PUBLICATIONS

Manuscripts

2017

  • Slobodin B, Han R, Calderone V, Vrielink JA, Loayza-Puch F, Elkon R*, Agami R.* Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation. Cell. 2017 Apr 6;169(2):326-337. (* Co-corresponding authors [PubMed]

  • Matern M, Vijayakumar S, Margulies Z, Milon B, Song Y, Elkon R, Zhang X, Jones SM, Hertzano R. Gfi1(Cre) mice have early onset progressive hearing loss and induce recombination in numerous inner ear non-hair cells. Sci Rep. 2017 Feb 9;7:42079.   [PubMed]

2016

  • Drost R, Dhillon KK, van der Gulden H, van der Heijden I, Brandsma I, Cruz C, Chondronasiou D, Castroviejo-Bermejo M, Boon U, Schut E, van der Burg E, Wientjens E, Pieterse M, Klijn C, Klarenbeek S, Loayza-Puch F, Elkon R, van Deemter L, Rottenberg S, van de Ven M, Dekkers  H, Demmers JA, van Gent DC, Agami R, Balmaña J, Serra V, Taniguchi T, Bouwman P, Jonkers J. BRCA1185delAG tumors may acquire therapy resistance through expression of RING-less BRCA1. J Clin Invest. 2016 Aug 1;126(8):2903-18. [PubMed]

  • Hoffman Y, Bublik DR, Ugalde AP, Elkon R, Biniashvili T, Agami R, Oren M, Pilpel Y. 3’UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells. PLoS Genet. 2016 Feb 23;12(2):e1005879. {PubMed]

  • Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R, Myacheva K, Zwart W, Elkon R* , Agami R*. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat Biotechnol. 2016 Feb;34(2):192-8. (* Co-corresponding authors) [PubMed]

  • Friedman-Mazursky O, Elkon R, Efrat S. Redifferentiation of expanded human islet β cells by inhibition of ARX. Sci Rep. 2016 Feb 9;6:20698. [PubMed]

  • Creemers EE, Bawazeer A, Ugalde AP, van Deutekom HW, van der Made I, de Groot NE, Adriaens ME, Cook SA, Bezzina CR, Hubner N, van der Velden J, Elkon R, Agami R, Pinto YM. Genome-Wide Polyadenylation Maps Reveal Dynamic mRNA 3′-End Formation in the Failing Human Heart. Circ Res. 2016 Feb 5;118(3):433-8. [PubMed]

2015

  • Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AF, Wolf E, Lorenzin F, Eilers M, Agami R. Myc  coordinates transcription and translation to enhance transformation and suppress invasiveness. EMBO Rep. 2015 Dec;16(12):1723-36.  [PubMed]

  • Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M, Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD, Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W, Hertzano R. RFX transcription factors are essential for hearing in mice. Nat Commun. 2015 Oct 15;6:8549  [PubMed]

2014

  • Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, Chobod Y, Paz A, Amstislavskiy V, Sultan M, Safer H, Nietfeld W, Lehrach H, Shamir R, Yaspo ML, Shiloh Y. Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Sci Signal. 2014 May 13;7(325):rs3.  [PubMed]

2013

  • Elkon R, Ugalde AP, Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet. 2013 Jul;14(7):496-506. doi: 10.1038/nrg3482. Review [PubMed]

  • Loayza-Puch F, Drost J, Rooijers K, Lopes R, Elkon R* , Agami R*. p53 induces transcriptional and translational programs to suppress cell proliferation and growth. Genome Biol. 2013 Apr 17;14(4):R32. (* Co-corresponding authors) [PubMed]

  • Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, LÃveillà N, Kalluri R, de Laat W, Agami R. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell. 2013 Feb 7;49(3):524-35. [PubMed]

2012

  • Morris AR, Bos A, Diosdado B, Rooijers K, Elkon R, Bolijn AS, Carvalho B, Meijer GA, Agami R. Alternative cleavage and polyadenylation during colorectal cancer development. Clin Cancer Res. 2012 Oct 1;18(19):5256-66.   [PubMed]

  • Elkon R, Drost J, van Haaften G, Jenal M, Schrier M, Oude Vrielink JA, Agami  R. E2F mediates enhanced alternative polyadenylation in proliferation. Genome Biol. 2012 Jul 2;13(7):R59 [PubMed]

  • Hertzano R, Elkon R. High throughput gene expression analysis of the inner ear. Hear Res. 2012 Jun;288(1-2):77-88 [PubMed]

  • Jenal M, Elkon R, Loayza-Puch F, van Haaften G, Kuhn U, Menzies FM, Oude Vrielink JA, Bos AJ, Drost J, Rooijers K, Rubinsztein DC, Agami R. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell. 2012 Apr 27;149(3):538-53.  [PubMed]

2011

  • LÃveillà N, Elkon R, Davalos V, Manoharan V, Hollingworth D, Oude Vrielink J, le Sage C, Melo CA, Horlings HM, Wesseling J, Ule J, Esteller M, Ramos A, Agami R. Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity. Nat Commun. 2011 Oct 25;2:513.  [PubMed]

  • 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. [PubMed]

  • 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. [PubMed]

  • 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. [PubMed]

  • 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. {PubMed]

2010

  • 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.   [PubMed]

  • 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.  [PubMed]

  • 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.   [PubMed]

  • 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.  [PubMed]

  • 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 [PubMed]

  • 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 Feb;5(2):303-22. [PubMed]

Before 2010

  • 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. [PubMed]

  • 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. [PubMed]

  • 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. [PubMed]

  • 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. [PubMed]

  • 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 15;6(8):972-81. [PubMed]

  • 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, De Bortoli M, 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. [PubMed]

  • 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 [PubMed]

  • Rashi-Elkeles S, Elkon R, Weizman N, Linhart C, Amariglio N, Sternberg G, Rechavi G, Barzilai A, Shamir R, Shiloh Y. Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue. Oncogene. 2006 Mar 9;25(10):1584-92. [PubMed]

  • Linhart C, Elkon R, Shiloh Y, Shamir R. Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle. 2005 Dec;4(12):1788-97 [PubMed]

  • Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R. EXPANDER – an integrative program suite for microarray data analysis. BMC Bioinformatics. 2005 Sep 21;6:232. [PubMed]

  • Ziv S, Brenner O, Amariglio N, Smorodinsky NI, Galron R, Carrion DV, Zhang W, Sharma GG, Pandita RK, Agarwal M, Elkon R, Katzin N, Bar-Am I, Pandita TK, Kucherlapati R, Rechavi G, Shiloh Y, Barzilai A. Impaired genomic stability and increased oxidative stress exacerbate different features of Ataxia-telangiectasia. Hum Mol Genet. 2005 Oct 1;14(19):2929-43. [PubMed]

  • 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 Dec;20(3):709-18 [PubMed]

  • 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. [PubMed]

  • Elkon R, Zeller KI, Linhart C, Dang CV, Shamir R, Shiloh Y. In silico identification of transcriptional regulators associated with c-Myc. Nucleic Acids Res. 2004 Sep 23;32(17):4955-61. [PubMed]

  • Hertzano R, Montcouquiol M, Rashi-Elkeles S, Elkon R, Yücel R, Frankel WN, Rechavi G, MÃrÃy T, Friedman TB, Kelley MW, Avraham KB. Transcription profiling of inner ears from Pou4f3(ddl/ddl) identifies Gfi1 as a target of the Pou4f3 deafness gene. Hum Mol Genet. 2004 Sep 15;13(18):2143-53. [PubMed]

  • 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. [PubMed]

  • 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. [PubMed]

Book chapters

  • Sharan R, Elkon R, Shamir R. Cluster analysis and its applications to gene expression data. In: Bioinformatics and Genome Analysis. Ernst Schering Res Found Workshop (HW. Mewes, H. Seidel and B. Weiss, eds.) 2002; 38:83-108. Springer, Berlin. 2.
  • Elkon R, Rashi-Elkeles S, Shamir R, Shiloh Y. Transcriptional Responses to DNA Damage: Systems-Level Delineation by Functional Genomics. In: Shannon MF, Rao S. Microarrays and Transcription Networks. Georgetown: Landes Bioscience, 2006; 98-113.