Bioinformatics publications

  1. Yosef R, Pilpel N, Papismadov N, Gal H, Ovadya Y, Vadai E, Miller S, Porat Z, Ben-Dor S, Krizhanovsky V. p21 maintains senescent cell viability under persistent DNA damage response by restraining JNK and caspase signaling. EMBO J. 2017 Jun 12. pii: e201695553. doi: 10.15252/embj.201695553. [Epub ahead of print] PMID: 28607003
  2. Schroeder M, Jakovcevski M, Polacheck T, Lebow M, Drori Y, Engel M, Ben-Dor S, Chen A. A Methyl-Balanced Diet Prevents CRF-Induced Prenatal Stress-Triggered Predisposition to Binge Eating-like Phenotype. Cell Metab. 2017 Jun 6;25(6):1269-1281.e6. doi: 10.1016/j.cmet.2017.05.001. Epub 2017 May 30. PMID: 28576418
  3. Eszter Bakos, Christoph A. Thaiss, Matthias P. Kramer, Sivan Cohen, Lihi Radomir, Irit Orr, Nathali Kaushansky, Avraham Ben-Nun, Shirly Becker-Herman and Idit Shachar. CCR2 Regulates the Immune Response by Modulating the Interconversion and Function of Effector and Regulatory T Cells. J Immunol June 15, 2017, 198 (12) 4659-4671; DOI: https://doi.org/10.4049/jimmunol.1601458
  4. Volpert G, Ben-Dor S, Tarcic O, Duan J, Saada A, Merrill AH Jr, Pewzner-Jung Y, Futerman AH. Oxidative stress elicited by modifying the ceramide acyl chain length reduces the rate of clathrin-mediated endocytosis. J Cell Sci. 2017 Mar 9. pii: jcs.199968. doi: 10.1242/jcs.199968. [Epub ahead of print] PMID: 28280117
  5. Gilad O, Shemer OS, Nevo M, Dgany O, Krasnov T, Noy-Lotan S, Rabinowicz R, Amitai N, Ben-Dor S, Yaniv I, Yacobovich J, Tamary H. Molecular diagnosis of α-thalassemia in a multi ethnic population. Eur J Haematol. 2017 Feb 3. doi: 10.1111/ejh.12866 [Epub ahead of print] PMID: 28160324
  6. Herzig Y, Nevo S, Bornstein C, Brezis MR, Ben-Hur S, Shkedy A, Eisenberg-Bord M, Levi B, Delacher M, Goldfarb Y, David E, Weinberger L, Viukov S, Ben-Dor S, Giraud M, Hanna JH, Breiling A, Lyko F, Amit I, Feuerer, Abramson J.Transcriptional programs that control expression of the autoimmune regulator gene Aire.Nat Immunol. 2017 Feb;18(2):161-172. doi: 10.1038/ni.3638.PMID: 27941786
  7. Maor-Nof M, Romi E, Shalom HS, Ulisse V, Raanan C, Nof A, Leshkowitz D, Lang R, Yaron A. Axonal Degeneration Is Regulated by a Transcriptional Program that Coordinates Expression of Pro- and Anti-degenerative Factors. Neuron. 2016 Nov 21. pii: S0896-6273(16)30835-2. doi: 10.1016/j.neuron.2016.10.061. [Epub ahead of print] PMID: 27889097
  8. Itkin M, Davidovich-Rikanati R, Cohen S, Portnoy V, Doron-Faigenboim A, Oren E, Freilich S, Tzuri G, Baranes N, Shen S, Petreikov M, Sertchook R, Ben-Dor S, Gottlieb H, Hernandez A, Nelson DR, Paris HS, Tadmor Y, Burger Y, Lewinsohn E, Katzir N, Schaffer A. The biosynthetic pathway of the nonsugar, high-intensity sweetener mogroside V from Siraitia grosvenorii. Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):E7619-E7628.
  9. Gibbs-Bar L, Tempelhof H, Ben-Hamo R, Ely Y, Brandis A, Hofi R, Almog G, Braun T, Feldmesser E, Efroni S, Yaniv K:Autotaxin-Lysophosphatidic Acid Axis Acts Downstream of Apoprotein B Lipoproteins in Endothelial Cells. Arterioscler Thromb Vasc Biol 2016, 36(10):2058-67.
  10. Oren R, Addadi Y, Narunsky Haziza L, Dafni H, Rotkopf R, Meir G, Fishman A, Neeman M:Fibroblast recruitment as a tool for ovarian cancer detection and targeted therapy. Int J Cancer 2016, 139(8):1788-98.
  11. Yoffe Y, David M, Kalaora R, Povodovski L, Friedlander G, Feldmesser E, Ainbinder E, Saada A, Bialik S, Kimchi A:Cap-independent translation by DAP5 controls cell fate decisions in human embryonic stem cells. Genes Dev 2016, 30(17):1991-2004.
  12. Appel E, Weissmann S, Salzberg Y, Orlovsky K, Negreanu V, Tsoory M, Raanan C, Feldmesser E , Bernstein Y, Wolstein O, Levanon D, Groner Y.An ensemble of regulatory elements controls Runx3 spatiotemporal expression in subsets of dorsal root ganglia proprioceptive neurons.Genes Dev. 2016 Dec 1;30(23):2607-2622. doi: 10.1101/gad.291484.116.
  13. Klein A D, Ferreira N S, Ben-Dor S, Duan J, Hardy J, Cox T M, Merrill A H, Futerman A H:Identification of Modifier Genes in a Mouse Model of Gaucher Disease. Cell Rep 2016, 16(10):2546-53.
  14. Fridmann-Sirkis Y, Milrot E, Mutsafi Y, Ben-Dor S, Levin Y, Savidor A, Kartvelishvily E, Minsky A:Efficiency in Complexity: Composition and Dynamic Nature of Mimivirus Replication Factories. J Virol 2016, ():.
  15. Redmond S A, Mei F, Eshed-Eisenbach Y, Osso L A, Leshkowitz D, Shen Y A, Kay J N, Aurrand-Lions M, Lyons D A, Peles E, Chan J R:Somatodendritic Expression of JAM2 Inhibits Oligodendrocyte Myelination. Neuron 2016, 91(4):824-36.
  16. Sheyn U, Rosenwasser S, Ben-Dor S, Porat Z, Vardi A:Modulation of host ROS metabolism is essential for viral infection of a bloom-forming coccolithophore in the ocean. ISME J 2016, 10(7):1742-54.
  17. Malitsky S, Ziv C, Rosenwasser S, Zheng S, Schatz D, Porat Z, Ben-Dor S, Aharoni A, Vardi A:Viral infection of the marine alga Emiliania huxleyi triggers lipidome remodeling and induces the production of highly saturated triacylglycerol. New Phytol 2016, 210(1):88-96.
  18. Yofe I, Weill U, Meurer M, Chuartzman S, Zalckvar E, Goldman O, Ben-Dor S, Schütze C, Wiedemann N, Knop M, Khmelinskii A, Schuldiner M:One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods 2016, 13(4):371-8.
  19. Aylon Y, Gershoni A, Rotkopf R, Biton I E, Porat Z, Koh A P, Sun X, Lee Y, Fiel M I, Hoshida Y, Friedman S L, Johnson R L, Oren M:The LATS2 tumor suppressor inhibits SREBP and suppresses hepatic cholesterol accumulation. Genes Dev 2016, 30(7):786-97.
  20. Machluf Y, Fink D, Farkash R, Rotkopf R, Pirogovsky A, Tal O, Shohat T, Weisz G, Ringler E, Dagan D, Chaiter Y:Adolescent BMI at Northern Israel: From Trends, to Associated Variables and Comorbidities, and to Medical Signatures. Medicine (Baltimore) 2016, 95(12):e3022.
  21. Elharar Y, Roth Z, Hecht N, Rotkopf R, Khalaila I, Gur E:Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system. Proc Natl Acad Sci U S A 2016, 113(12):E1605-14.
  22. Ziv C, Malitsky S, Othman A, Ben-Dor S, Wei Y, Zheng S, Aharoni A, Hornemann T, Vardi A:Viral serine palmitoyltransferase induces metabolic switch in sphingolipid biosynthesis and is required for infection of a marine alga. Proc Natl Acad Sci U S A 2016, 113(13):E1907-16.
  23. Tarcic O, Pateras I S, Cooks T, Shema E, Kanterman J, Ashkenazi H, Boocholez H, Hubert A, Rotkopf R, Baniyash M, Pikarsky E, Gorgoulis V G, Oren M:RNF20 Links Histone H2B Ubiquitylation with Inflammation and Inflammation-Associated Cancer. Cell Rep 2016, 14(6):1462-76.
  24. Sagiv A, Burton D G, Moshayev Z, Vadai E, Wensveen F, Ben-Dor S, Golani O, Polic B, Krizhanovsky V:NKG2D ligands mediate immunosurveillance of senescent cells. Aging (Albany NY) 2016, 8(2):328-44.
  25. Machluf Y, Gelbart H, Ben-Dor S, Yarden A:Making authentic science accessible-the benefits and challenges of integrating bioinformatics into a high-school science curriculum. Brief Bioinform 2016, ():.
  26. Cohen Y, Dafni H, Avni R, Fellus L, Bochner F, Rotkopf R, Raz T, Benjamin L E, Walsh K, Neeman M:Genetic and Pharmacological Modulation of Akt1 for Improving Ovarian Graft Revascularization in a Mouse Model. Biol Reprod 2016, 94(1):14.
  27. Ohad S, Ben-Dor S, Prilusky J, Kravitz V, Dassa B, Chalifa-Caspi V, Kashi Y, Rorman E:The Development of a Novel qPCR Assay-Set for Identifying Fecal Contamination Originating from Domestic Fowls and Waterfowl in Israel. Front Microbiol 2016, 7():145.
  28. Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S:Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PLoS One 2016, 11(4):e0153782.
  29. Diamant G, Eisenbaum T, Leshkowitz D, Dikstein R:Analysis of Subcellular RNA Fractions Revealed a Transcription-Independent Effect of Tumor Necrosis Factor Alpha on Splicing, Mediated by Spt5. Mol Cell Biol 2016, 36(9):1342-53.
  30. Vitner E B, Farfel-Becker T, Ferreira N S, Leshkowitz D, Sharma P, Lang K S, Futerman A H:Induction of the type I interferon response in neurological forms of Gaucher disease. J Neuroinflammation 2016, 13(1):104.
  31. Aviram R, Manella G, Kopelman N, Neufeld-Cohen A, Zwighaft Z, Elimelech M, Adamovich Y, Golik M, Wang C, Han X, Asher G:Lipidomics Analyses Reveal Temporal and Spatial Lipid Organization and Uncover Daily Oscillations in Intracellular Organelles. Mol Cell 2016, 62(4):636-48.
  32. Umansky K B, Feldmesser E, Groner Y:Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration. Genom Data 2015, 6():120-2.
  33. Arafeh R, Qutob N, Emmanuel R, Keren-Paz A, Madore J, Elkahloun A, Wilmott J S, Gartner J J, Di Pizio A, Winograd-Katz S, Sindiri S, Rotkopf R, Dutton-Regester K, Johansson P, Pritchard A L, Waddell N, Hill V K, Lin J C, Hevroni Y, Rosenberg S A, Khan J, Ben-Dor S, Niv M Y, Ulitsky I, Mann G J, Scolyer R A, Hayward N K, Samuels Y:Recurrent inactivating RASA2 mutations in melanoma. Nat Genet 2015, 47(12):1408-10.
  34. Fattal I, Shental N, Ben-Dor S, Molad Y, Gabrielli A, Pokroy-Shapira E, Oren S, Livneh A, Langevitz P, Zandman-Goddard G, Sarig O, Margalit R, Gafter U, Domany E, Cohen I R:Guanine polynucleotides are self-antigens for human natural autoantibodies and are significantly reduced in the human genome. Immunology 2015, 146(3):401-10.
  35. Rozen S, Füzesi-Levi M G, Ben-Nissan G, Mizrachi L, Gabashvili A, Levin Y, Ben-Dor S, Eisenstein M, Sharon M:CSNAP Is a Stoichiometric Subunit of the COP9 Signalosome. Cell Rep 2015, 13(3):585-98.
  36. Kopelman N M, Mayzel J, Jakobsson M, Rosenberg N A, Mayrose I:Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 2015, 15(5):1179-91.
  37. Umansky K B, Gruenbaum-Cohen Y, Tsoory M, Feldmesser E, Goldenberg D, Brenner O, Groner Y:Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration. PLoS Genet 2015, 11(8):e1005457.
  38. Nicenboim J, Malkinson G, Lupo T, Asaf L, Sela Y, Mayseless O, Gibbs-Bar L, Senderovich N, Hashimshony T, Shin M, Jerafi-Vider A, Avraham-Davidi I, Krupalnik V, Hofi R, Almog G, Astin J W, Golani O, Ben-Dor S, Crosier P S, Herzog W, Lawson N D, Hanna J H, Yanai I, Yaniv K:Lymphatic vessels arise from specialized angioblasts within a venous niche. Nature 2015, 522(7554):56-61.
  39. Alcolombri U, Ben-Dor S, Feldmesser E, Levin Y, Tawfik D S, Vardi A:MARINE SULFUR CYCLE. Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle. Science 2015, 348(6242):1466-9.
  40. Harari D, Orr I, Rotkopf R, Baranzini S E, Schreiber G:A robust type I interferon gene signature from blood RNA defines quantitative but not qualitative differences between three major IFNβ drugs in the treatment of multiple sclerosis. Hum Mol Genet 2015, 24(11):3192-205.
  41. Shemi A, Ben-Dor S, Vardi A:Elucidating the composition and conservation of the autophagy pathway in photosynthetic eukaryotes. Autophagy 2015, 11(4):701-15.
  42. Rice A, Glick L, Abadi S, Einhorn M, Kopelman N M, Salman-Minkov A, Mayzel J, Chay O, Mayrose I:The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers. New Phytol 2015, 206(1):19-26.
  43. Ma X, Shatil-Cohen A, Ben-Dor S, Wigoda N, Perera I Y, Im Y J, Diminshtein S, Yu L, Boss W F, Moshelion M, Moran N:Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway?. Planta 2015, 241(3):741-55.
  44. Dekel Y, Machluf Y, Ben-Dor S, Yifa O, Stoler A, Ben-Shlomo I, Bercovich D:Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency. BMC Genomics 2015, 16():53.
  45. Ram D, Leshkowitz D, Gonzalez D, Forer R, Levy I, Chowers M, Lorber M, Hindiyeh M, Mendelson E, Mor O:Evaluation of GS Junior and MiSeq next-generation sequencing technologies as an alternative to Trugene population sequencing in the clinical HIV laboratory. J Virol Methods 2015, 212():12-6.
  46. Davidi L, Levin Y, Ben-Dor S, Pick U:Proteome analysis of cytoplasmatic and plastidic β-carotene lipid droplets in Dunaliella bardawil. Plant Physiol 2015, 167(1):60-79.
  47. Sharoni S, Trainic M, Schatz D, Lehahn Y, Flores M J, Bidle K D, Ben-Dor S, Rudich Y, Koren I, Vardi A:Infection of phytoplankton by aerosolized marine viruses. Proc Natl Acad Sci U S A 2015, 112(21):6643-7.
  48. Schatz D, Shemi A, Rosenwasser S, Sabanay H, Wolf S G, Ben-Dor S, Vardi A:Hijacking of an autophagy-like process is critical for the life cycle of a DNA virus infecting oceanic algal blooms. New Phytol 2014, 204(4):854-63.
  49. Frada M J, Schatz D, Farstey V, Ossolinski J E, Sabanay H, Ben-Dor S, Koren I, Vardi A:Zooplankton may serve as transmission vectors for viruses infecting algal blooms in the ocean. Curr Biol 2014, 24(21):2592-7.
  50. Shalev M, Aviram R, Adamovich Y, Kraut-Cohen J, Shamia T, Ben-Dor S, Golik M, Asher G:The PXDLS linear motif regulates circadian rhythmicity through protein-protein interactions. Nucleic Acids Res 2014, 42(19):11879-90.
  51. Eshel O, Shirak A, Dor L, Band M, Zak T, Markovich-Gordon M, Chalifa-Caspi V, Feldmesser E, Weller J I, Seroussi E, Hulata G, Ron M:Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus). BMC Genomics 2014, 15():774.
  52. Shoshani O, Ravid O, Massalha H, Aharonov A, Ovadya Y, Pevsner-Fischer M, Leshkowitz D, Zipori D:Cell isolation induces fate changes of bone marrow mesenchymal cells leading to loss or alternatively to acquisition of new differentiation potentials. Stem Cells 2014, 32(8):2008-20.
  53. Cohen S, Itkin M, Yeselson Y, Tzuri G, Portnoy V, Harel-Baja R, Lev S, Sa'ar U, Davidovitz-Rikanati R, Baranes N, Bar E, Wolf D, Petreikov M, Shen S, Ben-Dor S, Rogachev I, Aharoni A, Ast T, Schuldiner M, Belausov E, Eshed R, Ophir R, Sherman A, Frei B, Neuhaus H E, Xu Y, Fei Z, Giovannoni J, Lewinsohn E, Tadmor Y, Paris H S, Katzir N, Burger Y, Schaffer A A:The PH gene determines fruit acidity and contributes to the evolution of sweet melons. Nat Commun 2014, 5():4026.
  54. Rosenwasser S, Mausz M A, Schatz D, Sheyn U, Malitsky S, Aharoni A, Weinstock E, Tzfadia O, Ben-Dor S, Feldmesser E, Pohnert G, Vardi A:Rewiring Host Lipid Metabolism by Large Viruses Determines the Fate of Emiliania huxleyi, a Bloom-Forming Alga in the Ocean. Plant Cell 2014, 26(6):2689-2707.
  55. Levanon D, Negreanu V, Lotem J, Bone K R, Brenner O, Leshkowitz D, Groner Y:Transcription factor Runx3 regulates interleukin-15-dependent natural killer cell activation. Mol Cell Biol 2014, 34(6):1158-69.
  56. Minis A, Dahary D, Manor O, Leshkowitz D, Pilpel Y, Yaron A:Subcellular transcriptomics-dissection of the mRNA composition in the axonal compartment of sensory neurons. Dev Neurobiol 2014, 74(3):365-81.
  57. Feldmesser E, Rosenwasser S, Vardi A, Ben-Dor S:Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi. BMC Genomics 2014, 15():148.
  58. Rosenwasser S, Graff van Creveld S, Schatz D, Malitsky S, Tzfadia O, Aharoni A, Levin Y, Gabashvili A, Feldmesser E, Vardi A:Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment. Proc Natl Acad Sci U S A 2014, 111(7):2740-5.
  59. Kotkamp K, Kur E, Wendik B, Polok B K, Ben-Dor S, Onichtchouk D, Driever W:Pou5f1/Oct4 promotes cell survival via direct activation of mych expression during zebrafish gastrulation. PLoS One 2014, 9(3):e92356.
  60. Behar D M, Metspalu M, Baran Y, Kopelman N M, Yunusbayev B, Gladstein A, Tzur S, Sahakyan H, Bahmanimehr A, Yepiskoposyan L, Tambets K, Khusnutdinova E K, Kushniarevich A, Balanovsky O, Balanovsky E, Kovacevic L, Marjanovic D, Mihailov E, Kouvatsi A, Triantaphyllidis C, King R J, Semino O, Torroni A, Hammer M F, Metspalu E, Skorecki K, Rosset S, Halperin E, Villems R, Rosenberg N A:No evidence from genome-wide data of a Khazar origin for the Ashkenazi Jews. Hum Biol 2013, 85(6):859-900.
  61. Ben-Ami O, Friedman D, Leshkowitz D, Goldenberg D, Orlovsky K, Pencovich N, Lotem J, Tanay A, Groner Y:Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1. Cell Rep 2013, 4(6):1131-43.
  62. Leshkowitz D, Horn-Saban S, Parmet Y, Feldmesser E:Differences in microRNA detection levels are technology and sequence dependent. RNA 2013, 19(4):527-38.
  63. Limor-Waisberg K, Ben-Dor S, Fass D:Diversification of quiescin sulfhydryl oxidase in a preserved framework for redox relay. BMC Evol Biol 2013, 13():70.
  64. Mildner A, Chapnik E, Manor O, Yona S, Kim K W, Aychek T, Varol D, Beck G, Itzhaki Z B, Feldmesser E, Amit I, Hornstein E, Jung S:Mononuclear phagocyte miRNome analysis identifies miR-142 as critical regulator of murine dendritic cell homeostasis. Blood 2013, 121(6):1016-27.
  65. Shi J X, Adato A, Alkan N, He Y, Lashbrooke J, Matas A J, Meir S, Malitsky S, Isaacson T, Prusky D, Leshkowitz D, Schreiber L, Granell A R, Widemann E, Grausem B, Pinot F, Rose J K, Rogachev I, Rothan C, Aharoni A:The tomato SlSHINE3 transcription factor regulates fruit cuticle formation and epidermal patterning. New Phytol 2013, 197(2):468-80.
  66. Keydar I, Ben-Asher E, Feldmesser E, Nativ N, Oshimoto A, Restrepo D, Matsunami H, Chien M S, Pinto J M, Gilad Y, Olender T, Lancet D:General olfactory sensitivity database (GOSdb): candidate genes and their genomic variations. Hum Mutat 2013, 34(1):32-41.
  67. Lotem J, Levanon D, Negreanu V, Leshkowitz D, Friedlander G, Groner Y:Runx3-mediated transcriptional program in cytotoxic lymphocytes. PLoS One 2013, 8(11):e80467.
  68. Leviatan N, Alkan N, Leshkowitz D, Fluhr R:Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray. PLoS One 2013, 8(6):e66511.
  69. Sela D, Buxdorf K, Shi J X, Feldmesser E, Schreiber L, Aharoni A, Levy M:Overexpression of AtSHN1/WIN1 provokes unique defense responses. PLoS One 2013, 8(7):e70146.
  70. Kopelman N M, Stone L, Gascuel O, Rosenberg N A:The behavior of admixed populations in neighbor-joining inference of population trees. Pac Symp Biocomput 2013, ():273-84.
  71. Dicken J, Mildner A, Leshkowitz D, Touw I P, Hantisteanu S, Jung S, Groner Y:Transcriptional reprogramming of CD11b+Esam(hi) dendritic cell identity and function by loss of Runx3. PLoS One 2013, 8(10):e77490.
  72. Shoshani O, Massalha H, Shani N, Kagan S, Ravid O, Madar S, Trakhtenbrot L, Leshkowitz D, Rechavi G, Zipori D:Polyploidization of murine mesenchymal cells is associated with suppression of the long noncoding RNA H19 and reduced tumorigenicity. Cancer Res 2012, 72(24):6403-13.
  73. Landau G, Ran A, Bercovich Z, Feldmesser E, Horn-Saban S, Korkotian E, Jacob-Hirsh J, Rechavi G, Ron D, Kahana C:Expression profiling and biochemical analysis suggest stress response as a potential mechanism inhibiting proliferation of polyamine-depleted cells. J Biol Chem 2012, 287(43):35825-37.
  74. Fuchs G, Shema E, Vesterman R, Kotler E, Wolchinsky Z, Wilder S, Golomb L, Pribluda A, Zhang F, Haj-Yahya M, Feldmesser E, Brik A, Yu X, Hanna J, Aberdam D, Domany E, Oren M:RNF20 and USP44 regulate stem cell differentiation by modulating H2B monoubiquitylation. Mol Cell 2012, 46(5):662-73.
  75. Biran J, Palevitch O, Ben-Dor S, Levavi-Sivan B:Neurokinin Bs and neurokinin B receptors in zebrafish-potential role in controlling fish reproduction. Proc Natl Acad Sci U S A 2012, 109(26):10269-74.
  76. Teper-Bamnolker P, Buskila Y, Lopesco Y, Ben-Dor S, Saad I, Holdengreber V, Belausov E, Zemach H, Ori N, Lers A, Eshel D:Release of apical dominance in potato tuber is accompanied by programmed cell death in the apical bud meristem. Plant Physiol 2012, 158(4):2053-67.
  77. Alon M, Elbaz M, Ben-Zvi M M, Feldmesser E, Vainstein A, Morin S:Insights into the transcriptomics of polyphagy: Bemisia tabaci adaptability to phenylpropanoids involves coordinated expression of defense and metabolic genes. Insect Biochem Mol Biol 2012, 42(4):251-63.
  78. Sirota-Madi A, Olender T, Helman Y, Brainis I, Finkelshtein A, Roth D, Hagai E, Leshkowitz D, Brodsky L, Galatenko V, Nikolaev V, Gutnick D L, Lancet D, Ben-Jacob E:Genome sequence of the pattern-forming social bacterium Paenibacillus dendritiformis C454 chiral morphotype. J Bacteriol 2012, 194(8):2127-8.
  79. Tidhar R, Ben-Dor S, Wang E, Kelly S, Merrill A H, Futerman A H:Acyl chain specificity of ceramide synthases is determined within a region of 150 residues in the Tram-Lag-CLN8 (TLC) domain. J Biol Chem 2012, 287(5):3197-206.
  80. Blechman J, Amir-Zilberstein L, Gutnick A, Ben-Dor S, Levkowitz G:The metabolic regulator PGC-1α directly controls the expression of the hypothalamic neuropeptide oxytocin. J Neurosci 2011, 31(42):14835-40.
  81. Mendoza-Fandino G A, Gee J M, Ben-Dor S, Gonzalez-Quevedo C, Lee K, Kobayashi Y, Hartiala J, Myers R M, Leal S M, Allayee H, Patel P I:A novel g.-1258G>A mutation in a conserved putative regulatory element of PAX9 is associated with autosomal dominant molar hypodontia. Clin Genet 2011, 80(3):265-72.
  82. Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy A A:Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 2011, 188(2):263-72.
  83. Tietel Z, Feldmesser E, Lewinsohn E, Fallik E, Porat R:Changes in the transcriptome of 'Mor' mandarin flesh during storage: emphasis on molecular regulation of fruit flavor deterioration. J Agric Food Chem 2011, 59(8):3819-27.
  84. Shkolnik K, Tadmor A, Ben-Dor S, Nevo N, Galiani D, Dekel N:Reactive oxygen species are indispensable in ovulation. Proc Natl Acad Sci U S A 2011, 108(4):1462-7.
  85. 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:Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics 2010, 11():710.
  86. Amit M, Weisberg S J, Nadler-Holly M, McCormack E A, Feldmesser E, Kaganovich D, Willison K R, Horovitz A:Equivalent mutations in the eight subunits of the chaperonin CCT produce dramatically different cellular and gene expression phenotypes. J Mol Biol 2010, 401(3):532-43..
  87. Galon Y, Aloni R, Nachmias D, Snir O, Feldmesser E, Scrase-Field S, Boyce J M, Bouché N, Knight M R, Fromm H:Calmodulin-binding transcription activator 1 mediates auxin signaling and responds to stresses in Arabidopsis. Planta 2010, 232(1):165-78.
  88. Tietel Z, Bar E, Lewinsohn E, Feldmesser E, Fallik E, Porat R:Effects of wax coatings and postharvest storage on sensory quality and aroma volatile composition of 'Mor' mandarins. J Sci Food Agric 2010, 90(6):995-1007.
  89. 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 A H, Futerman A H:A critical role for ceramide synthase 2 in liver homeostasis: II. insights into molecular changes leading to hepatopathy. J Biol Chem 2010, 285(14):10911-23.
  90. Sapoznik S, Cohen B, Tzuman Y, Meir G, Ben-Dor S, Harmelin A, Neeman M:Gonadotropin-regulated lymphangiogenesis in ovarian cancer is mediated by LEDGF-induced expression of VEGF-C. Cancer Res 2009, 69(24):9306-14.
  91. Angelovici R, Fait A, Zhu X, Szymanski J, Feldmesser E, Fernie A R, Galili G:Deciphering transcriptional and metabolic networks associated with lysine metabolism during Arabidopsis seed development. Plant Physiol 2009, 151(4):2058-72.
  92. Manevich-Mendelson E, Feigelson S W, 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:Loss of Kindlin-3 in LAD-III eliminates LFA-1 but not VLA-4 adhesiveness developed under shear flow conditions. Blood 2009, 114(11):2344-53.
  93. Cohen B, Addadi Y, Sapoznik S, Meir G, Kalchenko V, Harmelin A, Ben-Dor S, Neeman M:Transcriptional regulation of vascular endothelial growth factor C by oxidative and thermal stress is mediated by lens epithelium-derived growth factor/p75. Neoplasia 2009, 11(9):921-33.
  94. Biran J, Ben-Dor S, Levavi-Sivan B:Molecular identification and functional characterization of the kisspeptin/kisspeptin receptor system in lower vertebrates. Biol Reprod 2008, 79(4):776-86.
  95. Shkolnik K, Ben-Dor S, Galiani D, Hourvitz A, Dekel N:Molecular characterization and bioinformatics analysis of Ncoa7B, a novel ovulation-associated and reproduction system-specific Ncoa7 isoform. Reproduction 2008, 135(3):321-33.
  96. Shkolnik K, Ben-Dor S, Galiani D, Hourvitz A, Dekel N:A novel ovary-specific and ovulation-associated variant of epoxide hydrolase 2. FEBS Lett 2007, 581(25):4891-8.
  97. Mesika A, Ben-Dor S, Laviad E L, Futerman A H:A new functional motif in Hox domain-containing ceramide synthases: identification of a novel region flanking the Hox and TLC domains essential for activity. J Biol Chem 2007, 282(37):27366-73.
  98. Pasvolsky R, Feigelson S W, Kilic S S, Simon A J, Tal-Lapidot G, Grabovsky V, Crittenden J R, Amariglio N, Safran M, Graybiel A M, Rechavi G, Ben-Dor S, Etzioni A, Alon R:A LAD-III syndrome is associated with defective expression of the Rap-1 activator CalDAG-GEFI in lymphocytes, neutrophils, and platelets. J Exp Med 2007, 204(7):1571-82.
  99. Pewzner-Jung Y, Ben-Dor S, Futerman A H:When do Lasses (longevity assurance genes) become CerS (ceramide synthases)?: Insights into the regulation of ceramide synthesis. J Biol Chem 2006, 281(35):25001-5.
  100. Reiner O, Coquelle F M, Peter B, Levy T, Kaplan A, Sapir T, Orr I, Barkai N, Eichele G, Bergmann S:The evolving doublecortin (DCX) superfamily. BMC Genomics 2006, 7():188.
  101. Ben-Dor S, Esterman N, Rubin E, Sharon N:Biases and complex patterns in the residues flanking protein N-glycosylation sites. Glycobiology 2004, 14(2):95-101.

Book Chapter

  • Non Mammalian Models for Neurohypophyseal Peptides. Wircer E, Ben-Dor S, Levkowitz G. International Neuroendocrine Federation (INF) Masterclass Series, Volume 4: Molecular f)Neuroendocrinology: “From genome to physiology” Editors: David Murphy, University of Bristol, UK and Hal Gainer, NIH, USA (2015) Wiley-Blackwell, In press.
     
  • The genetic basis of olfactory deficits. “Genomic Disorders: The Genomic Basis of Disease”,  Menashe I., Feldmesser E., Lancet D. (2006). edited by JR Lupski and P Stankiewicz, Humana Press Inc., Totowa, NJ.
     

Acknowledgments

  • Nucleolin-Mediated RNA Localization Regulates Neuron Growth and Cycling Cell Size. (2016). Rotem Ben-Tov Perry, Ida Rishal,Ella Doron-Mandel,Alma L. Burlingame, Jeffery L. Twiss,Mike Fainzilber; Cell Reports 16, 1664–1676, August 9, 2016 ª 2016 The Author(s). http://dx.doi.org/10.1016/j.celrep.2016.07.005 (for Ofra Golani and Shifra Ben-Dor)
     
  • Localization of cofilin mRNA to the leading edge of migrating cells promotes directed cell migration. (2016). Yael Maizels, Froma Oberman, Rachel Miloslavski, Nava Ginzach, Malka Berman, Joel K. Yisraeli. J Cell Sci 2015 128: 1922-1933; doi: 10.1242/jcs.163972. http://jcs.biologists.org/content/128/10/1922.short (for Ofra Golani).
     
  • The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions. (2016). Osnat Tirosh ,Yifat Cohen ,Alina Shitrit, Odem Shani, Vu Thuy Khanh Le-Trilling, Mirko Trilling, Gilgi Friedlander, Marvin Tanenbaum, Noam Stern-Ginossar http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1005288 (for Ofra Golani).
     
  • Early and late HIV-1 membrane fusion events are impaired by sphinganine lipidated peptides that target the fusion site. (2016). Yoel A. Klug, Avraham Ashkenazi, Mathias Viard, Ziv Porat, Robert Blumenthal, Yechiel Shai. Biochemical Journal Jul 15, 2014, 461 (2) 213-222; DOI: 10.1042/BJ20140189 http://www.biochemj.org/content/461/2/213.abstract (for Ofra Golani)
     
  • Delineating pathological pathways in a chemically-induced mouse model of Gaucher disease. (2016). Vardi A1, Zigdon H1, Meshcheriakova A1, Klein AD1, Yaacobi C1, Eilam R2, Kenwood BM3, Rahim AA4, Massaro G4, Merrill AH Jr3, Vitner EB1, Futerman AH1. J Pathol. 2016 May 28. doi: 10.1002/path.4751. [Epub ahead of print]. (for Shifra Ben-Dor and Irit Orr)
     
  • A Krebs Cycle Component Limits Caspase Activation Rate Through Mitochondrial Surface Restriction of Crl Activation.(2016). Aram, L; Braun, T; Braverman, C; Kaplan, Y; Ravid, L; Levin-Zaidman, S; Arama, E. http://www.sciencedirect.com/science/article/pii/S1534580716300806 (for Ofra Golani).
     
  • Astrocyte morphology is confined by cortical functional boundaries in mammals ranging from mice to human. (2016). R Eilam, R Aharoni, R Arnon, R Malach. eLife, https://elifesciences.org/content/5/e15915  (for Ron Rotkopf)
     
  • Distinct bone marrow blood vessels differentially regulate haematopoiesis.(2016). Tomer Itkin, Shiri Gur-Cohen, Joel A. Spencer, Amir Schajnovitz, Saravana K. Ramasamy, Anjali P. Kusumbe, Guy Ledergor, Yookyung Jung, Idan Milo, Michael G. Poulos, Alexander Kalinkovich, Aya Ludin, Orit Kollet, Guy Shakhar, Jason M. Butler, Shahin Rafii, Ralf H. Adams, David T. Scadden, Charles P. Lin & Tsvee Lapidot. Nature 2016. doi:10.1038/nature17624  http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17624.html (for Ron Rotkopf)
     
  • MR Imaging–derived Oxygen-Hemoglobin Dissociation Curves and Fetal-Placental Oxygen-Hemoglobin Affinities. (2016). Reut Avni, Ofra Golani, Ayelet Akselrod-Ballin, Yonni Cohen,, Inbal Biton, Joel R. Garbow, Michal Neeman. Radiology online, http://pubs.rsna.org/doi/abs/10.1148/radiol.2015150721, (for Ron Rotkopf)
     
  • Volume 164, Issues 1–2, 14 January 2016, Pages 170–182. http://www.sciencedirect.com/science/article/pii/S0092867415015664 (for Ron Rotkopf)
     
  • Isometric Scaling in Developing Long Bones Is Achieved by an Optimal Epiphyseal Growth Balance.(2015). Stern T, Aviram R, Rot C, Galili T, Sharir A, Kalish Achrai N, et al. PLoS Biol 13(8):e1002212. doi:10.1371/journal.pbio.1002212  (for Ofra Golani)
     
  • A Novel Intravital Imaging Window for Longitudinal Microscopy of the Mouse Ovary. Filip Bochner, Liat Fellus-Alyagor, Vyacheslav Kalchenko, Shiri Shinar & Michal Neeman.
    Scientific Reports 5, Article number: 12446, Published online: 24 July 2015,  http://www.nature.com/articles/srep12446  (for Ofra Golani)​
     
  • Developmental Axon Pruning Requires Destabilization of Cell Adhesion by JNK Signaling. Bornstein, B., Zahavi, Eitan E., Gelley, S., Zoosman, M., Yaniv, Shiri P., Fuchs, O., Porat, Z., Perlson, E., & Schuldiner, O. (2015). Neuron. doi:10.1016/j.neuron.2015.10.023  (for Ron Rotkopf)
     
  • Paternal Mitochondrial Destruction after Fertilization Is Mediated by a Common Endocytic and Autophagic Pathway in Drosophila. Yoav Politi1, 3, Liron Gal1, 3, Yossi Kalifa1, Liat Ravid1, Zvulun Elazar2, Eli Arama1. Developmental Cell, Volume 29, Issue 3, 12 May 2014, Pages 305–320, doi:10.1016/j.devcel.2014.04.005.  http://www.sciencedirect.com/science/article/pii/S1534580714002044 (for Ofra Golani)
     
  • PAR1 signaling regulates the retention and recruitment of EPCR-expressing bone marrow hematopoietic stem cells. Cohen, S.G., Itkin, T., Chakrabarty, S., Graf, C., Kollet, O., Ludin, A., Golan, K., Kalinkovich, A., Ledergor, G., Wong, E., Niemeyer, E., Porat, Z., Erez, A., Sagi, I., Esmon, C.T., Ruf, W., & Lapidot, T. (2015) . Nature Medicine, advance online publication. doi:10.1038/nm.3960,  http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3960.html   (for Ron Rotkopf)
     
  • Mitotic Golgi translocation of ERK1c is mediated by PI4KIIIβ/14-3-3γ shuttling complex. Inbal Wortzel, Tamar Hanoch, Ziv Porat, Angelika Hausser, Rony Seger.  J Cell Sci 2015 : doi: 10.1242/jcs.170910. http://jcs.biologists.org/content/early/2015/10/08/jcs.170910  (for Ron Rotkopf)
     
  • Preconditioning allows engraftment of mouse and human embryonic lung cells, enabling lung repair in mice. Rosen, C., Shezen, E., Aronovich, A., Klionsky, Y.Z., Yaakov, Y., Assayag, M., Biton, I.E., Tal, O., Shakhar, G., Ben-Hur, H., Shneider, D., Vaknin, Z., Sadan, O., Evron, S., Freud, E., Shoseyov, D., Wilschanski, M., Berkman, N., Fibbe, W.E., Hagin, D., Hillel-Karniel, C., Krentsis, I.M., Bachar-Lustig, E., & Reisner, Y. (2015). Nature Medicine, advance online publication. http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3889.html (for Ron Rotkopf)
     
  • Appropriate expression of Ube2C and Ube2S controls the progression of the first meiotic division. Ben-Eliezer, I., Pomerantz, Y., Galiani, D., Nevo, N., & Dekel, N. (2015), The FASEB Journal. http://www.fasebj.org/content/early/2015/07/23/fj.15-274522.abstract (for Ron Rotkopf)
     
  • Nature Medicine (2015)  doi:10.1038/nm.3889, 13 July 2015 (for Ofra Golani and Ron Rotkopf)
     
  • Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment. Rosenwasser S, Graff van Creveld S, Schatz D, Malitsky S, Tzfadia O, Aharoni A, Levin Y, Gabashvili A, Feldmesser E, Vardi A (2014) Proc Natl Acad Sci U S A, 111(7):2740-5 ( for Ester Feldmesser)
     
  • Plum, an Immunoglobulin Superfamily Protein, Regulates Axon Pruning by Facilitating TGF-? Signaling. Yu M. Y., Gutman I., Mosca T. J., Iram T., O' zkan E.,Garcia K. C., Luo L., Schuldiner O. , Neuron, Volume 22, Issue 3, 456-468 (2013) (for Ofra Golani)
     
  • Overexpression of AtSHN1/WIN1 provokes inappropriate defense responses. Sela D, Buxdorf  K, Jian Xin S, Feldmesser E, Schreiber L, Aharoni A, Levy M (2013) PLoS One, 8(7):1-13 (for Ester Feldmesser)
     

Conference Tutorial

Tutorial at ISMB (Intelligent Systems for Molecular Biology, 2003) Training and Support for Bioinformatics: Theoretical and Practical Aspects Ben-Dor S, Butcher S, Iyer LK, Kelso J, LittleJohn T, Shachak A, and Rubin E.