Russia) Marital Status: Married+4 Citizenship: Israeli Mailing address: Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel 76100 Email: [email protected] Homepage: http://www.weizmann.ac.il/~igoru Education / Positions held 8/2013- Senior Scientist, Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel 9/2009-8/2013 Postdoctoral Fellow at the Bartel Lab, Whitehead Institute for Biomedical Research, Cambridge MA 7/2004-7/2009 Ph.D. (direct track) in Computer Science, Tel Aviv University, (awarded 5/2010) Advisor: Prof. Ron Shamir. Thesis: Algorithmic methods for integrating heterogeneous biological data for disease modeling. 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). Fellowships and Awards 2015-2020 ERC Starting Grant award 2014-2017 Alon fellowship (“Milgat Alon”), Israel Council for Higher Education 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 International schools 4th international course on the noncoding genome @Institute Curie, Paris, February 2014 EMBO practical course “‘Non-coding RNAs: From discovery to function”, Brno, July 2015 @Weizmann RNA World (w/ Prof. Rotem Sorek and Dr. Eran Hornstein) 2014/15,2015/16 Systems Biology 101 (w/ other lecturers) 2014/15,2015/16 Advanced seminar on Post-transcriptional fate of mRNAs 2013/14,2015/16 @MIT Advanced undergraduate seminars on Biological networks and Post- transcriptional fate of mRNAs 2010/2011, 2011/2012, 2012/2013 Teaching assistant @Tel-Aviv University: Computational Genomics 2006/2007, 2007/2008, 2008/2009 Analysis of Gene Expression Data, DNA Chips and Gene Networks 2006/2007 Course instructor @Tel Aviv University: Tools in Bioinformatics 2006/2007, 2007/2008, 2008/2009 Professional Activities Editorial board: Cell Reports Conference organization: EMBO workshop on “Systems Biology of Noncoding RNAs”, February 2016; 19th Israeli Bioinformatics Symposium, May 2017; Keystone Meeting on Long Noncoding RNAs, 2018 Scientific reviewer for granting agencies: European Research Council (ERC), NSF, Israeli Science Foundation, Austrian Science Fund (FWF), French National Research Agency’s (ANR), Israeli Cancer Association, The Wellcome Trust/DBT India Alliance, Cancer Research UK Program Committee: ISMB 2012, ISMB 2013/ECCB, ISMB 2014, ISMB/ECCB 2015, ISMB 2016 Journal reviewing: Nature, Science, Cell, Nature Genetics, Nature Methods, Nature Communications, Genome Research, Molecular Cell, Cell Reports, PNAS, Genome Biology, Nucleic Acids Research, RNA journal, PLoS Computational Biology, PLoS One, Bioinformatics, BMC Genomics, BMC Bioinformatics, BMC Systems Biology, Journal of Metabolic Engineering, IEEE Transactions on Computational Biology and Bioinformatics, Molecular Biology of the Cell, Molecular Biology and Evolution, Biochimie, BBA Gene Regulatory Mechanisms, DNA Research, Gene 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 2012-2016 Consulting services to Kailos Genetics, Huntsville AL 2009,2011 Consulting services to NextBio, Cupertino CA 2004-2005 Computational biologist in Biolog Technologies Publications Scientific journals 1. R. Ben Tov Perry and I. Ulitsky. The functions of long noncoding RNAs in development and stem cells. Development. In press (2016) (Peer-reviewed review article). 2. I. Ulitsky. Evolution to the rescue: understanding long noncoding RNAs through comparative genomics. Nature Reviews Genetics. 17, 601–614 (2016) (Peer- reviewed review article). 3. A. Tichon, N. Gil, Y. Lubelsky, T.H. Solomon, D. Lemze, S. Itzkovitz, N. Stern- Ginossar, and I. Ulitsky. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nature Communications, 7:12209 (2016). 4. A. Sas-Chen, M.R. Aure, L. Leibovich, … , I. Ulitsky, S. Diederichs, S. Wiemann, Z. Yakhini, V.N. Kristensen, A.L. Børresen-Dale and Y. Yarden. LIMT, a novel metastasis inhibiting lncRNA is suppressed by EGF and down-regulated in aggressive breast cancer. EMBO Molecular Medicine. 8(9):1052-64 (2016) 5. G. Housman and I. Ulitsky. Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs. BBA – Gene Regulatory Mechanisms. 1859(1):31-40 (2016) 6. Y. Enuka, M. Lauriola, M.E. Feldman, A. Sas-Chen, I. Ulitsky, Y. Yarden. Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor. Nucleic Acids Research. 44(3):1370-83. (2016) 7. K. Bahar Halpern, I. Caspi, D. Lemze, M. Levy, S. Landen, E. Elinav, I. Ulitsky, S. Itzkovitz. Nuclear retention of mRNA in mammalian tissues. Cell Reports. 13(12):2653-62 (2015) 8. S. Rabinovich, L. Adler, K. Yizhak, A. Sarver, A. Silberman, S. Agron, N. Stettner, Q. Sun, A. Brandis, D. Helbling, S. Korman, S. Itzkovitz, D. Dimmock, I. Ulitsky, SCS Nagamani, E. Ruppin, A. Erez. Diversion of aspartate in ASS1-deficient tumors fosters de novo pyrimidine synthesis. Nature. 527(7578):379-83 (2015) 9. R. Arafeh, N. Qutob, R. Emmanuel, … , I Ulitsky, GJ Mann, RA Scolyer, NK Hayward, Y. Samuels. Recurrent inactivating RASA2 mutations in melanoma. Nature Genetics. 47(12):1408-10 (2015) 10. H. Hezroni, D. Koppstein, M.G. Schwartz, A. Avrutin, D.P. Bartel, I. Ulitsky. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Reports. 11(7):1110-22 (2015) 11. I. Ulitsky and D.P. Bartel. “lincRNAs: Genomics, Evolution, and Mechanisms”. Cell. 154(1):26-46 (2013) 12. V. Ayeung, I. Ulitsky, S.E. McGeary and D.P. Bartel. “Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing”. Cell. 152(4):844-58 (2013) 13. 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) 14. 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) 15. 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) 16. 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) 17. 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) 18. I. Ulitsky, L.C. Laurent and R. Shamir. “Towards computational prediction of microRNA function and activity”. Nucleic Acids Research 38(15):e160 (2010) 19. 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) 20. 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) 21. 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) 22. 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) 23. 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) 24. I. Ulitsky, N.J. Krogan and R. Shamir. “Towards accurate imputation of quantitative genetic interactions”. Genome Biology 10:R140 (2009) 25. I. Ulitsky and R. Shamir. “Identifying functional modules using expression profiles and confidence-scored protein
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