Ron Shamir

Research interests

Publications

• NEMO: cancer subtyping by integration of partial multi-omic data

  Bioinformatics · 2019 · 10.1093/bioinformatics/btz058

• Multi-omic and multi-view clustering algorithms: review and cancer benchmark

  Nucleic Acids Research · 2018 · https://doi.org/10.1093/nar/gky889

• Environmental Stresses Disrupt Telomere Length Homeostasis

  PLoS Genetics · 2013 · https://doi.org/10.1371/journal.pgen.1003721

• Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

  Cell stem cell · 2011 · https://doi.org/10.1016/j.stem.2010.12.003

• Expander: from expression microarrays to networks and functions

  Nature Protocols · 2010 · https://doi.org/10.1038/nprot.2009.230

• Regulatory networks define phenotypic classes of human stem cell lines

  Nature · 2008 · 10.1038/nature07213

• Modelling and analysis of gene regulatory networks

  Nature Reviews Molecular Cell Biology · 2008 · https://doi.org/10.1038/nrm2503

• Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence

  Stem Cells · 2008 · 10.1634/stemcells.2007-1081

• Identification of functional modules using network topology and high-throughput data

  BMC Systems Biology · 2007 · 10.1186/1752-0509-1-8

• Network‐based prediction of protein function

  Molecular Systems Biology · 2007 · https://doi.org/10.1038/msb4100129

• Quantification of protein half-lives in the budding yeast proteome

  Proceedings of the National Academy of Sciences · 2006 · https://doi.org/10.1073/pnas.0605420103

• Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

  Journal of Computational Biology · 2005 · https://doi.org/10.1089/cmb.2005.12.835

• EXPANDER – an integrative program suite for microarray data analysis

  BMC Bioinformatics · 2005 · https://doi.org/10.1186/1471-2105-6-232

• A global view of pleiotropy and phenotypically derived gene function in yeast

  Molecular Systems Biology · 2005 · https://doi.org/10.1038/msb4100004

• Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast

  Proceedings of the National Academy of Sciences · 2005 · https://doi.org/10.1073/pnas.0502521102

• Cluster graph modification problems

  Discrete Applied Mathematics · 2004 · https://doi.org/10.1016/j.dam.2004.01.007

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

  Proceedings of the National Academy of Sciences · 2004 · https://doi.org/10.1073/pnas.0308661100

• How prevalent is functional alternative splicing in the human genome?

  Trends in Genetics · 2003 · 10.1016/j.tig.2003.12.004

• Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells

  Genome Research · 2003 · https://doi.org/10.1101/gr.947203

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

  Bioinformatics · 2003 · https://doi.org/10.1093/bioinformatics/btg232

• Discovering statistically significant biclusters in gene expression data

  Bioinformatics · 2002 · https://doi.org/10.1093/bioinformatics/18.suppl_1.s136

• Complexity classification of some edge modification problems

  Discrete Applied Mathematics · 2001 · https://doi.org/10.1016/s0166-218x(00)00391-7

• CLICK: a clustering algorithm with applications to gene expression analysis.

  PubMed · 2000

• A clustering algorithm based on graph connectivity

  Information Processing Letters · 2000 · 10.1016/s0020-0190(00)00142-3

• A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences

  Molecular Biology and Evolution · 2000 · 10.1093/oxfordjournals.molbev.a026369

• Clustering Gene Expression Patterns

  Journal of Computational Biology · 1999 · https://doi.org/10.1089/106652799318274

• Four Strikes Against Physical Mapping of DNA

  Journal of Computational Biology · 1995 · 10.1089/cmb.1995.2.139

Current projects

No projects listed.