Eytan Ruppin - Once          And today...  

My Lab (Make lab no war..): The people, research and downloads

Our Lab seminar

Papers

Selected Publications

  • Translation efficiency is determined by both codon bias and folding energy
    (T. Tuller, Y. Walman, M. Kupiec, E. Ruppin)
    Proceedings of the National Academy of Sciences (PNAS), to appear.
  • Reconstructing ancestral gene content by co-evolution
    (T. Tuller, H. Birin, U. Gophna, M. Kupiec, E. Ruppin)
    Genome Research, November 2009, doi:10.1101/gr.096115.109.
  • Predicting metabolic biomarkers of human inborn errors of metabolism
    (T. Shlomi, M. N. Cabili, E. Ruppin)
    Molecular Systems Biology (MSB), 5:263, doi:10.1038/msb.2009.22, May 2009.
  • Toward accurate reconstruction of functional protein networks
    (N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec, E. Ruppin, R. Sharan)
    Molecular Systems Biology (MSB), doi:10.1038/msb.2009.5, March 2009.
  • Large scale reconstruction and phylogenetic analysis of metabolic environments.
    (E. Borenstein, M. Kupiec, M.W. Feldman, E. Ruppin)
    Proceedings of the National Academy of Sciences (PNAS), 105(38), September 2008, and see also
    `Netwrok-based approaches for linking metabolism with environment' , by S Janga and MM Babu, Minireview, Genome Biology, November 2008.
  • Network based prediction of human tissue specific metabolism
    (T. Shlomi, M.N Cabili, M.J. Herrgard, B.O. Palsson, E. Ruppin)
    Nature Biotechnology, doi: 10.1038/nbt.1487, August 2008.
  • The evolution of modularity in bacterial metabolic networks
    (A. Kreimer, E. Borenstein, U. Gophna, E. Ruppin)
    Proceedings of the National Academy of Sciences (PNAS), 6976-6981, 105(19), May 2008.
  • Multiple knockouts analysis of genetic robustness in the yEast metabolic metwork
    (D. Deutscher, I. Meilijson, M. Kupiec, E. Ruppin)
    Nature Genetics, 38(9), 993-998, 2006.
  • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    (T. Shlomi, O. Berkman, E. Ruppin)
    proceedings of the National Academy of Sciences (PNAS), 102(21), 7695-7700, 2005.
  • Evolutionary AutonomousAgents: A Neuroscience Perspective
    (E. Ruppin)
    Nature Reviews Neuroscience, 3(2), (2002), 132-141.

    • Recent Publications: 2009 --

  • Translation efficiency in humans: tissue specificity, global optimization and the differences between developmental stages
    (Y. Walman, T. Tuller, T. Shlomi, R. Sharan, E. Ruppin)
    Nucleic Acids Research (NAR), to appear.
  • A systems level strategy for analyzing the cell death network: Implication in exploring the apoptosis/autophagy connection
    (E. Zalckvar, N. Yosef, S. Reef, Y. Ber, A. Rubinstein, R. Sharan, E. Ruppin, A. Kimchi)
    Cell Death and Differentiation (CDD), to appear.
  • Translation efficiency is determined by both codon bias and folding energy
    (T. Tuller, Y. Walman, M. Kupiec, E. Ruppin)
    Proceedings of the National Academy of Sciences (PNAS), to appear.
  • Decoupling environmental-dependent and independent genetic robustness across bacterial species
    (S. Freilich*, A. Kreimer*, E. Borenstein, U. Gophna, R. Sharan, E. Ruppin; *equal contribution)
    PLoS Computational Biology, to appear.
  • Associating genes and protein complexes with disease via network propagation
    (O. Vanunu, O. Magger, E. Ruppin, T. Shlomi, R. Sharan)
    PLoS Computational Biology, to appear.
  • Network-free prediction of knockout effects in yeast
    (T. Peleg, N. Yosef, E. Ruppin, R. Sharan)
    PLoS Computational Biology, to appear.
  • Reconstructing ancestral gene content by co-evolution
    (T. Tuller, H. Birin, U. Gophna, M. Kupiec, E. Ruppin)
    Genome Research, November 2009, doi:10.1101/gr.096115.109.
  • TP53 cancerous mutations exhibit selection for translation efficiency
    (Y. Waldman, T. Tuller, R. Sharan, E. Ruppin )
    Cancer Research, 69: (22), 8807-8813, November 2009.
  • Properties of untranslated regions of the S. cerevisiae genome
    (T. Tuller, E. Ruppin, M. Kupiec)
    BMC Genomics, 10: 391, August 2009.
  • Metabolic network-based analysis of yeast gene-nutrient interactions
    (I. Diamant, Y. Eldar, O. Rokhlenko, E. Ruppin, T. Shlomi)
    Molecular Biosystems, doi: 10.1039/b823287n, 2009.
  • Metabolic-network driven analysis of bacterial ecological strategies
    (S. Freilich, A. Kreimer, E. Borenstein, R. Sharan, U. Gophna, E. Ruppin)
    Genome Biology, 10(6):R61, June 5, 2009.
  • Increased microRNA activity in human cancers
    (A. Israel, R. Sharan, E. Ruppin, E. Galun)
    PLoS One, 4(6):e6045, June 25, 2009.
  • A complex-centric view of protein network evolution
    (N. Yosef, M. Kupiec, E. Ruppin, R. Sharan)
    Nucleic Acids Research (NAR), doi:10.1093/nar/gkp414, May 2009.
  • Co-evolutionary networks of genes and cellular processes across fungal species
    (T. Tuller, M. Kupiec, E. Ruppin)
    Genome Biology, 10:R48, doi:10.1186/gb-2009-5-r48, May 2009.
  • A genome-wide screen for essential yeast genes that affect telomere length maintenance.
    (L. Ungar, N. Yosef, Y. Sela, R. Sharan, E. Ruppin, M. Kupiec)
    Nucleic Acids Research (NAR), doi:10.1093/nar/gkp259, April 2009.
  • Multi-perturbation analysis of distributed neural networks: the case of spatial neglect.
    (A. Kaufman, C. Serfaty, L.Y. Deouell, E. Ruppin, N. Soroker)
    Human Brain Mapping (HBM), May 15,2009.
  • Network-based prediction of metabolic enzymes subcellular localization
    (S. Mintz, A. Aharoni, E. Ruppin, T. Shlomi)
    Bioinformatics (ISMB 2009 Proceedings), 25(12):i247-52, June 15, 2009.
  • Predicting metabolic biomarkers of human inborn errors of metabolism
    (T. Shlomi, M. N. Cabili, E. Ruppin)
    Molecular Systems Biology (MSB), 5:263, doi:10.1038/msb.2009.22, May 2009.
  • Toward accurate reconstruction of functional protein networks
    (N. Yosef, L. Ungar, E. Zalckvar, A. Kimchi, M. Kupiec, E. Ruppin, R. Sharan)
    Molecular Systems Biology (MSB), 5:248, doi:10.1038/msb.2009.5, March 2009.
  • Higher-order genomic organization of cellular functions in yeast
    (T. Tuller, U. Rubinstein, D. Bar, M. Gurevitch, E. Ruppin, M. Kupiec)
    Journal of Computational Biology, Feb 2009, 16(2), 303-316.

    • Papers in Computational Biology

    Constraint-based Metabolic Modeling
    Protein & Signalling Networks
    Evolutionary Systems Biology
    Others

    Papers in Past Research Topics

    Machine Learning and Natural Language Processing
    Artificial Life and Evolutionary Computation
    Neural Modeling of Brain Disorders
    Cognitive Neuroscience Modeling
    Dynamics of Neural Networks
    Others

    Books

    1. Neural Modeling of Brain and Cognitive Disorders -- Reggia, Ruppin, Berndt (1996)
    2. Brain, Behavioral and Cognitive Disorders: The Computational Perspective -- Reggia, Ruppin, Glanzman (1999)

    Teaching

    1. Computational Systems Biology Seminar (2009)
    2. Computational Systems Biology (2008)
    3. Computer Structure (2007)
    4. Adios Workshop (Sadna, 2005)
    5. Computer Structure (2005) -- a pointer to Yehuda Afek's page
    6. Artificial Life Workshop (Sadna, 2004)
    7. Artificial Life Workshop (Sadna, 2003)
    8. NLP: The IR Perspective (2001, 2002) --- Course notes (zip file)
    9. Seminar on Evolutionary Autonomous Agents and Neuroscience (2002) (Alife)
    10. Introduction to Artificial Intelligence (99,2000)
    11. Seminar on Evolutionary Autonomous Agents (99) (Alife)
    12. Seminar on Artificial life (98)
    13. Seminar on Neural Modeling of Brain Disorders (96/97)

    Links

    1. The Edmond J. Safra Bioinformatics Program at TAU
    2. Metabolic Networks Analysis
    3. Statistical Natural Language Processing
    4. Evoweb - European network of excellence in Evolutionary Computing
    5. Complex Adaptive Systems and Artificial Life
    6. Neural Computation
    7. Artificial Intelligence in Medicine

    Coordinates

     

    Professor Eytan Ruppin, MD, PhD

    School of Computer Sciences & School of Medicine

    Tel Aviv University

    Tel Aviv 69978, Israel

    email: ruppin@post.tau.ac.il

    +972-3-640-6528 (voice)

    +972-3-640-9357 (fax)

    +972-8-9261565 (home)