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List of works by Itamar Simon

A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors

A combined expression-interaction model for inferring the temporal activity of transcription factors

scientific article published on August 2009

A probabilistic generative model for GO enrichment analysis

scientific article published on August 2008

Allele-specific expression patterns of interleukin-2 and Pax-5 revealed by a sensitive single-cell RT-PCR analysis

scientific article published on 01 June 2000

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

scientific article

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

scientific article published on 16 June 2009

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

scientific article

Chromatin immunoprecipitation-on-chip reveals stress-dependent p53 occupancy in primary normal cells but not in established cell lines

scientific article published in December 2008

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

scientific article

Combined analysis reveals a core set of cycling genes

scientific article published on January 2007

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

scientific article published in December 2005

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

scientific article

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

scientific article published on 21 August 2003

Competition between small RNAs: a quantitative view

scientific article published on April 2012

Continuous hidden process model for time series expression experiments

scientific article

Continuous representations of time-series gene expression data

scientific article

DECOD: fast and accurate discriminative DNA motif finding

scientific article

DNA methylation and gene expression

scientific article published on 01 May 2010

Deconvolving cell cycle expression data with complementary information

scientific article

Developmental programming of CpG island methylation profiles in the human genome

scientific article

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

scientific article

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

scientific article

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

scientific article

From promoter sequence to expression

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

scientific article

Genome-wide analysis of androgen receptor targets reveals COUP-TF1 as a novel player in human prostate cancer

scientific article

Genome-wide analysis of the replication program in mammals

scientific article published on January 2010

Genome-wide location and function of DNA binding proteins

scientific article (publication date: 22 December 2000)

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

scholarly article

Global organization of replication time zones of the mouse genome

scientific article published on 30 July 2008

Higher-order association of extrachromosomal rDNA genes in Dictyostelium discoideum

scientific article published on 01 November 1994

Integrating multiple evidence sources to predict transcription factor binding in the human genome

scientific article

Integrative analysis of methylome and transcriptome reveals the importance of unmethylated CpGs in non-CpG island gene activation

scientific article published on 10 July 2013

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

scientific article published on 11 March 2015

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

scientific article

Modulation of the vitamin D3 response by cancer-associated mutant p53

scientific article

Molecular characteristics of liver metastases from uveal melanoma

scientific article published on November 2007

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

scientific article

Perturbations in the Replication Program Contribute to Genomic Instability in Cancer

scientific article published on 25 May 2017

Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling.

scientific article

Reconstructing dynamic regulatory maps

scientific article published on 16 January 2007

Serial regulation of transcriptional regulators in the yeast cell cycle

scientific article (publication date: 21 September 2001)

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

scientific article published on July 18, 2012

Systematic analysis of essential yeast TAFs in genome-wide transcription and preinitiation complex assembly

scientific article

Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization

scientific article

Tamoxifen induces heparanase expression in estrogen receptor-positive breast cancer

scientific article

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress

scientific article

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

scientific article

The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain

scientific article published on 01 March 2015

Transcriptional regulatory networks in Saccharomyces cerevisiae

scientific article

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