Bioinformatics: LSCF Publications

  1. Sirota-Madi A., Olender T., Helman Y., Ingham C., Brainis I., Roth D., Hagi E., Brodsky L., Leshkowitz D., Galatenko V., Nikolaev V., Mugasimangalam R. C., Bransburg-Zabary S., Gutnick D. L., Lancet D. & Ben-Jacob E. (2010). Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments.  BMC Genomics. 2010 Dec 17 , 11 (1).
  2. Pewzner-Jung Y., Brenner O., Braun S., Laviad E. L., Ben-Dor S., Feldmesser E., Horn-Saban S., Amann Zalcenstein D., Raanan C., Berkutzki T., Erez Roman R., Ben David O., Levy M., Holzman D., Park H., Nyska A., Merrill, Jr. A. H. & Futerman A. H. (2010). A critical role for ceramide synthase 2 in liver homeostasis II. Insights into molecular changes leading to hepatopathy.  Journal of Biological Chemistry. 2010 Apr 2 , 285 (14):10911-10923.
  3. Stelzer G., Inger A., Olender T., Iny Stein S. T., Dalah I., Harel A., Safran M. & Lancet D. (2009). GeneDecks: Paralog hunting and gene-set distillation with genecards annotation.  Omics-A Journal Of Integrative Biology. 2009 Dec 1 , 13 (6):477-487.
  4. Hodis E., Prilusky J. & Sussman J. L. (2009). Tools to Make 3D Structural Data More Comprehensible:  Emovie & Proteopedia.  . 2009, :169-182.
  5. Frenkel-Morgenstern M., Cohen A., Geva Zatorsky Z. N., Eden E., Prilusky J., Issaeva I., Sigal A., Cohen-Saidon C., Liron Y., Cohen L., Danon T., Perzov N. & Alon U. (2009). Dynamic proteomics: A database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells.  Nucleic Acids Research. 2009 Oct 9 , 38 (SUPPL.1):D508-D512.
  6. Manevich-Mendelson E., Feigelson S., Pasvolsky R., Aker M., Grabovsky V., Shulman Z., Kilic S. S., Rosenthal-Allieri M. A., Ben-Dor S., Mory A., Bernard A., Moser M., Etzioni A. & Alon R. (2009). Loss of kindlin-3 in LAD-III eliminates LFA-1 but not VLA-4 adhesiveness developed under shear flow conditions.  Blood. 2009, 114 (11):2344-2353.
  7. Noivirt-Brik O., Prilusky J. & Sussman J. L. (2009). Assessment of disorder predictions in CASP8.  Proteins-Structure Function And Bioinformatics. 2009, 77 (SUPPL. 9):210-216.
  8. Prilusky J. & Bibi E. (2009). Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs.  Proceedings of the National Academy of Sciences of the United States of America. 2009 Apr 21 , 106 (16):6662-6666.
  9. Harel A., Inger A., Stelzer G., Strichman-Almashanu L., Dalah I., Safran M. & Lancet D. (2009). GIFtS: Annotation landscape analysis with GeneCards.  BMC Bioinformatics. 2009 Oct 23 , 10 .
  10. Ben David D. M., Noivirt-Brik O., Paz A., Prilusky J., Sussman J. & Levy Y. (2009). Assessment of CASP8 structure predictions for template free targets.  Proteins-Structure Function And Bioinformatics. 2009, 77 (SUPPL. 9):50-65.
  11. Sapoznik S., Cohen B., Tzuman Y., Meir G., Ben-Dor S., Harmelin A. & Neeman M. (2009). Gonadotropin-regulated lymphangiogenesis in ovarian cancer is mediated by LEDGF-induced expression of VEGF-C.  Cancer Research. 2009 Dec 15 , 69 (24):9306-9314.
  12. Cohen B., Addadi Y., Sapoznik S., Meir G., Kalchenko V., Harmelin A., Ben-Dor S. & Neeman M. (2009). Transcriptional regulation of vascular endothelial growth factor C by oxidative and thermal stress is mediated by lens epithelium-derived growth factor/p751,2.  Neoplasia. 2009 Sept , 11 (9):921-933.
  13. Dassa B., London N., Stoddard B. L., Schueler-Furman O. & Pietrokovski S. (2009). Fractured genes: A novel genomic arrangement involving new split inteins and a new homing endonuclease family.  Nucleic Acids Research. 2009, 37 (8):2560-2573.
  14. Dori-Bachash M., Dassa B., Peleg O., Pineiro S. A., Jurkevitch E. & Pietrokovski S. (2009). Bacterial intein-like domains of predatory bacteria: A new domain type characterized in Bdellovibrio bacteriovorus.  Functional & Integrative Genomics. 2009, 9 (2):153-166.
  15. Tompa P., Prilusky J., Silman I. & Sussman J. (2008). Structural disorder serves as a weak signal for intracellular protein degradation.  Proteins-Structure Function And Bioinformatics. 2008 May 1 , 71 (2):903-909.
  16. Graslund S., Peleg Y., Albeck S., Unger T., Dym O., Prilusky J. & Sussman J. L. (2008). Protein production and purification.  Nature Methods. 2008 Feb , 5 (2):135-146.
  17. Hodis E., Prilusky J., Martz E., Silman I., Moult J. & Sussman J. L. (2008). Proteopedia - A scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.  GENOME BIOLOGY. 2008 Aug 3 , 9 (8).
  18. Biran J., Ben-Dor S. & Levavi-Sivan B. (2008). Molecular identification and functional characterization of the kisspeptin/kisspeptin receptor system in lower vertebrates.  Biology of Reproduction. 2008 Oct , 79 (4):776-786.
  19. Shkolnik K., Ben-Dor S., Galianil D., Hourvitz A. & Dekel N. (2008). Molecular characterization and bioinformatics analysis of Ncoa7B, a novel ovulation-associated and reproduction system-specific Ncoa7 isoform.  Reproduction. 2008 Mar , 135 (3):321-333.
  20. Dori-Bachash M., Dassa B., Pietrokovski S. & Jurkevitch E. (2008). Proteome-based comparative analyses of growth stages reveal new cell cycle-dependent functions in the predatory bacterium Bdellovibrio bacteriovorus.  Applied and Environmental Microbiology. 2008 Dec , 74 (23):7152-7162.