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Fields of interest

• Computational Biology / Bioinformatics
• Transcriptional networks
• Microarray data analysis

Academic Degrees

B.Sc. - Physics, Tel Aviv University, 1993.
M.Sc. - Human Genetics, Tel Aviv University, 2001.
Ph.D. - Human Genetics, Tel Aviv University, 2006.

Publications

• Hertzano R, Elkon R, Kurima K, Morrisson A, Chan SL, Sallin M, Biedlingmaier A, Darling DS, Griffith AJ, Eisenman DJ, Strome SE. Cell Type-Specific Transcriptome Analysis Reveals a Major Role for Zeb1 and miR-200b in Mouse Inner Ear Morphogenesis. PLoS Genet. 2011 Sep;7(9):e1002309.
• Salton M, Elkon R, Borodina T, Davydov A, Yaspo ML, Halperin E, Shiloh Y. Matrin 3 binds and stabilizes mRNA. PLoS One. 2011;6(8):e23882.
• Rashi-Elkeles S, Elkon R, Shavit S, Lerenthal Y, Linhart C, Kupershtein A, Amariglio N, Rechavi G, Shamir R, Shiloh Y. Transcriptional modulation induced by ionizing radiation: p53 remains a central player. Mol Oncol. 2011 Aug;5(4):336-48.
• Elkan-Miller T, Ulitsky I, Hertzano R, Rudnicki A, Dror AA, Lenz DR, Elkon R, Irmler M, Beckers J, Shamir R, Avraham KB. Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PLoS One. 2011 Apr 5;6(4):e18195.
• Bensimon A, Schmidt A, Ziv Y, Elkon R, Wang SY, Chen DJ, Aebersold R, Shiloh Y. ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Sci Signal. 2010 Dec 7;3(151):rs3.
• Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R. SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9.
• Kedde M, van Kouwenhove M, Zwart W, Oude Vrielink JA, Elkon R, Agami R. A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol. 2010 Oct;12(10):1014-20.
• Elkon R, Zlotorynski E, Zeller KI, Agami R. Major role for mRNA stability in shaping the kinetics of gene induction. BMC Genomics. 2010 Apr 21;11:259.
• Drost J, Mantovani F, Tocco F, Elkon R, Comel A, Holstege H, Kerkhoven R, Jonkers J, Voorhoeve PM, Agami R, Del Sal G. BRD7 is a candidate tumour suppressor gene required for p53 function. Nat Cell Biol. 2010 Apr;12(4):380-9.
• Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Expander: from expression microarrays to networks and functions. Nat Protoc. 2010;5(2):303-22.
• Elkon R, Agami R. Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs. PLoS Comput Biol. 2008 Oct 3;4(10):e1000189.
• Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R, Assa J, Shiloh Y, Shamir R. SPIKE - a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics. 2008 Feb 20;9:110.
• Elkon R, Linhart C, Halperin Y, Shiloh Y, Shamir R. Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics. 2007 Oct 29;8:394.
• Blum R, Elkon R, Yaari S, Zundelevich A, Jacob-Hirsch J, Rechavi G, Shamir R, Kloog Y. Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid). Cancer Res. 2007 Apr 1;67(7):3320-8
• Zhou T, Chou J, Mullen TE, Elkon R, Zhou Y, Simpson DA, Bushel PR, Paules RS, Lobenhofer EK, Hurban P, Kaufmann WK. Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. Cell Cycle. 2007 Apr;6(8):972-81.
• Blum R, Elkon R, Yaari S, Zundelevich A, Jacob-Hirsch J, Rechavi G, Shamir R, Kloog Y. Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid). Cancer Res. 2007 Apr 1;67(7):3320-8.
• Rashi-Elkeles S, Elkon R, Weizman N, Linhart C, Amariglio N, Sternberg G, Rechavi G, Barzilai A, Shamir R, and Shiloh Y. Parallel induction of ATM-dependent pro- and anti-apoptotic signals in response to ionizing radiation in murine lymphoid tissue. Oncogene. 2006 Mar 9;25(10):1584-92.
• Blum R, Nakdimon I, Goldberg L, Elkon R, Shamir R, Rechavi G, Kloog Y. E2F1 identified by promoter and biochemical analysis as a central target of glioblastoma cell-cycle arrest in response to Ras inhibition. Int J Cancer. 2006 Aug 1;119(3):527-38.
• Scafoglio C, Ambrosino C, Cicatiello L, Altucci L, Ardovino M, Bontempo P, Medici N, Molinari AM, Nebbioso A, Facchiano A, Calogero RA, Elkon R, Menini N, Ponzone R, Biglia N, Sismondi P, Bortoli MD, Weisz A. Comparative gene expression profiling reveals partially overlapping but distinct genomic actions of different antiestrogens in human breast cancer cells. J Cell Biochem. 2006 Aug 1;98(5):1163-84.
• Linhart C, Elkon R, Shiloh Y, and Shamir R. Deciphering transcriptional regulatory elements that encode specific cell-cycle phasing by comparative genomics analysis. Cell Cycle. 2005 Dec 13;4(12).
• Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, and Elkon R. EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinformatics 2005, 6:232.
• Ziv S, Brenner O, Amariglio N, Galron N, Smorodinsky N, Carrion D, Zhang W, Sharma G, Pandita R, Agarwal M, Elkon R, Katzin N, Bar-Am N, Pandita T, Kucherlapati R, Rechavi G, Shiloh Y, and Barzilai A. Increased oxidative stress and impaired genomic stability exacerbate different features of A-T. Hum Mol Genet. 2005 Oct 1;14(19):2929-43.
• Elkon R, Rashi-Elkeles S, Lerenthal Y, Linhart C, Tenne T, Amariglio N, Rechavi G, Shamir R, Shiloh Y. Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biol. 2005;6(5):R43.
• Ophir G, Amariglio N, Jacob-Hirsch J, Elkon R, Rechavi G, Michaelson DM. Apolipoprotein E4 enhances brain inflammation by modulation of the NF-kappaB signaling cascade. Neurobiol Dis. 2005 Jun 22.
• Elkon R, Zeller KI, Linhart C, Dang CV, Shamir R, and Shiloh Y. In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Research 2004 32(17):4955-4961
• Hertzano R, Montcouquiol M, Rashi-Elkeles S, Elkon R, Yucel R, Frankel WN, Rechavi G, Moroy T, Friedman TB, Kelley MW, Avraham KB. Transcription profiling of inner ears from Pou4f3ddl/ddl identifies Gfi1 as a target of the Pou4f3 deafness gene. Hum Mol Genet. 2004; 13(18):2143-53.
• Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res. 2003 May;13(5):773-80 ,
• Fuchs T, Malecova B, Linhart C, Sharan R, Khen M, Herwig R, Shmulevich D, Elkon R, Steinfath M, O'Brien JK, Radelof U, Lehrach H, Lancet D, Shamir R. DEFOG: a practical scheme for deciphering families of genes. Genomics. 2002 Sep;80(3):295-302.
• Sharan Roded, Elkon Ran, Shamir Ron. Cluster analysis and its applications to gene expression data. Ernst Schering Res Found Workshop. 2002;(38):83-108. Review
 

Projects

• PRIMA (PRomoter Integration in Microarray Analysis),
• EXPANDER (EXpression Analyzer and DisplayER)
• SPIKE (Signaling Pathway Integrated Knowledge Engine)

Ron Shamir's Group

• Homepage
• Publications

Other

• Edmond J. Safra Bioinformatics Program