Igor Ulitsky

Postdoctoral associate in the Bartel lab at the Whitehead Institute. Previously, I was a PhD student at the School of Computer Science in Tel Aviv University, under the guidance of Prof. Ron Shamir.

Lab: Room 621, 9 Cambridge Ct., Cambridge, MA 02142

Lab phone: (617) 258 8346
E-mail: ulitsky { at } wi.mit.edu

My CV

Current interests & projects:

Currently, my main interest is in the evolution, regulation and functions of long intervening noncoding RNAs (lincRNAs)
- 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)
Alternative polyadenylation
- I. Ulitsky, A. Shkumatava, C. Jan, A.O. Subtelny, D. Koppstein, G. Bell, H. Sive and D.P. Bartel. Extensive Alternative Polyadenylation during Zebrafish Development. Genome Research 22:2054-2066 (2012)
MicroRNA biogenesis
- V. Ayeung, I. Ulitsky, and D.P. Bartel. Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell. In press.

Previous interests & projects:

Function of regulatory RNAs
- I. Ulitsky, L.C. Laurent and R. Shamir. Towards computational prediction of microRNA function and activity. Nucleic Acids Research 38(15):e160 (2010) .
- L.C. Laurent, J. Chen, I. Ulitsky, F.J Mueller, C. Lu, R.Shamir, J.B. Fan and J.F. Loring. Human embryonic stem cell microRNAs share characteristic functions, seed sequences, and genomic locations. Stem Cells 26(6):1506-16 (2008)
- T. Elkan-Miller, I. Ulitsky, R. Hertzano, A. Rudnicki, A. A. Dror, D. R. Lenz, R. Elkon, M. Irmler, J. Beckers, R. Shamir, K.B. Avraham. Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear. PLoS One , Volume 6,Issue 4, e18195, 2011
Identifying functional modules using network and expression data
- MATISSE (download)
  - I. Ulitsky and R. Shamir
    Identification of Functional Modules using Network Topology and High-Throughput Data. BMC Systems Biology 1:8 (2007).
  - F.J. Mueller, D. Kostka, L. Laurent, I. Ulitsky, R. Williams, C. Lu, M.S. Rao, R. Shamir, P.H. Schwartz, N.O. Schmidt, J.F. Loring
    Regulatory networks define phenotypic classes of human stem cell lines. Nature. Vol. 455 No. 7211 p. 401-405 (2008).
- CEZANNE (available as part of MATISSE)
  - I. Ulitsky and R. Shamir
    Identifying functional modules using expression profiles and confidence-scored protein interactions
    Bioinformatics (2009) 25(9):1158-1164 doi: 10.1093/bioinformatics/btp118
- DEGAS (available as part of MATISSE)
  - 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)
  - I. Ulitsky, R.M. Karp and R. Shamir. Detecting disease-specific disregulated pathways via analysis of clinical expression profiles. Proceedings of RECOMB 2008 Lecture Notes in Computer Science Vol. 4955
- Modules correlated with clinical parameters (available as part of MATISSE)
  - I. Ulitsky and R. Shamir
    Detecting pathways transcriptionally correlated with clinical parameters
    Proceedings of CSB 2008
Transcription regulatory networks and analysis of microarray data
- ALEGRO
  - Y. Halperin, C. Linhart, I., Ulitsky and R. Shamir. Analyzing expression and sequence in concert to discover regulatory programs Nucleic Acids Research Advance Online publication doi:10.1093/nar/gkn1064
- MetaReg
  - I. Ulitsky*, I. Gat-Viks* and R. Shamir. MetaReg application: a graphical interface for modeling and evaluation of biological systems. Genome Biology (2008) Vol. 9 No. R1
- SPIKE
  - R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, N. Orlev, G. Sternberg, R. Blekhman, , I. Zohar, G. Mass, J. Assa, Y. Shiloh and R. Shamir. SPIKE: A Database, Visualization and Analysis Tool of Cellular Signaling Pathways. BMC Bioinformatics (2008) 9:110
- Expander
  - 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, In Press
- 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. 2011;6(10):e26992. .
Genetic interaction networks
- I. Ulitsky, N.J. Krogan and R. Shamir. Towards accurate prediction of quantitative genetic interactions. Genome Biology, In Press.
- 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 (2008) doi:10.1038/msb.2008.42
- I. Ulitsky and R. Shamir
  Pathway Redundancy and Protein Essentiality Revealed in the S. cerevisiae Interaction Networks. Molecular Systems Biology 3:104
- P.S. Aguilar, F. Fr?hlich, M. Rehman, M. Shales, I. Ulitsky, A. Olivera-Couto, H. Braberg, R. Shamir, P. Walter, M. Mann, C.S. Ejsing, N.J. Krogan and T.C. Walther. A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking. Nature Structural and Molecular Biology , Vol. 17 no. 7, pp 901-909 (2010)
Other biological networks
- G.H. Romano, Y. Gurevich, O. Lavi, I. Ulitsky, R. Shamir and M. Kupiec
  Dissection of the Complex Genetic Network Determining Natural Genetic Variability. Submitted.
- Roded Sharan*,Igor Ulitsky* and Ron Shamir. Network-based prediction of protein function.
  Molecular Systems Biology 3:88
Whole genome phylogeny

Igor Ulitsky, David Burstein, Tamir Tuller and Benny Chor
The ASC approach to Phylogenomic Reconstruction.
Journal of Computational Biology (JCB) 13(2):336-50, 2006.
David Burstein, Igor Ulitsky, Tamir Tuller and Benny Chor
Information Theoretic Approaches to Whole Genome Phylogenomics.
The Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005), Cambridge, MA, USA, May 14-18, 2005. Proceedings p. 283

Other stuff (past & present):

A guide for following the scientific literature