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שלח באימייל הדפס
Name: Shiri Freilich, Ph.D. (Researcher)
Units: Newe Ya'arResearch teams-Newe Yaar
Research Interests / Job description  
Tel:  049539533 0506220047
Cell: 050-6220047
Email:    shiri@volcani.agri.gov.il


Research Interests / Job description
Systems Biology in Ecology & Agriculture: In the group we apply and develop computational approaches towards the study of complex ecological systems with the goal of improving existing practices. Projects include: (1) the educated design of bacterial communities towards improved bio-degradation and bio-production and the rational design of bio-control strategies. (2) Using next generation sequencing for developing improved plant traits. For more details please see our group site at http://app.agri.gov.il/shiri/http://app.agri.gov.il/shiri/

  List of Publications

  • Freilich S., Oron E, Kapp Y, Nevo-Caspi Y, Orgad S, Segal D, Chamovitz DA: The COP9 signalosome is essential for development of Drosophila melanogaster. Curr Biol 1999, 9:1187-1190.
  •  Freilich, S., Spriggs, R. V., George, R. A., Al-Lazikani, B., Swindells, M. & Thornton, J. M.: The complement of enzymatic sets in different species. J Mol Biol 2005, 349, 745-6.
  • Freilich, S., Massingham, T., Bhattacharyya, S., Ponsting, H., Lyons, P. A., Freeman, T. C. & Thornton, J. M.: Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biology 2005, 6.
  • Freilich S., Massingham T., Blanc E., Goldovsky L., Thornton, J. M: Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biology 2006, 7.
  •  Freeman, T. C., Goldovsky L., Brosch M.,Van Dongen S., Maziere P., Athanasios Grocock R. J., Freilich S., Thornton, J. M., & Enright A. J. E.: Construction, visualization and clustering of transcription networks from microarray expression data. PLOS Computational Biology 2007, 3:2032-2042.
  • Kamburov A., Goldovsky L., Freilich S., Kapazoglou A., Kunin V., Enright A. J. E., Tsaftaris A., & Ouzounis C. A: Denoising functional networks by domain interaction filtering. BMC Bioinformatics 2007, 8:460.
  •  Freilich S, Goldovsky L, Ouzounis CA, Thornton JM: Metabolic innovations towards the human lineage. BMC Evolutionary Biology 2008, 8:247.
  • Huminiecki L, Goldovsky L, Freilich S, Moustakas A, Ouzounis C, Heldin CH: Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom. BMC evolutionary biology 2009, 9:28.
  • Freilich S, Kreimer A, Borenstein E, Yosef N, Sharan R, Gophna U, Ruppin E: Metabolic-network-driven analysis of bacterial ecological strategies. Genome Biology 2009, 10(6):R61.
  • Freilich S, Goldovsky L, Gottlieb A, Blanc E, Tsoka S, Ouzounis C: Stratification of co-evolving genomic groups using ranked phylogenetic profile. BMC Bioinformatics 2009, 10:355.
  • Freilich S, Kreimer A, Borenstein E, Gophna U, Sharan R, Ruppin E: Decoupling environment-dependent and independent genetic robustness across bacterial species. PLoS Computational Biology 2010,6.
  • Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E: The large scale organization of the bacterial interactions network. Nucleic Acid Research 2010, 38:3857.
  • Tuller T, Gir Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E: Translation efficiency plays a role in determining horizontal gene transfer. Nucleic Acid Research Nucleic Acid Research 2011, 39:4743.
  • Chrysanthi A, Simon M, Freilich S, Espinosa O, Hazelwood L, Tsoka S, Ouzounis CA, Hancock JM: Protein coalitions in a core mammalian biochemical network linked by rapidly evolving protein. BMC Evolutionary Biology 2011, 25;11.
  • Freilich S & Eytan Ruppin. Towards the educated design of bacterial communities. Book chapter in "Bene?cial Microorganisms in Multicellular Life Forms" 2011 (Springer publishin, Hidelberg).
  • Freilich S, Zarecki R, Eilam O, Shtifman-Segal E, Kupieck M, Gophna U, Sharan R, Ruppin E: Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications 2011,10.1038/ncomms1597.
  • Kreimer A, Doron-Faigenboim A, Borenstein E, Freilich S. (2012). NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species. Bioinformatics 28:2195-2197.
    • Zarecki R, Oberhardt, M, Yizhak K, Wagner A, Shtifman Segal E, Freilich S, Henry CS, Gophna U & Ruppin E (2014). Maximal Sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms. PloS One 27;9(5):e98372.
    • Zchori-Fein E, Lahav T, Freilich S (2014). Variations in the identity and complexity of endosymbiont combinations in whitefly hosts. Front Microbiol. 4;5:310.
    Freilich S, Lev S, Gonda I, Reuveni E, Portnoy V, Oren E, Lohse M, Galpaz N, Bar E, Tzuri G, Wissotsky G, Meir A, Burger J, Tadmor Y, Schaffer A, Fei Z, Giovannoni J, Lewinsohn E, Katzir N. (2015). Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits. BMC Plant Biology 3;15.
    • Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich and Elhanan Borenstein (2015). NetCooperate: A network-based tool for inferring host-microbe and microbe-microbe cooperation. BMC Bioinformatics 17;16:164.
    • Itay Mayrose & Shiri Freilich. The interplay between scientific overlap and cooperation and the resulting gain in co-authorship interactions (2015). PloS One 15;10(9):e0137856.
  • Chen K, Zhang L, Xu X, Gou Z, Li S, Freilich S & Jiang J. Plasmidome comparison of four Comamonas catabolic plasmids reveals the evolution of pBHB for haloaromatics catabolism (2015). Applied and Environmental Microbiology. 18;82(5):1401-11.
    • Lahav T, Zchori-Fein E, Naor V, Freilich S & Iasur-Kruh L. Draft Genome Sequence of a Dyella-Like bacterium from the planthopper Hyalesthes obsoletus. (2016). Genome Announcements 4(4) pii: e00686-16.
    • Widder S et al. Challenges in microbial ecology: building predictive understanding of community function and dynamics (2016). ISME J. 10(11):2557-2568.
    • Zhang L, Chen XL, Hu Q, Chen K, Yan X, Shun-Peng L, Freilich S & Jiang J. Haoranjiania flava gen. nov., sp. nov., a new member of the family Chitinophagaceae, isolated from an activated sludge (2017) . International Journal of Systematic and Evolutionary Microbiology 66(11):4686-4691.
    • Yadav B, Lahav T, Reuveni E, Chamovitz SA, Freilich S. Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana.(2016). Plant Mol Biol 92(6):689-699.
    • Itkin M, et al. The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii (2016). Proc. Natl. Acad. Sci. U.S.A. 113: E7619-E7628.
    • Mazzola M & Freilich S. Prospects for Biological Soilborne Disease Control: Application of Indigenous Versus Synthetic Microbiomes (2017). Phytopathology 107(3):256-263.
    • Iasur Kruh L, Lahav T, Abu-Nassar J, Achdari G, Salami R, Freilich S, Aly R. Host-Parasite-Bacteria Triangle: The Microbiome of the Parasitic Weed Phelipanche aegyptiaca and Tomato-Solanum lycopersicum (Mill.) as a Host (2017). Front Plant Sci. 1;8:269.
    • Gupta S, Yadav BS, Raj U, Freilich S, Varadwaj PK. Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency (2017). Front Plant Sci. 22;8:1025.
    • Shany Ofaim, Maya Ofek-Lalzar, Noa Sela, Jiandong Jiang, Yechezkel Kashi, Dror Minz, Shiri Freilich. Analysis of microbial functions in the rhizosphere using a metabolic-network based framework for metagenomics interpretation (Accepted). Front Microbiol.
Updated on: 13/08/17 17:39
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