Bioinformatics: LSCF Publications

  1. Turner M., Danino Y., Barshai M., Yacovzada N., Cohen Y., Olender T., Rotkopf R., Monchaud D., Hornstein E. & Orenstein Y. (2022). rG4detector, a novel RNA G-quadruplex predictor, uncovers their impact on stress granule formation.  Nucleic Acids Research. 2022 Nov 11 , 50 (20):11426-11441.
  2. Swain U., Friedlander G., Sehrawat U., Sarusi-Portuguez A., Rotkopf R., Ebert C., Paz-Elizur T., Dikstein R., Carell T., Geacintov N. E. & Livneh Z. (2021). Tent4a noncanonical poly(A) polymerase regulates dnadamage tolerance via multiple pathways that are mutated in endometrial cancer.  International Journal of Molecular Sciences. 2021 Jul 1 , 22 (13).
  3. Bar J., Sarig O., Lotan-Pompan M., Dassa B., Miodovnik M., Weinberger A., Sprecher E., Segal E. & Samuelov L. (2021). Evidence for cutaneous dysbiosis in dystrophic epidermolysis bullosa.  Clinical and Experimental Dermatology. 2021 Oct , 46 (7):1223-1229.
  4. Peri A., Greenstein E., Alon M., Pai J. A., Dingjan T., Reich-Zeliger S., Barnea E., Barbolin C., Levy R., Arnedo-Pac C., Kalaora S., Dassa B., Feldmesser E., Shang P., Greenberg P., Levin Y., Benedek G., Levesque M. P., Adams D. J., Lotem M., Wilmott J. S., Scolyer R. A., Jönsson G. B., Admon A., Rosenberg S. A., Cohen C. J., Niv M. Y., Lopez-Bigas N., Satpathy A. T., Friedman N. & Samuels Y. (2021). Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma.  Journal of Clinical Investigation. 2021, 131 (20).
  5. Goldfarb Y., Givony T., Dobeš J., Kadouri N., Zalayat I., Peligero-Cruz C., Damari G., Dassa B., Ben-Dor S., Gruper Y., Oftedal B. E., Bratland E., Erichsen M. M., Berger A., Avin A., Nevo S., Haljasorg U., Kuperman Y., Ulman A., Porat Z., Haffner-Krausz R., Atasoy U., Leshkowitz D., Husebye E. S. & Abramson J. (2021). Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE autoregulation.  Journal of Experimental Medicine. 2021 Nov , 218 (11).
  6. Goldfarb Y., Givony T., Dobeš J., Kadouri N., Zalayat I., Peligero-Cruz C., Damari G., Dassa B., Ben-Dor S., Gruper Y., Oftedal B. E., Bratland E., Erichsen M. M., Berger A., Avin A., Nevo S., Haljasorg U., Kuperman Y., Ulman A., Porat Z., Haffner-Krausz R., Atasoy U., Leshkowitz D., Husebye E. S. & Abramson J. (2021). Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE autoregulation.  Journal of Experimental Medicine. 2021 Nov , 218 (11).
  7. Goldfarb Y., Givony T., Dobeš J., Kadouri N., Zalayat I., Peligero-Cruz C., Damari G., Dassa B., Ben-Dor S., Gruper Y., Oftedal B. E., Bratland E., Erichsen M. M., Berger A., Avin A., Nevo S., Haljasorg U., Kuperman Y., Ulman A., Porat Z., Haffner-Krausz R., Atasoy U., Leshkowitz D., Husebye E. S. & Abramson J. (2021). Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE autoregulation.  Journal of Experimental Medicine. 2021 Nov , 218 (11).
  8. Castro C., Johnson R. J., Kieffer B., Means J. A., Taylor A., Telford J., Thompson L. K., Sussman J. L., Prilusky J. & Theis K. (2021). A practical guide to teaching with Proteopedia.  Biochemistry and Molecular Biology Education. 2021 Sept 1 , 49 (5):707-719.
  9. Tsamir-Rimon M., Ben-Dor S., Feldmesser E., Oppenhimer-Shaanan Y., David-Schwartz R., Samach A. & Klein T. (2021). Rapid starch degradation in the wood of olive trees under heat and drought is permitted by three stress-specific beta amylases.  New Phytologist. 2021 Feb , 229 (3):1398-1414.
  10. Pewzner-Jung Y., Joseph T., Blumenreich S., Vardi A., Ferreira N. S., Cho S. M., Eilam R., Tsoory M., Biton I. E., Brumfeld V., Haffner-Krausz R., Brenner O., Sharabi N., Addadi Y., Salame T. M., Rotkopf R., Wigoda N., Yayon N., Merrill A. H., Schiffmann R. & Futerman A. H. (2021). Brain pathology and cerebellar purkinje cell loss in a mouse model of chronic neuronopathic Gaucher disease.  Progress in Neurobiology. 2021 Feb , 197 .
  11. Pewzner-Jung Y., Joseph T., Blumenreich S., Vardi A., Ferreira N. S., Cho S. M., Eilam R., Tsoory M., Biton I. E., Brumfeld V., Haffner-Krausz R., Brenner O., Sharabi N., Addadi Y., Salame T. M., Rotkopf R., Wigoda N., Yayon N., Merrill A. H., Schiffmann R. & Futerman A. H. (2021). Brain pathology and cerebellar purkinje cell loss in a mouse model of chronic neuronopathic Gaucher disease.  Progress in Neurobiology. 2021 Feb , 197 .
  12. Dekel E., Yaffe D., Rosenhek-Goldian I., Ben-Nissan G., Ofir-Birin Y., Morandi M. I., Ziv T., Sisquella X., Pimentel M. A., Nebl T., Kapp E., Ohana Daniel Y., Karam P. A., Alfandari D., Rotkopf R., Malihi S., Temin T. B., Mullick D., Revach O. Y., Rudik A., Gov N. S., Azuri I., Porat Z., Bergamaschi G., Sorkin R., Wuite G. J., Avinoam O., Carvalho T. G., Cohen S. R., Sharon M. & Regev-Rudzki N. (2021). 20S proteasomes secreted by the malaria parasite promote its growth.  Nature Communications. 2021 Feb 19 , 12 (1).
  13. Ulman A., Levin T., Dassa B., Javitt A., Kacen A., Shmueli M. D., Eisenberg-Lerner A., Sheban D., Fishllevich S., Levy E. D. & Merbl Y. (2021). Altered Protein Abundance and Localization Inferred from Sites of Alternative Modification by Ubiquitin and SUMO: Revealing new insights into protein function from Sites of Alternative Modifications (SAM).  Journal of Molecular Biology. 2021 Oct 15 , 433 (21).
  14. Doron E., Koppel I., Abraham O., Rishal I., Smith T. P., Buchanan C. N., Sahoo P. K., Kadlec J., Oses-Prieto J. A., Kawaguchi R., Alber S., Zahavi E. E., Di Matteo P., Di Pizio A., Song D. A., Okladnikova N., Gordon D., Ben-Dor S., Haffner-Krausz R., Coppola G., Burlingame A. L., Jungwirth P., Twiss J. L. & Fainzilber M. (2021). The glycine arginine-rich domain of the RNA-binding protein nucleolin regulates its subcellular localization.  EMBO Journal. 2021 Oct 18 , 40 (20).
  15. Raz A., Dahan-Meir T., Melamed-Bessudo C., Leshkowitz D. & Levy A. A. (2021). Redistribution of Meiotic Crossovers Along Wheat Chromosomes by Virus-Induced Gene Silencing.  Frontiers in Plant Science. 2021 Feb 4 , 11 .
  16. Daniel E., Maksimainen M. M., Smith N., Ratas V., Biterova E., Murthy S. N., Tanvir Rahman M., Kiema T. R., Sridhar S., Cordara G., Dalwani S., Venkatesan R., Prilusky J., Dym O., Lehtio L., Kristian Koski M., Ashton A. W., Sussman J. L. & Wierenga R. K. (2021). IceBear: An intuitive and versatile web application for research-data tracking from crystallization experiment to PDB deposition.  Acta Crystallographica Section D: Structural Biology. 2021 Feb 1 , 77 (2):151-163.
  17. Soll M., Goldshtein H., Rotkopf R., Russek-Blum N. & Gross Z. (2021). A synthetic sod/catalase mimic compound for the treatment of als.  Antioxidants. 2021 Jun , 10 (6).
  18. Benjamin A., Kuperman Y., Eren N., Rotkopf R., Amitai M., Rossman H., Shilo S., Meir T., Keshet A., Nuttman-Shwartz O., Segal E. & Chen A. (2021). Stress-related emotional and behavioural impact following the first COVID-19 outbreak peak.  Molecular Psychiatry. 2021 Nov , 26 (11):6149-6158.
  19. Mevorach T., Taler M., Dar S., Lebow M., Sapir I. S., Rotkopf R., Apter A., Fennig S., Chen A., Weizman A. & Amitai M. (2021). The relationship between the plasma proinflammatory cytokine levels of depressed/anxious children and their parents.  Scientific Reports. 2021 Dec , 11 (1).
  20. Camargo S., Leshkowitz D., Dassa B., Mariscal V., Flores E., Stavans J. & Arbel-Goren R. (2021). Impaired cell-cell communication in the multicellular cyanobacterium Anabaena affects carbon uptake, photosynthesis, and the cell wall.  iScience. 2021 Jan 22 , 24 (1).