The Freilich Lab

Publications

Peer review articles
Kreimer A, Doron-Faigenboim A, Borenstein E, Freilich S: NetCmpt: A network-based tool for calculating the metabolic       competition between bacterial species. Bioinformatics 2012. [abs].
Persi E, Weingart U, Freilich S, Horn D: Peptide markers of Aminoacyl tRNA Synthetases facilitate taxa counting in metagenomic data. BMC Genomics 2012 13:65.[abs] [pdf].
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. [abs] [pdf].
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 Evol Biol 2011, 25;11. [abs] [pdf].
Tuller T, Gir Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E: Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acid Research 2011, 39:4743. [abs] [pdf].
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. [abs] [pdf].
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. [abs] [pdf].
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. [abs] [pdf].
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. [abs] [pdf].
Huminiecki L, Goldovsky L, Freilich S, Moustakas A, Ouzounis C, Heldin CH: Emergence, development and diversification of the TGF-beta signaling pathway within the animal kingdom. BMC evolutionary biology 2009, 9:28. [abs] [pdf].
Freilich S, Goldovsky L, Ouzounis CA, Thornton JM: Metabolic innovations towards the human lineage. BMC Evolutionary Biology 2008, 8:247. [abs] [pdf].
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. [abs] [pdf].
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.[abs] [pdf].
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. [abs] [pdf].
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. [abs] [pdf].
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, 745-63. [abs] [pdf].
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. [abs] [pdf].


Book chapters

Freilich S & Eytan Ruppin. Towards the educated design of bacterial communities. Book chapter in  “Microorganisms in Multicellular Life Forms”‚ (Springer publishin, Hidelberg 2011). [
abs] [pdf].


Tutorials

For a friendly, basic, introduction (in Hebrew) about metabolic-driven approaches in System Biology click here.