Tomer Shlomi

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. pmc A direct comparison of protein interaction confidence assignment schemes
    Silpa Suthram
    Department of Bioengineering, University of California, San Diego, CA 92093, USA
    BMC Bioinformatics 7:360. 2006
  2. pmc Systematic condition-dependent annotation of metabolic genes
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Res 17:1626-33. 2007
  3. pmc QPath: a method for querying pathways in a protein-protein interaction network
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 7:199. 2006
  4. pmc A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:101. 2007
  5. doi Network-based prediction of human tissue-specific metabolism
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nat Biotechnol 26:1003-10. 2008
  6. ncbi Pepitope: epitope mapping from affinity-selected peptides
    Itay Mayrose
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 23:3244-6. 2007
  7. ncbi SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    Oved Ourfali
    School of Computer Science, School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 23:i359-66. 2007
  8. pmc Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes
    Elhanan Borenstein
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 35:e7. 2007
  9. doi A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism
    Idit Diamant
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Biosyst 5:1732-9. 2009
  10. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010

Detail Information

Publications23

  1. pmc A direct comparison of protein interaction confidence assignment schemes
    Silpa Suthram
    Department of Bioengineering, University of California, San Diego, CA 92093, USA
    BMC Bioinformatics 7:360. 2006
    ..Here, we perform a rigorous comparative analysis and performance assessment among these different methods...
  2. pmc Systematic condition-dependent annotation of metabolic genes
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Res 17:1626-33. 2007
    ..The CDA presented is likely to serve as a new reference source for metabolic gene annotation...
  3. pmc QPath: a method for querying pathways in a protein-protein interaction network
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 7:199. 2006
    ..The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks...
  4. pmc A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 3:101. 2007
    ..Overall, SR-FBA enables one to address a host of new questions concerning the interplay between regulation and metabolism...
  5. doi Network-based prediction of human tissue-specific metabolism
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nat Biotechnol 26:1003-10. 2008
    ..Our results establish a computational basis for the genome-wide study of normal and abnormal human metabolism in a tissue-specific manner...
  6. ncbi Pepitope: epitope mapping from affinity-selected peptides
    Itay Mayrose
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 23:3244-6. 2007
    ..Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/..
  7. ncbi SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
    Oved Ourfali
    School of Computer Science, School of Medicine, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 23:i359-66. 2007
    ....
  8. pmc Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes
    Elhanan Borenstein
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Nucleic Acids Res 35:e7. 2007
    ....
  9. doi A network-based method for predicting gene-nutrient interactions and its application to yeast amino-acid metabolism
    Idit Diamant
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Mol Biosyst 5:1732-9. 2009
    ....
  10. pmc Associating genes and protein complexes with disease via network propagation
    Oron Vanunu
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    PLoS Comput Biol 6:e1000641. 2010
    ..PRINCE's predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation...
  11. pmc Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
    Keren Yizhak
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Bioinformatics 26:i255-60. 2010
    ....
  12. pmc Predicting selective drug targets in cancer through metabolic networks
    Ori Folger
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 7:501. 2011
    ..Finally, potential selective treatments for specific cancers that depend on cancer type-specific downregulation of gene expression and somatic mutations are compiled...
  13. pmc Evolutionary conservation and over-representation of functionally enriched network patterns in the yeast regulatory network
    Ofer Meshi
    School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    BMC Syst Biol 1:1. 2007
    ..This paper examines the functional significance of regulatory network patterns via their biological annotation and evolutionary conservation...
  14. pmc Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm
    Itay Mayrose
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv 69978, Israel
    Nucleic Acids Res 35:69-78. 2007
    ..We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs...
  15. pmc Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    Tomer Shlomi
    School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 102:7695-700. 2005
    ..Further work is needed to identify metrics that characterize the complete trajectory from the initial to the final metabolic steady states after genetic perturbations...
  16. doi iMAT: an integrative metabolic analysis tool
    Hadas Zur
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Bioinformatics 26:3140-2. 2010
    ..Availability and Implementation: http://imat.cs.tau.ac.il/...
  17. pmc Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    Livnat Jerby
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
    Mol Syst Biol 6:401. 2010
    ..67 versus 0.59). The approach presented can be used to construct other human tissue-specific models, and be applied to other organisms...
  18. pmc Flux balance analysis accounting for metabolite dilution
    Tomer Benyamini
    The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
    Genome Biol 11:R43. 2010
    ..Here, we present metabolite dilution flux balance analysis, which addresses this problem, resulting in improved metabolic phenotype predictions...
  19. pmc Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages
    Yedael Y Waldman
    Blavatnik School of Computer Science, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 38:2964-74. 2010
    ..Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms...
  20. pmc From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions
    Igor Ulitsky
    School of Computer Science, Tel Aviv University, Ramat Aviv, Israel
    Mol Syst Biol 4:209. 2008
    ..We show how the resulting map of modules provides clues for the elucidation of function both at the level of individual genes and at the level of functional modules...
  21. pmc Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states
    Yonatan Bilu
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Comput Biol 2:e106. 2006
    ..This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states...
  22. pmc Transcriptional regulation of protein complexes within and across species
    Kai Tan
    Department of Bioengineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 104:1283-8. 2007
    ..Our results demonstrate how multiple molecular interaction types can be integrated toward a global wiring diagram of the cell, and they provide insights into the evolutionary dynamics of protein complex regulation...
  23. ncbi Constraint-based functional similarity of metabolic genes: going beyond network topology
    Oleg Rokhlenko
    Department of Computer Science, Technion, Haifa 32000, Israel
    Bioinformatics 23:2139-46. 2007
    ..However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data...