Publications by authors named "Ran Elkon"

61Publications

Expression pattern of cochlear microRNAs in the mammalian auditory hindbrain.

Cell Tissue Res 2020 Nov 6. Epub 2020 Nov 6.

Neurogenetics Group and Cluster of Excellence Hearing4All, School of Medicine and Health Sciences, Carl Von Ossietzky University Oldenburg, 26111, Oldenburg, Germany.

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http://dx.doi.org/10.1007/s00441-020-03290-xDOI Listing
November 2020

Identification and characterization of key long non-coding RNAs in the mouse cochlea.

RNA Biol 2020 Nov 1:1-10. Epub 2020 Nov 1.

Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University , Tel Aviv, Israel.

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http://dx.doi.org/10.1080/15476286.2020.1836456DOI Listing
November 2020

GFI1 functions to repress neuronal gene expression in the developing inner ear hair cells.

Development 2020 Sep 11;147(17). Epub 2020 Sep 11.

Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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http://dx.doi.org/10.1242/dev.186015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7502595PMC
September 2020

Systematic identification of functional SNPs interrupting 3'UTR polyadenylation signals.

PLoS Genet 2020 08 17;16(8):e1008977. Epub 2020 Aug 17.

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1371/journal.pgen.1008977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7451987PMC
August 2020

Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels.

Mol Cell 2020 05 14;78(3):434-444.e5. Epub 2020 Apr 14.

Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.03.022DOI Listing
May 2020

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias.

PLoS Biol 2019 11 12;17(11):e3000481. Epub 2019 Nov 12.

Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1371/journal.pbio.3000481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850523PMC
November 2019

Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data.

Nucleic Acids Res 2019 11;47(19):10027-10039

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1093/nar/gkz781DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821429PMC
November 2019

The EXPANDER Integrated Platform for Transcriptome Analysis.

J Mol Biol 2019 06 14;431(13):2398-2406. Epub 2019 May 14.

The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.05.013DOI Listing
June 2019

Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions.

Epigenetics Chromatin 2018 08 29;11(1):49. Epub 2018 Aug 29.

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.

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http://dx.doi.org/10.1186/s13072-018-0220-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114837PMC
August 2018

CUEDC1 is a primary target of ERα essential for the growth of breast cancer cells.

Cancer Lett 2018 11 23;436:87-95. Epub 2018 Aug 23.

Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.canlet.2018.08.018DOI Listing
November 2018

Activity-dependent neuroprotective protein (ADNP) is an alcohol-responsive gene and negative regulator of alcohol consumption in female mice.

Neuropsychopharmacology 2019 01 27;44(2):415-424. Epub 2018 Jun 27.

Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel.

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http://www.nature.com/articles/s41386-018-0132-7
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http://dx.doi.org/10.1038/s41386-018-0132-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300527PMC
January 2019

Pax6 regulation of in the mouse retinal pigmented epithelium controls its timely differentiation and choroid vasculature development.

Development 2018 08 9;145(15). Epub 2018 Aug 9.

Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neurosciences, Tel Aviv University, Tel Aviv 69978, Israel

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http://dev.biologists.org/lookup/doi/10.1242/dev.163691
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http://dx.doi.org/10.1242/dev.163691DOI Listing
August 2018

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map.

Genome Biol 2018 05 1;19(1):56. Epub 2018 May 1.

Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel.

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http://dx.doi.org/10.1186/s13059-018-1432-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930446PMC
May 2018

Characterization of noncoding regulatory DNA in the human genome.

Nat Biotechnol 2017 Aug;35(8):732-746

Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/nbt.3863DOI Listing
August 2017

Proteomic analysis of polyribosomes identifies splicing factors as potential regulators of translation during mitosis.

Nucleic Acids Res 2017 Jun;45(10):5945-5957

Department of Cell Research & Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkx326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449605PMC
June 2017

Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation.

Cell 2017 04;169(2):326-337.e12

Division of Oncogenomics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2017.03.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388891PMC
April 2017

Gfi1 mice have early onset progressive hearing loss and induce recombination in numerous inner ear non-hair cells.

Sci Rep 2017 02 9;7:42079. Epub 2017 Feb 9.

Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1038/srep42079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299610PMC
February 2017

Redifferentiation of expanded human islet β cells by inhibition of ARX.

Sci Rep 2016 Feb 9;6:20698. Epub 2016 Feb 9.

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1038/srep20698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746595PMC
February 2016

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9.

Nat Biotechnol 2016 Feb 11;34(2):192-8. Epub 2016 Jan 11.

Division of Biological Stress Response, the Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://www.nature.com/articles/nbt.3450
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http://dx.doi.org/10.1038/nbt.3450DOI Listing
February 2016

Genome-Wide Polyadenylation Maps Reveal Dynamic mRNA 3'-End Formation in the Failing Human Heart.

Circ Res 2016 Feb 15;118(3):433-8. Epub 2015 Dec 15.

From the Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands (E.E.C., A.B., H.W.M.D., I.M., N.E.G., M.E.A., C.R.B., Y.M.P.); Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands (A.P.U., R.E., R.A.); National Heart and Lung Institute, Imperial College, London, United Kingdom (S.A.C.); Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany (N.H.); and Department of Physiology, VU University Medical Center, Amsterdam, The Netherlands (J.V.).

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http://dx.doi.org/10.1161/CIRCRESAHA.115.307082DOI Listing
February 2016

Myc coordinates transcription and translation to enhance transformation and suppress invasiveness.

EMBO Rep 2015 Dec 4;16(12):1723-36. Epub 2015 Nov 4.

Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands Erasmus MC, Rotterdam University, Rotterdam, The Netherlands

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http://dx.doi.org/10.15252/embr.201540717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4687422PMC
December 2015

Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation.

Sci Signal 2014 May 13;7(325):rs3. Epub 2014 May 13.

The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1126/scisignal.2005032DOI Listing
May 2014

Alternative cleavage and polyadenylation: extent, regulation and function.

Nat Rev Genet 2013 Jul;14(7):496-506

Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/nrg3482DOI Listing
July 2013

eRNAs are required for p53-dependent enhancer activity and gene transcription.

Mol Cell 2013 Feb 27;49(3):524-35. Epub 2012 Dec 27.

Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands; Doctoral Programme in Biomedicine and Experimental Biology, Centre for Neuroscience and Cell Biology, 3004-517 Coimbra, Portugal.

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http://dx.doi.org/10.1016/j.molcel.2012.11.021DOI Listing
February 2013

Alternative cleavage and polyadenylation during colorectal cancer development.

Clin Cancer Res 2012 Oct 8;18(19):5256-66. Epub 2012 Aug 8.

The Netherlands Cancer Institute, The Netherlands.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-0543DOI Listing
October 2012

High throughput gene expression analysis of the inner ear.

Hear Res 2012 Jun 8;288(1-2):77-88. Epub 2012 Feb 8.

Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland, 16 S Eutaw St. Suite 500, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1016/j.heares.2012.01.002DOI Listing
June 2012

The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites.

Cell 2012 Apr 12;149(3):538-53. Epub 2012 Apr 12.

Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.cell.2012.03.022DOI Listing
April 2012

Matrin 3 binds and stabilizes mRNA.

PLoS One 2011 17;6(8):e23882. Epub 2011 Aug 17.

The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023882PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157474PMC
February 2012

Transcriptional modulation induced by ionizing radiation: p53 remains a central player.

Mol Oncol 2011 Aug 7;5(4):336-48. Epub 2011 Jul 7.

The David and Inez Myers Laboratory for Genetic Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Room 1022, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1016/j.molonc.2011.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528315PMC
August 2011

ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage.

Sci Signal 2010 Dec 7;3(151):rs3. Epub 2010 Dec 7.

David and Inez Myers Laboratory for Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://stke.sciencemag.org/cgi/doi/10.1126/scisignal.2001034
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http://dx.doi.org/10.1126/scisignal.2001034DOI Listing
December 2010

SPIKE: a database of highly curated human signaling pathways.

Nucleic Acids Res 2011 Jan 19;39(Database issue):D793-9. Epub 2010 Nov 19.

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkq1167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014840PMC
January 2011

A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility.

Nat Cell Biol 2010 Oct 5;12(10):1014-20. Epub 2010 Sep 5.

Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/ncb2105DOI Listing
October 2010

Major role for mRNA stability in shaping the kinetics of gene induction.

BMC Genomics 2010 Apr 21;11:259. Epub 2010 Apr 21.

Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864252PMC
April 2010

BRD7 is a candidate tumour suppressor gene required for p53 function.

Nat Cell Biol 2010 Apr 14;12(4):380-9. Epub 2010 Mar 14.

The Netherlands Cancer Institute, Division of Gene Regulation, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.

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http://www.nature.com/articles/ncb2038
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http://dx.doi.org/10.1038/ncb2038DOI Listing
April 2010

Expander: from expression microarrays to networks and functions.

Nat Protoc 2010 Feb 28;5(2):303-22. Epub 2010 Jan 28.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.1038/nprot.2009.230DOI Listing
February 2010

Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs.

PLoS Comput Biol 2008 Oct 3;4(10):e1000189. Epub 2008 Oct 3.

Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1000189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2533120PMC
October 2008

SPIKE--a database, visualization and analysis tool of cellular signaling pathways.

BMC Bioinformatics 2008 Feb 20;9:110. Epub 2008 Feb 20.

The David and Inez Myers Laboratory for Genetic Research, Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1471-2105-9-110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263022PMC
February 2008

Functional genomic delineation of TLR-induced transcriptional networks.

BMC Genomics 2007 Oct 29;8:394. Epub 2007 Oct 29.

The David and Inez Myers Laboratory for Genetic Research, Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-8-394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175519PMC
October 2007

Gene expression signature of human cancer cell lines treated with the ras inhibitor salirasib (S-farnesylthiosalicylic acid).

Cancer Res 2007 Apr;67(7):3320-8

Department of Neurobiochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

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http://cancerres.aacrjournals.org/lookup/doi/10.1158/0008-54
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http://dx.doi.org/10.1158/0008-5472.CAN-06-4287DOI Listing
April 2007

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;119(3):527-38

Department of Neurobiochemistry, Sackler School of Medicine, Tel-Aviv University, and Safra Children's Hospital, Sheba Medical Center, Israel.

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http://dx.doi.org/10.1002/ijc.21735DOI Listing
August 2006

Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis.

Cell Cycle 2005 Dec 13;4(12):1788-97. Epub 2005 Dec 13.

School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

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http://dx.doi.org/10.4161/cc.4.12.2173DOI Listing
December 2005

EXPANDER--an integrative program suite for microarray data analysis.

BMC Bioinformatics 2005 Sep 21;6:232. Epub 2005 Sep 21.

School of Computer Science, Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1471-2105-6-232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1261157PMC
September 2005

Apolipoprotein E4 enhances brain inflammation by modulation of the NF-kappaB signaling cascade.

Neurobiol Dis 2005 Dec 23;20(3):709-18. Epub 2005 Jun 23.

Department of Neurobiochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1016/j.nbd.2005.05.002DOI Listing
December 2005

Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis.

Genome Biol 2005 13;6(5):R43. Epub 2005 Apr 13.

The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.

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http://dx.doi.org/10.1186/gb-2005-6-5-r43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175955PMC
May 2006

In silico identification of transcriptional regulators associated with c-Myc.

Nucleic Acids Res 2004 23;32(17):4955-61. Epub 2004 Sep 23.

The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, Tel Aviv University, Israel.

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http://dx.doi.org/10.1093/nar/gkh816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC521640PMC
September 2004

Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.

Genome Res 2003 May;13(5):773-80

The David and Inez Myers Laboratory for Genetic Research, Department of Human Genetics, Sackler School of Medicine, and School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1101/gr.947203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC430898PMC
May 2003