Works by Simon, Itamar

Results: 37

Genome-wide analysis of the replication program in mammals.

Published in:

Chromosome Research, 2010, v. 18, n. 1, p. 115, doi. 10.1007/s10577-009-9091-5

By:

Farkash-Amar, Shlomit;
Simon, Itamar

Publication type:

Article

Harnessing DNA replication stress to target RBM10 deficiency in lung adenocarcinoma.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-50882-0

By:

Machour, Feras E.;
R. Abu-Zhayia, Enas;
Kamar, Joyce;
Barisaac, Alma Sophia;
Simon, Itamar;
Ayoub, Nabieh

Publication type:

Article

Combined static and dynamic analysis for determining the quality of time-series expression profiles.

Published in:

Nature Biotechnology, 2005, v. 23, n. 12, p. 1503, doi. 10.1038/nbt1164

By:

Simon, Itamar;
Siegfried, Zahava;
Ernst, Jason;
Bar-Joseph, Ziv

Publication type:

Article

Persistence to anti-cancer treatments in the stationary to proliferating transition.

Published in:

Cell Cycle, 2016, v. 15, n. 24, p. 3442, doi. 10.1080/15384101.2016.1248006

By:

Pearl Mizrahi, Sivan;
Gefen, Orit;
Simon, Itamar;
Balaban, Nathalie Q.

Publication type:

Article

A probabilistic generative model for GO enrichment analysis.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 17, p. e109, doi. 10.1093/nar/gkn434

By:

Lu, Yong;
Rosenfeld, Roni;
Simon, Itamar;
Nau, Gerard J.;
Bar-Joseph, Ziv

Publication type:

Article

RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28588-y

By:

Feng, Sumin;
Ma, Sai;
Li, Kejiao;
Gao, Shengxian;
Ning, Shaokai;
Shang, Jinfeng;
Guo, Ruiyuan;
Chen, Yingying;
Blumenfeld, Britny;
Simon, Itamar;
Li, Qing;
Guo, Rong;
Xu, Dongyi

Publication type:

Article

Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer.

Published in:

Nature Genetics, 2007, v. 39, n. 2, p. 232, doi. 10.1038/ng1950

By:

Schlesinger, Yeshayahu;
Straussman, Ravid;
Keshet, Ilana;
Farkash, Shlomit;
Hecht, Merav;
Zimmerman, Joseph;
Eden, Eran;
Yakhini, Zohar;
Ben-Shushan, Etti;
Reubinoff, Benjamin E.;
Bergman, Yehudit;
Simon, Itamar;
Cedar, Howard

Publication type:

Article

Evidence for an instructive mechanism of de novo methylation in cancer cells.

Published in:

Nature Genetics, 2006, v. 38, n. 2, p. 149, doi. 10.1038/ng1719

By:

Keshet, Ilana;
Schlesinger, Yeshayahu;
Farkash, Shlomit;
Rand, Eyal;
Hecht, Merav;
Segal, Eran;
Pikarski, Eli;
Young, Richard A.;
Niveleau, Alain;
Cedar, Howard;
Simon, Itamar

Publication type:

Article

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture.

Published in:

PLoS Genetics, 2010, v. 6, n. 7, p. 1, doi. 10.1371/journal.pgen.1001011

By:

Yaffe, Eitan;
Farkash-Amar, Shlomit;
Polten, Andreas;
Yakhini, Zohar;
Tanay, Amos;
Simon, Itamar

Publication type:

Article

Continuous hidden process model for time series expression experiments.

Published in:

Bioinformatics, 2007, v. 23, n. 13, p. i459, doi. 10.1093/bioinformatics/btm218

By:

Yanxin Shi;
Michael Klustein;
Itamar Simon;
Tom Mitchell;
Ziv Bar-Joseph

Publication type:

Article

Deconvolving cell cycle expression data with complementary information.

Published in:

Bioinformatics, 2004, v. 20, n. suppl_1, p. i23, doi. 10.1093/bioinformatics/bth915

By:

Bar-Joseph, Ziv;
Farkash, Shlomit;
Gifford, David K.;
Simon, Itamar;
Rosenfeld, Roni

Publication type:

Article

Deconvolving cell cycle expression data with complementary information.

Published in:

Bioinformatics, 2004, v. 20, p. i23, doi. 10.1093/bioinformatics/bth915

By:

Bar-Joseph, Ziv;
Farkash, Shlomit;
Gifford, David K.;
Simon, Itamar;
Rosenfeld, Roni

Publication type:

Article

Mutational signatures association with replication timing in normal cells reveals similarities and differences with matched cancer tissues.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-34631-9

By:

Yaacov, Adar;
Rosenberg, Shai;
Simon, Itamar

Publication type:

Article

Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences.

Published in:

PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0172769

By:

Vardi, Oriya;
Shamir, Inbal;
Javasky, Elisheva;
Goren, Alon;
Simon, Itamar

Publication type:

Article

Characterization of Unidirectional Replication Forks in the Mouse Genome.

Published in:

International Journal of Molecular Sciences, 2023, v. 24, n. 11, p. 9611, doi. 10.3390/ijms24119611

By:

Zerbib, Avital;
Simon, Itamar

Publication type:

Article

Perturbations in the Replication Program Contribute to Genomic Instability in Cancer.

Published in:

International Journal of Molecular Sciences, 2017, v. 18, n. 6, p. 1138, doi. 10.3390/ijms18061138

By:

Blumenfeld, Britny;
Ben-Zimra, Micha;
Simon, Itamar

Publication type:

Article

Studying and modelling dynamic biological processes using time-series gene expression data.

Published in:

Nature Reviews Genetics, 2012, v. 13, n. 8, p. 552, doi. 10.1038/nrg3244

By:

Bar-Joseph, Ziv;
Gitter, Anthony;
Simon, Itamar

Publication type:

Article

DECOD: fast and accurate discriminative DNA motif finding.

Published in:

Bioinformatics, 2011, v. 27, n. 17, p. 2361, doi. 10.1093/bioinformatics/btr412

By:

Huggins, Peter;
Zhong, Shan;
Shiff, Idit;
Beckerman, Rachel;
Laptenko, Oleg;
Prives, Carol;
Schulz, Marcel H.;
Simon, Itamar;
Bar-Joseph, Ziv

Publication type:

Article

Distinguishing between stochasticity and determinism: Examples from cell cycle duration variability.

Published in:

BioEssays, 2016, v. 38, n. 1, p. 8, doi. 10.1002/bies.201500113

By:

Mizrahi, Sivan Pearl;
Sandler, Oded;
Lande-Diner, Laura;
Balaban, Nathalie Q.;
Simon, Itamar

Publication type:

Article

A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms.

Published in:

Biology (2079-7737), 2024, v. 13, n. 3, p. 175, doi. 10.3390/biology13030175

By:

Rapoport, Rachel;
Greenberg, Avraham;
Yakhini, Zohar;
Simon, Itamar

Publication type:

Article

S Phase Duration Is Determined by Local Rate and Global Organization of Replication.

Published in:

Biology (2079-7737), 2022, v. 11, n. 5, p. 718, doi. 10.3390/biology11050718

By:

Greenberg, Avraham;
Simon, Itamar

Publication type:

Article

MILANO -- custom annotation of microarray results using automatic literature searches.

Published in:

BMC Bioinformatics, 2005, v. 6, p. 1, doi. 10.1186/1471-2105-6-12

By:

Rubinstein, Ran;
Simon, Itamar

Publication type:

Article

Both cell autonomous and non-autonomous processes modulate the association between replication timing and mutation rate.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-39463-1

By:

Vardi-Yaacov, Oriya;
Yaacov, Adar;
Rosenberg, Shai;
Simon, Itamar

Publication type:

Article

Both cell autonomous and non-autonomous processes modulate the association between replication timing and mutation rate.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-39463-1

By:

Vardi-Yaacov, Oriya;
Yaacov, Adar;
Rosenberg, Shai;
Simon, Itamar

Publication type:

Article

The mutation spectrum in genomic late replication domains shapes mammalian GC content.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 9, p. 4222, doi. 10.1093/nar/gkw268

By:

Kenigsberg, Ephraim;
Yishai Yehuda;
Marjavaara, Lisette;
Keszthelyi, Andrea;
Chabes, Andrei;
Tanay, Amos;
Simon, Itamar

Publication type:

Article

Developmental regulation of DNA replication timing at the human ß globin locus.

Published in:

EMBO Journal, 2001, v. 20, n. 21, p. 6150, doi. 10.1093/emboj/20.21.6150

By:

Simon, Itamar;
Tenzen, Toyoaki;
Mostoslavsky, Raul;
Fibach, Eitan;
Lande, Laura;
Milot, Eric;
Gribnau, Joost;
Grosveld, Frank;
Fraser, Peter;
Cedar, Howard

Publication type:

Article

Backup in gene regulatory networks explains differences between binding and knockout results.

Published in:

Molecular Systems Biology, 2009, v. 5, n. 1, p. 276, doi. 10.1038/msb.2009.33

By:

Gitter, Anthony;
Siegfried, Zehava;
Klutstein, Michael;
Fornes, Oriol;
Oliva, Baldo;
Simon, Itamar;
Bar‐Joseph, Ziv

Publication type:

Article

Reconstructing dynamic regulatory maps.

Published in:

Molecular Systems Biology, 2007, v. 3, n. 1, p. 74, doi. 10.1038/msb4100115

By:

Ernst, Jason;
Vainas, Oded;
Harbison, Christopher T;
Simon, Itamar;
Bar‐Joseph, Ziv

Publication type:

Article

Developmental programming of CpG island methylation profiles in the human genome.

Published in:

Nature Structural & Molecular Biology, 2009, v. 16, n. 5, p. 564, doi. 10.1038/nsmb.1594

By:

Straussman, Ravid;
Nejman, Deborah;
Roberts, Douglas;
Steinfeld, Israel;
Blum, Barak;
Benvenisty, Nissim;
Simon, Itamar;
Yakhini, Zohar;
Cedar, Howard

Publication type:

Article

Asynchronous replication of imprinted genes is established in the gametes and maintained during...

Published in:

Nature, 1999, v. 401, n. 6756, p. 929, doi. 10.1038/44866

By:

Simon, Itamar;
Tenzen, Toyoaki

Publication type:

Article

Integrative Analysis of Methylome and Transcriptome Reveals the Importance of Unmethylated CpGs in Non-CpG Island Gene Activation.

Published in:

BioMed Research International, 2013, v. 2013, p. 1, doi. 10.1155/2013/785731

By:

Marx, Amichai;
Kahan, Tamar;
Simon, Itamar

Publication type:

Article

Chromosomal coordination and differential structure of asynchronous replicating regions.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21348-4

By:

Blumenfeld, Britny;
Masika, Hagit;
Farago, Marganit;
Yehuda, Yishai;
Halaseh, Lamia;
Vardi, Oriya;
Rapoport, Rachel;
Levin-Klein, Rena;
Cedar, Howard;
Bergman, Yehudit;
Simon, Itamar

Publication type:

Article

Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization.

Published in:

PLoS ONE, 2012, v. 7, n. 11, p. 1, doi. 10.1371/journal.pone.0048986

By:

Farkash-Amar, Shlomit;
David, Yaara;
Polten, Andreas;
Hezroni, Hadas;
Eldar, Yonina C.;
Meshorer, Eran;
Yakhini, Zohar;
Simon, Itamar

Publication type:

Article

Genome-Wide Analysis of Androgen Receptor Targets Reveals COUP-TF1 as a Novel Player in Human Prostate Cancer.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0046467

By:

Perets, Ruth;
Kaplan, Tommy;
Stein, Ilan;
Hidas, Guy;
Tayeb, Shay;
Avraham, Eti;
Ben-Neriah, Yinon;
Simon, Itamar;
Pikarsky, Eli

Publication type:

Article

Lineage correlations of single cell division time as a probe of cell-cycle dynamics.

Published in:

Nature, 2015, v. 519, n. 7544, p. 468, doi. 10.1038/nature14318

By:

Sandler, Oded;
Mizrahi, Sivan Pearl;
Weiss, Noga;
Agam, Oded;
Simon, Itamar;
Balaban, Nathalie Q.

Publication type:

Article

Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phasemeiosis genes.

Published in:

BMC Genomics, 2010, v. 11, p. 478, doi. 10.1186/1471-2164-11-478

By:

Klutstein, Michael;
Siegfried, Zahava;
Gispan, Ariel;
Farkash-Amar, Shlomit;
Zinman, Guy;
Bar-Joseph, Ziv;
Simchen, Giora;
Simon, Itamar

Publication type:

Article

An analysis of intra array repeats: the good, the bad and the non informative.

Published in:

BMC Genomics, 2006, v. 7, p. 136, doi. 10.1186/1471-2164-7-136

By:

Elbez, Yedid;
Farkash-Amar, Shlomit;
Simon, Itamar

Publication type:

Article