Noam Shomron

From OpenWetWare

Revision as of 07:03, 30 November 2008 by Nshomron (Talk | contribs)
(diff) ←Older revision | Current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

I am a Lecturer at Tel Aviv University's Sackler School of Medicine pursuing better understanding of mechanisms governing microRNA regulation and function.

See my homepage

My interests and goals lie within seeking better understanding of the mechanisms governing regulation of gene expression on the RNA level, in particular, regulation by microRNAs and also alternative splicing. I would like to decipher the role these processes play in molding the transcriptome and proteome and thus affect cellular fate during states of health and disease.

I explore microRNA and splicing regulation using bench work, computational biology and high-throughput techniques. I focus on several aspects that together shed light on these small non-coding RNAs and their roles in molecular biology and evolution. On the miRNA annotation level, I complemented the miRNA registry (miRbase) with hundreds of mammalian high-confidence miRNA homologs and looked into their genomic organization and regulation. Regarding miRNA roles, I proposed a new function for miRNAs in buffering developmental related gene expression and I linked miRNA regulation to oncofetal genes relevant to human cancer. For miRNA targeting, I deciphered determinants of targeting by endogenous (and exogenous) miRNAs (also applicable to siRNAs).

Also see: http://web.mit.edu/nshomron/www http://pag.csail.mit.edu/mirnaminer http://genes.mit.edu/targetrank http://people.csail.mit.edu/akiezun/miRviewer/


Selected Publications:

Friedman BA, Stadler MB, Shomron N, Ding Y, Burge CB. Ab initio identification of functionally interacting pairs of cis-regulatory elements. Genome Res. 2008 Oct;18(10):1643-51. Epub 2008 Sep 17.

Boyerinas B, Park SM, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter ME. Identification of let-7-regulated oncofetal genes. Cancer Res. 2008 Apr 15;68(8):2587-91.

Artzi S, Kiezun A, Shomron N. miRNAminer: a tool for homologous microRNA gene search. BMC Bioinformatics. 2008 Jan 23;9:39.

Amit M, Sela N, Keren H, Melamed Z, Muler I, Shomron N, Izraeli S, Ast G. Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene. BMC Mol Biol. 2007 Nov 29;8:109.

Nielsen CB, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge CB. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA. 2007 Nov;13(11):1894-910. Epub 2007 Sep 13.

Alberstein M, Amit M, Vaknin K, O'Donnell A, Farhy C, Lerenthal Y, Shomron N, Shaham O, Sharrocks AD, Ashery-Padan R, Ast G. Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing. RNA. 2007 Nov;13(11):1988-99. Epub 2007 Sep 5.

Stadler MB, Shomron N, Yeo GW, Schneider A, Xiao X, Burge CB. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet. 2006 Nov 24;2(11):e191. Epub 2006 Sep 28.

Ibrahim EC, Hims MM, Shomron N, Burge CB, Slaugenhaupt SA, Reed R. Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Hum Mutat. 2007 Jan;28(1):41-53. PMID: 16964593 [PubMed - indexed for MEDLINE]

Hornstein E, Shomron N. Canalization of development by microRNAs. Nat Genet. 2006 Jun;38 Suppl:S20-4. Review.

Ohler U, Shomron N, Burge CB. Recognition of unknown conserved alternatively spliced exons. PLoS Comput Biol. 2005 Jul;1(2):113-22. Epub 2005 Jul 8.

Shomron N, Alberstein M, Reznik M, Ast G. Stress alters the subcellular distribution of hSlu7 and thus modulates alternative splicing. J Cell Sci. 2005 Mar 15;118(Pt 6):1151-9. Epub 2005 Feb 22.

Shomron N, Reznik M, Ast G. Splicing factor hSlu7 contains a unique functional domain required to retain the protein within the nucleus. Mol Biol Cell. 2004 Aug;15(8):3782-95. Epub 2004 Jun 4.

Pessah N, Reznik M, Shamis M, Yantiri F, Xin H, Bowdish K, Shomron N, Ast G, Shabat D. Bioactivation of carbamate-based 20(S)-camptothecin prodrugs. Bioorg Med Chem. 2004 Apr 15;12(8):1859-66.

Shomron N, Ast G. Boric acid reversibly inhibits the second step of pre-mRNA splicing. FEBS Lett. 2003 Sep 25;552(2-3):219-24.

Lev-Maor G, Sorek R, Shomron N, Ast G. The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science. 2003 May 23;300(5623):1288-91.

Malca H, Shomron N, Ast G. The U1 snRNP base pairs with the 5' splice site within a penta-snRNP complex. Mol Cell Biol. 2003 May;23(10):3442-55.

Shomron N, Malca H, Vig I, Ast G. Reversible inhibition of the second step of splicing suggests a possible role of zinc in the second step of splicing. Nucleic Acids Res. 2002 Oct 1;30(19):4127-37.

Personal tools