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List of works by Ron Shamir

A Chemical-Distance-Based Test for Positive Darwinian Selection

A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem ⬇️

scientific article published on May 1, 2011

Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays ⬇️

scientific article published on October 1, 2003

CLICK and EXPANDER: a system for clustering and visualizing gene expression data

scientific article

CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps

scientific article published on 01 June 2022

Complexity and algorithms for copy-number evolution problems

scientific article

Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription Factor–DNA Interactions with Expression Data: An Entropy-Based Approach ⬇️

scientific article published on January 1, 2012

Copy-Number Evolution Problems: Complexity and Algorithms

DEFOG: a practical scheme for deciphering families of genes

scientific article

Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers

scientific article published on 24 March 2015

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.

scientific article published on 2 October 2017

Detecting excess radical replacements in phylogenetic trees

scientific article published on 01 November 2003

Discovering statistically significant biclusters in gene expression data

scientific article

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

scientific article

Drosophila TRF2 is a preferential core promoter regulator

scientific article

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing

scientific article published in 2024

EXPANDER--an integrative program suite for microarray data analysis

scientific article

ElemeNT: a computational tool for detecting core promoter elements

scientific article

Environmental stresses disrupt telomere length homeostasis

scientific article

Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism

scientific article published on 15 February 2016

Examination of exhaustive cloning attempts reveals that C. elegans piRNAs, transposons, and repeat sequences are efficiently cloned in yeast, but not in bacteria

scientific article published on 28 August 2014

Expander: from expression microarrays to networks and functions

scientific article

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.

scientific article published on 18 August 2017

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

scientific article published on April 2007

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

scientific article

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data

scientific article

Inaccuracy of the log-rank approximation in cancer data analysis

scientific article published on 01 August 2019

Incomplete Directed Perfect Phylogeny

scholarly article by Itsik Pe'er et al published January 2004 in SIAM Journal on Computing

Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets

scientific article published on 10 August 2015

Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy ⬇️

scientific article published on June 29, 2011

MONET: Multi-omic module discovery by omic selection

scientific article published on 15 September 2020

MicroRNAs are essential for differentiation of the retinal pigmented epithelium and maturation of adjacent photoreceptors

scientific article published on 10 June 2015

Network-Induced Classification Kernels for Gene Expression Profile Analysis ⬇️

scientific article published on June 1, 2012

Network-based prediction of protein function

scientific article

PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets

scientific article published on 26 December 2019

Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD

scientific article published on 08 August 2019

PrtT-Regulated Proteins Secreted by Aspergillus fumigatus Activate MAPK Signaling in Exposed A549 Lung Cells Leading to Necrotic Cell Death ⬇️

scientific article published on March 11, 2011

Reconstructing chain functions in genetic networks

scientific article published in January 2004

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

scientific article

Strongly Polynomial Algorithms for the High Multiplicity Scheduling Problem

scientific article published in 1991

TORQUE: topology-free querying of protein interaction networks

scientific article published on 2 June 2009

The DOMINO web-server for active module identification analysis

scientific article published in 2022

Topology-free querying of protein interaction networks

scientific article published in March 2010

Transcription Factor/microRNA Axis Blocks Melanoma Invasion Program by miR-211 Targeting NUAK1 ⬇️

scientific article published on August 9, 2013

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.

scientific article published on 06 February 2017

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

scientific article published on 07 July 2011

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