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The Faculty of Medicine - Microbiology and Molecular Genetics: Simon Itamar

Researchers

 Last updated June 2021 - School of Pharmacy

List of Publications

(1) Blumenfeld B, Masika H, Farago M, Yehuda Y, Halaseh L, Vardi O, et al. Chromosomal coordination and differential structure of asynchronous replicating regions. Nat Commun 2021;12(1).

(2) Bar-Joseph Z, Simon I. Special issue focused on regulatory genomics. Curr Opin Syst 2020;24:153-154.

(3) Greenberg A, Blumenfeld B, Simon I. The delicate relationship between DNA replication timing and gene expression. Curr Opin Syst 2020;19:8-15.

(4) Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, et al. Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns. Genome Res 2018;28(10):1455-1466.

(5) Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, et al. Germline DNA replication timing shapes mammalian genome composition. Nucleic Acids Res 2018;46(16):8299-8310.

(6) Blumenfeld B, Ben-Zimra M, Simon I. Perturbations in the replication program contribute to genomic instability in cancer. Int J Mol Sci 2017;18(6).

(7) Vardi O, Shamir I, Javasky E, Goren A, Simon I. Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences. PLoS ONE 2017;12(2).

(8) Yehuda Y, Blumenfeld B, Lehmann D, Simon I. Genome-wide determination of mammalian replication timing by DNA content measurement. J Visualized Exp 2017;2017(119).

(9) Pearl Mizrahi S, Gefen O, Simon I, Balaban NQ. Persistence to anti-cancer treatments in the stationary to proliferating transition. Cell Cycle 2016;15(24):3442-3453.

(10) Kenigsberg E, Yehuda Y, Marjavaara L, Keszthelyi A, Chabes A, Tanay A, et al. The mutation spectrum in genomic late replication domains shapes mammalian GC content. Nucleic Acids Res 2016;44(9):4222-4232.

(11) Pearl Mizrahi S, Sandler O, Lande-Diner L, Balaban NQ, Simon I. Distinguishing between stochasticity and determinism: Examples from cell cycle duration variability. Bioessays 2016;38(1):8-13.

(12) Sandler O, Mizrahi SP, Weiss N, Agam O, Simon I, Balaban NQ. Lineage correlations of single cell division time as a probe of cell-cycle dynamics. Nature 2015;519(7544):468-471.

(13) Laptenko O, Shiff I, Freed-Pastor W, Zupnick A, Mattia M, Freulich E, et al. The p53 C Terminus Controls Site-Specific DNA Binding and Promotes Structural Changes within the Central DNA Binding Domain. Mol Cell 2015;57(6):1034-1046.

(14) Marx A, Kahan T, Simon I. Integrative analysis of methylome and transcriptome reveals the importance of unmethylated CpGs in non-CpG island gene activation. BioMed Res Int 2013;2013.

(15) Farkash-Amar S, David Y, Polten A, Hezroni H, Eldar YC, Meshorer E, et al. Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization. PLoS ONE 2012;7(11).

(16) Perets R, Kaplan T, Stein I, Hidas G, Tayeb S, Avraham E, et al. Genome-Wide Analysis of Androgen Receptor Targets Reveals COUP-TF1 as a Novel Player in Human Prostate Cancer. PLoS ONE 2012;7(10).

(17) Bar-Joseph Z, Gitter A, Simon I. Studying and modelling dynamic biological processes using time-series gene expression data. Nat Rev Gen 2012;13(8):552-564.

(18) Loinger A, Shemla Y, Simon I, Margalit H, Biham O. Competition between small RNAs: A quantitative view. Biophys J 2012;102(8):1712-1721.

(19) Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, et al. DECOD: Fast and accurate discriminative DNA motif finding. Bioinformatics 2011;27(17):2361-2367.

(20) Klutstein M, Siegfried Z, Gispan A, Farkash-Amar S, Zinman G, Bar-Joseph Z, et al. Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. BMC Genomics 2010;11(1).

(21) Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I. Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet 2010;6(7):1-12.

(22) Stambolsky P, Tabach Y, Fontemaggi G, Weisz L, Maor-Aloni R, Siegfried Z, et al. Erratum: Modulation of the Vitamin D3 Response by Cancer-Associated Mutant p53 (DOI:10.1016/j.ccr.2009.11.025). Cancer Cell 2010;17(5):523.

(23) Siegfried Z, Simon I. DNA methylation and gene expression. Wiley Interdiscip Rev Syst Biol Med 2010;2(3):362-371.

(24) Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res 2010;20(4):526-536.

(25) Stambolsky P, Tabach Y, Fontemaggi G, Weisz L, Maor-Aloni R, Sigfried Z, et al. Modulation of the Vitamin D3 Response by Cancer-Associated Mutant p53. Cancer Cell 2010;17(3):273-285.

(26) Farkash-Amar S, Simon I. Genome-wide analysis of the replication program in mammals. Chromosome Res 2010;18(1):115-125.

(27) Shi Y, Klutstein M, Simon I, Mitchell T, Bar-Joseph Z. A combined expression-interaction model for inferring the temporal activity of transcription factors. J Comput Biol 2009;16(8):1035-1049.

(28) Straussman R, Nejman D, Roberts D, Steinfeld I, Blum B, Benvenisty N, et al. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 2009;16(5):564-571.

(29) Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, et al. Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol 2009;5.

(30) Shaked H, Shiff I, Kott-Gutkowski M, Siegfried Z, Haupt Y, Simon I. Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines. Cancer Res 2008;68(23):9671-9677.

(31) Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z, et al. Global organization of replication time zones of the mouse genome. Genome Res 2008;18(10):1562-1570.

(32) Shi Y, Simon I, Mitchell T, Bar-Joseph Z. A combined expression-interaction model for inferring the temporal activity of transcription factors. Lect Notes Comput Sci 2008;4955 LNBI:82-97.

(33) Bar-Joseph Z, Siegfried Z, Brandeis M, Brors B, Lu Y, Eils R, et al. Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc Natl Acad Sci U S A 2008;105(3):955-960.

(34) Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z. A probabilistic generative model for GO enrichment analysis. Nucleic Acids Res 2008;36(17).

(35) Meir T, Dror R, Yu X, Qian J, Simon I, Pe'er J, et al. Molecular characteristics of liver metastases from uveal melanoma. Invest Ophthalmol Vis Sci 2007;48(11):4890-4896.

(36) Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, et al. Combined analysis reveals a core set of cycling genes. Genome Biol 2007;8(7).

(37) Cohen I, Maly B, Simon I, Meirovitz A, Pikarsky E, Zcharia E, et al. Tamoxifen induces heparanase expression in estrogen receptor - Positive breast cancer. Clin Cancer Res 2007;13(14):4069-4077.

(38) Shi Y, Klustein M, Simon I, Mitchell T, Bar-Joseph Z. Continuous hidden process model for time series expression experiments. Bioinformatics 2007;23(13):i459-i467.

(39) Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Reconstructing dynamic regulatory maps. Mol Syst Biol 2007;3.

(40) Schlesinger Y, Straussman R, Keshet I, Farkash S, Hecht M, Zimmerman J, et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 2007;39(2):232-236.

(41) Elbez Y, Farkash-Amar S, Simon I. An analysis of intra array repeats: The good, the bad and the non informative. BMC Genomics 2006;7.

(42) Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat Genet 2006;38(2):149-153.

(43) Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nat Biotechnol 2005;23(12):1503-1508.

(44) Rubinstein R, Simon I. MILANO - Custom annotation of microarray results using automatic literature searches. BMC Bioinform 2005;6.

(45) Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Deconvolving cell cycle expression data with complementary information. Bioinformatics 2004;20(SUPPL. 1):i23-i30.

(46) Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous Representations of Time-Series Gene Expression Data. J Comput Biol 2003;10(3-4):341-356.

(47) Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A 2003;100(18):10146-10151.

(48) Shen W-, Bhaumik SR, Causton HC, Simon I, Zhu X, Jennings EG, et al. Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly. EMBO J 2003;22(13):3395-3402.

(49) Zeitlinger J, Simon I, Harbison CT, Hannett NM, Volkert TL, Fink GR, et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 2003;113(3):395-404.

(50) Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002;298(5594):799-804.

(51) A new approach to analyzing gene expression time series data. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB; 2002.

(52) From promoter sequence to expression: A probabilistic framework. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB; 2002.

(53) Damelin M, Simon I, Moy TI, Wilson B, Komili S, Tempst P, et al. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol Cell 2002;9(3):563-573.

(54) Simon I, Tenzen T, Mostoslavsky R, Fibach E, Lande L, Milot E, et al. Developmental regulation of DNA replication timing at the human β globin locus. EMBO J 2001;20(21):6150-6157.

(55) Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 2001;106(6):697-708.

(56) Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, et al. Genome-wide location and function of DNA binding proteins. Science 2000;290(5500):2306-2309.

(57) Rhoades KL, Singh N, Simon I, Glidden B, Cedar H, Chess A. Allele-specific expression patterns of interleukin-2 end Pax-5 revealed by a sensitive single-cell RT-PCR analysis. Curr Biol 2000;10(13):789-792.

(58) Simon I, Tenzen T, Reubinoff BE, Hillman D, McCarrey JR, Cedar H. Asynchronous replication of imprinted genes is established in the gametes and maintained during development. Nature 1999;401(6756):929-932.

(59) Simon I, Olins DE. Higher-order association of extrachromosomal rDNA genes in Dictyostelium discoideum. Cell Biol Int 1994;18(11):1091-1094.

(60) Chess A, Simon I, Cedar H, Axel R. Allelic inactivation regulates olfactory receptor gene expression. Cell 1994;78(5):823-834.

(61) Kitsberg D, Selig S, Brandels M, Simon I, Keshet I, Driscoll DJ, et al. Allele-specific replication timing of imprinted gene regions. Nature 1993;364(6436):459-463.