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Itamar Simon

Research Profile

Procedures

Devices

Oligonucleotide Array Sequence Analysis

Chemicals & Drugs

Living Beings

Saccharomyces cerevisiae

Occupations

Computational Biology

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Physiology

Genes & Molecular Sequences

Phenomena

Protein Binding

Anatomy

Cells, Cultured

Co-author Network

Publications

TOP 3
Ziv Bar-Joseph; Anthony Gitter; Itamar Simon
Studying and modelling dynamic biological processes using time-series gene expression data.
Shlomit Farkash-Amar; Hadas Hezroni; Eran Meshorer; Andreas Polten; Yaara David; Yonina C Eldar; Zohar Yakhini; Itamar Simon
Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.
Zahava Siegfried; Itamar Simon
DNA methylation and gene expression.

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All Publications

2012: Ziv Bar-Joseph; Anthony Gitter; Itamar Simon
Studying and modelling dynamic biological processes using time-series gene expression data.
Nature reviews. Genetics 2012;13(8):552-64.
2012: Shlomit Farkash-Amar; Hadas Hezroni; Eran Meshorer; Andreas Polten; Yaara David; Yonina C Eldar; Zohar Yakhini; Itamar Simon
Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.
PloS one 2012;7(11):e48986.
2010: Zahava Siegfried; Itamar Simon
DNA methylation and gene expression.
Wiley interdisciplinary reviews. Systems biology and medicine 2010;2(3):362-71.
2010: Jason Ernst; Heather L Plasterer; Itamar Simon; Ziv Bar-Joseph
Integrating multiple evidence sources to predict transcription factor binding in the human genome.
Genome research 2010;20(4):526-36.
2010: Michael Klutstein; Zahava Siegfried; Ariel Gispan; Shlomit Farkash-Amar; Guy Zinman; Ziv Bar-Joseph; Giora Simchen; Itamar Simon
Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes.
BMC genomics 2010;11():478.
2010: Shlomit Farkash-Amar; Itamar Simon
Genome-wide analysis of the replication program in mammals.
Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 2010;18(1):115-25.
2009: Yanxin Shi; Michael Klutstein; Itamar Simon; Tom Mitchell; Ziv Bar-Joseph
A combined expression-interaction model for inferring the temporal activity of transcription factors.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(8):1035-49.
2009: Ravid Straussman; Deborah Nejman; Douglas Roberts; Israel Steinfeld; Barak Blum; Nissim Benvenisty; Itamar Simon; Zohar Yakhini; Howard Cedar
Developmental programming of CpG island methylation profiles in the human genome.
Nature structural & molecular biology 2009;16(5):564-71.
2009: Anthony Gitter; Zehava Siegfried; Michael Klutstein; Oriol Fornes; Baldo Oliva; Itamar Simon; Ziv Bar-Joseph
Backup in gene regulatory networks explains differences between binding and knockout results.
Molecular systems biology 2009;5():276.
2008: Helena Shaked; Idit Shiff; Miriam Kott-Gutkowski; Zahava Siegfried; Ygal Haupt; Itamar Simon
Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines.
Cancer research 2008;68(23):9671-7.
2008: Yong Lu; Roni Rosenfeld; Itamar Simon; Gerard J Nau; Ziv Bar-Joseph
A probabilistic generative model for GO enrichment analysis.
Nucleic acids research 2008;36(17):e109.
2008: Shlomit Farkash-Amar; Doron Lipson; Andreas Polten; Alon Goren; Charles E Helmstetter; Zohar Yakhini; Itamar Simon
Global organization of replication time zones of the mouse genome.
Genome research 2008;18(10):1562-70.
2008: Ziv Bar-Joseph; Zahava Siegfried; Michael Brandeis; Benedikt Brors; Yong Lu; Roland Eils; Brian David Dynlacht; Itamar Simon
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(3):955-60.
2007: Tal Meir; Rinat Dror; Xueping Yu; Jiang Qian; Itamar Simon; Jacob Pe'er; Itay Chowers
Molecular characteristics of liver metastases from uveal melanoma.
Investigative ophthalmology & visual science 2007;48(11):4890-6.
2007: Irit Cohen; Bella Maly; Itamar Simon; Amichay Meirovitz; Eli Pikarsky; Eyal Zcharia; Tamar Peretz; Israel Vlodavsky; Michael Elkin
Tamoxifen induces heparanase expression in estrogen receptor-positive breast cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2007;13(14):4069-77.
2007: Yanxin Shi; Michael Klustein; Itamar Simon; Tom Mitchell; Ziv Bar-Joseph
Continuous hidden process model for time series expression experiments.
Bioinformatics (Oxford, England) 2007;23(13):i459-67.
2007: Yeshayahu Schlesinger; Ravid Straussman; Ilana Keshet; Shlomit Farkash; Merav Hecht; Joseph Zimmerman; Eran Eden; Zohar Yakhini; Etti Ben-Shushan; Benjamin E Reubinoff; Yehudit Bergman; Itamar Simon; Howard Cedar
Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer.
Nature genetics 2007;39(2):232-6.
2007: Yong Lu; Shaun Mahony; Panayiotis V Benos; Roni Rosenfeld; Itamar Simon; Linda L Breeden; Ziv Bar-Joseph
Combined analysis reveals a core set of cycling genes.
Genome biology 2007;8(7):R146.
2007: Jason Ernst; Oded Vainas; Christopher T Harbison; Itamar Simon; Ziv Bar-Joseph
Reconstructing dynamic regulatory maps.
Molecular systems biology 2007;3():74.
2006: Ilana Keshet; Yeshayahu Schlesinger; Shlomit Farkash; Eyal Rand; Merav Hecht; Eran Segal; Eli Pikarski; Richard A Young; Alain Niveleau; Howard Cedar; Itamar Simon
Evidence for an instructive mechanism of de novo methylation in cancer cells.
Nature genetics 2006;38(2):149-53.
2005: Itamar Simon; Zahava Siegfried; Jason Ernst; Ziv Bar-Joseph
Combined static and dynamic analysis for determining the quality of time-series expression profiles.
Nature biotechnology 2005;23(12):1503-8.
2005: Ran Rubinstein; Itamar Simon
MILANO--custom annotation of microarray results using automatic literature searches.
BMC bioinformatics 2005;6():12.
2004: Ziv Bar-Joseph; Shlomit Farkash; David K Gifford; Itamar Simon; Roni Rosenfeld
Deconvolving cell cycle expression data with complementary information.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i23-30.
2003: Ziv Bar-Joseph; Georg Gerber; Itamar Simon; David K Gifford; Tommi S Jaakkola
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(18):10146-51.
2003: Wu-Cheng Shen; Sukesh R Bhaumik; Helen C Causton; Itamar Simon; Xiaochun Zhu; Ezra Jennings; Tseng-Hsing Wang; Richard A Young; Michael R Green
Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly.
The EMBO journal 2003;22(13):3395-402.
2003: Julia Zeitlinger; Itamar Simon; Christopher T Harbison; Nancy M Hannett; Thomas L Volkert; Gerald R Fink; Richard A Young
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.
Cell 2003;113(3):395-404.
2003: Ziv Bar-Joseph; Georg Gerber; David K Gifford; Tommi S Jaakkola; Itamar Simon
Continuous representations of time-series gene expression data.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):341-56.
2002: Tong Ihn Lee; Nicola J Rinaldi; François Robert; Duncan T Odom; Ziv Bar-Joseph; Georg Gerber; Nancy M Hannett; Christopher T Harbison; Craig M Thompson; Itamar Simon; Julia Zeitlinger; Ezra Jennings; Heather L Murray; D Benjamin Gordon; Bing Ren; John J Wyrick; Jean-Bosco Tagne; Thomas L Volkert; Ernest Fraenkel; David K Gifford; Richard A Young
Transcriptional regulatory networks in Saccharomyces cerevisiae.
Science (New York, N.Y.) 2002;298(5594):799-804.
2001: Itamar Simon; T Tenzen; Raul Mostoslavsky; Eitan Fibach; L Lande; E Milot; J Gribnau; Frank Grosveld; P Fraser; Howard Cedar
Developmental regulation of DNA replication timing at the human beta globin locus.
The EMBO journal 2001;20(21):6150-7.
2001: Itamar Simon; J Barnett; Nancy M Hannett; Christopher T Harbison; Nicola J Rinaldi; Thomas L Volkert; John J Wyrick; Julia Zeitlinger; David K Gifford; Tommi S Jaakkola; Richard A Young
Serial regulation of transcriptional regulators in the yeast cell cycle.
Cell 2001;106(6):697-708.
2000: Bing Ren; François Robert; John J Wyrick; Oscar M Aparicio; Ezra Jennings; Itamar Simon; Julia Zeitlinger; Joerg Schreiber; Nancy M Hannett; E Kanin; Thomas L Volkert; C J Wilson; Stephen P Bell; Richard A Young
Genome-wide location and function of DNA binding proteins.
Science (New York, N.Y.) 2000;290(5500):2306-9.
1999: Itamar Simon; T Tenzen; Benjamin E Reubinoff; D Hillman; John R McCarrey; Howard Cedar
Asynchronous replication of imprinted genes is established in the gametes and maintained during development.
Nature 1999;401(6756):929-32.