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 interactions”. Bioinformatics 25:1158-1164 (2009) 26. Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir. "Discovering transcriptional modules by combined analysis of expression profiles and regulatory sequences". Nucleic Acids Research 37:1566-1579 (2009) 27. 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) 28. 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) 29. 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) 30. 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) 31. 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) 32. I. Ulitsky and R. Shamir. “Pathway redundancy and protein essentiality revealed in the S. cerevisiae interaction networks”. Molecular Systems Biology 3:104 (2007) 33. R. Sharan*, I. Ulitsky* and R. Shamir. “Network-based prediction of protein function”. Molecular Systems Biology 3:88 (2007) (* - equal contribution). Review. 34. I. Ulitsky and R. Shamir. “Identification of functional modules using network topology and high-throughput data”. BMC Systems Biology 1:8 (2007) 35. 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 1. Ulitsky and R. Shamir. "Detecting pathways transcriptionally correlated with clinical parameters". Proceedings of CSB 2008 249-258, Imperial College Press, London, UK (2008) 2. 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 3. 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 since appointment to Senior Scientist • Invited Speaker, Computation RNA biology conference, Wellcome Genome Campus, Hinxon, UK, October 2016 • Invited Seminar, Cancer Research UK, Cambridge, UK • Invited Speaker, Villars Symposium on “Non-coding RNAs: from Function to Evolution”, Villars, Switzerland, September 2016 • Invited seminar, Hebrew University, March 2016 • Invited seminar, Ben Gurion University, March 2016 • Invited speaker, Batsheva de Rothschild Seminar on RNA regulatory circuits in infectious diseases and man, Weizmann Institute, December 2015 • Selected abstract, EMBL/EMBO Symposium The Noncoding Genome. EMBL Heidelberg, October 2015 • Invited seminar, EMBL Gernoble, France, July 2015 • Invited seminar, Ben Guiron University, Beer Sheva, Israel, May 2015 • Invited speaker, 17th meeting of the Israeli Bioinformatics Society, Tel Aviv University, May 2015 • Invited speaker, Centre for Genomic Regulation (CRG), Barcelona, Spain, February 2015 • Invited seminar, Institut Pasteur, Paris, France, February 2015 • Invited speaker, 14th Tokyo RNA club, Tokyo, Japan, November 2014 • Invited speaker, 14th Molecular Biology Society of Japan, Workshop on, Yokohama, Japan, November 2014 • Invited speaker, Department of Cell Research & Immunology, Tel Aviv University, Israel, November 2014 • Invited speaker, Research seminar at the Sheba Medical Center, Tel HaShomer, Israel, October 2014 • Selected abstract, EMBO/ESF meeting on Long Regulatory RNAs, Poltusk, Poland, September 2014 • Invited speaker, WIS/Karolinska Institute conference, Stockholm, Sweden, June 2014 • Invited seminar, Oslo University Hospital research, Oslo, Norway, May 2014 • Invited seminar, Hebrew University Medical School, Jerusalem, Israel, May 2014 • Invited seminar, BioClub at Hebrew University, Jerusalem, Israel, March 2014 • Selected abstract, Keystone meeting on Long Noncoding RNAs, Santa Fe, March 2014 • 7th Congress of the Federation of the Israel Societies for Experimental Biology (FISEB/ILANIT), February 2014 • Invited speaker, The Helmsley Stem Cells Symposium, Weizmann Institute, December 2013 • Invited speaker, Bar Ilan University seminar series October 2013 • Selected abstract, The Noncoding Genome meeting, EMBL, October 2013

National and International Research Grants

Year Duration Agency Title Total amount (years) 2013-2015 5 ISF (I- Chromatin and RNA I-CORE 1,500,000 NIS CORE) 2014-2017 3 Fritz An Interdisciplinary Approach 120,000 € Thyssen for Studying the Functions of Stiftung Long Noncoding RNAs during Neurogenesis and in Neurological Diseases 2014-2019 5 ISF Computational and 1,650,000 NIS (research experimental methods for grant) identification of functional domains in long noncoding RNAs 2015-2018 3 Minerva Co-transcriptional and post- 150,000 € foundation transcriptional functions of long noncoding RNA genes in endodermal differentiation 2015-2019 5 European lincSAFARI – Sequence and 1,500,000 € Research Function Relationships in Council Long Intervening Noncoding (ERC) RNAs 2016-2019 4 United Global analysis of expression $90,000 States- patterns and roles of long Israel noncoding RNAs during Binational differentiation towards Science pancreatic and hepatic cell Foundation fates

Internal Research Grants

Year Duration Title Total amount (years) 2013-2014 1 Kimmel Stem Cell Center $30,000 support 2014-2015 1 Rising Tide Foundation $100,000 support 2014-2015 1 Benozio Center for $30,000 Neurological disease 2015-2016 1 Benozio Center for $10,000 Neurological disease

Students and Postdoctoral Fellows Master students Aviv Rom (2014-2015) - linc-Chd2 - a conserved long noncoding RNA regulator of Chd2 activity Alexandra Avrutin (2014-2016) - The regulatory circuitry and the involvement of lincRNA Pvt1 in breast cancer Gali Housman (2014-2016) - The regulatory roles of short open reading frames in long non- coding RNAs PhD students Hadas Hezroni (2013-) Neta Degani (2014-) Noa Gil (2014-) Aviv Rom (2015-) Binyamin Zuckerman (2016-) Postdoctoral fellows Ailone Tichon (2014-) Senior interns/ Visiting scientists Yoav Lubelsky (2013-) Miriam Rosenberg (2015-) Rotem Ben Tov Perry (2015-) Visiting students Florain Deckert (8-10/2016) – Visiting student from master student at Ludwig-Maximlian- University Munich Master of Biology program Nate Swetlitz (6-8/2014) – Visiting undergraduate student from Yale University Katharina Holzer (10-12/2014) – Visiting student from Tübingen Master of Biochemistry program