Bioinformatics: LSCF Publications

  1. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  2. Weller C., Bartok O., McGinnis C. S., Palashati H., Chang T. G., Malko D., Shmueli M. D., Nagao A., Hayoun D., Murayama A., Sakaguchi Y., Poulis P., Khatib A., Erlanger Avigdor B., Gordon S., Cohen Shvefel S., Zemanek M. J., Nielsen M. M., Boura-Halfon S., Sagie S., Gumpert N., Yang W., Alexeev D., Kyriakidou P., Yao W., Zerbib M., Greenberg P., Benedek G., Litchfield K., Petrovich-Kopitman E., Nagler A., Oren R., Ben-Dor S., Levin Y., Pilpel Y., Rodnina M., Cox J., Merbl Y., Satpathy A. T., Carmi Y., Erhard F., Suzuki T., Buskirk A. R., Olweus J., Ruppin E., Schlosser A. & Samuels Y. (2025). Translation dysregulation in cancer as a source for targetable antigens.  Cancer Cell. 2025 Mar 27 , 43 (5):823-840.e18.
  3. Chourasia S., Petucci C., Shoffler C., Abbasian D., Wang H., Han X., Sivan E., Brandis A., Mehlman T., Malitsky S., Itkin M., Sharp A., Rotkopf R., Dassa B., Regev L., Zaltsman Y. & Gross A. (2025). MTCH2 controls energy demand and expenditure to fuel anabolism during adipogenesis.  EMBO Journal. 2025 Jan 3 , 44 (4):1007-1038.
  4. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  5. Mizrachi A., Sadeh M., Ben-Dor S., Dym O., Ku C., Feldmesser E., Zarfin A., Brunson J. K., Allen A. E., Jinkerson R. E., Schatz D. & Vardi A. (2025). Cathepsin X is a conserved cell death protein involved in algal response to environmental stress.  Current Biology. 2025 Apr 14 , .
  6. Chourasia S., Petucci C., Shoffler C., Abbasian D., Wang H., Han X., Sivan E., Brandis A., Mehlman T., Malitsky S., Itkin M., Sharp A., Rotkopf R., Dassa B., Regev L., Zaltsman Y. & Gross A. (2025). MTCH2 controls energy demand and expenditure to fuel anabolism during adipogenesis.  EMBO Journal. 2025 Jan 3 , 44 (4):1007-1038.
  7. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  8. Kozela E., Petrovich-Kopitman E., Berger Y., Camacho A. C., Shoham Y., Morandi M. I., Rosenhek-Goldian I., Rotkopf R. & Regev-Rudzki N. (2025). Spectral flow cytometry for detecting DNA cargo in malaria parasitederived extracellular vesicles.  Journal of Biological Chemistry. 2025 May , 301 (5).
  9. Furth N., Cohen N., Spitzer A., Salame T. M., Dassa B., Mehlman T., Brandis A., Moussaieff A., Friedmann-Morvinski D., Castro M. G., Fortin J., Suvà M. L., Tirosh I., Erez A., Ron G. & Shema E. (2025). Oncogenic IDH1mut drives robust loss of histone acetylation and increases chromatin heterogeneity.  Proceedings of the National Academy of Sciences - PNAS. 2025 Jan 7 , 122 (1).
  10. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  11. Zahavi E. E., Koppel I., Kawaguchi R., Oses-Prieto J. A., Briner A., Monavarfeshani A., Dalla Costa I., van Niekerk E., Lee J., Matoo S., Hegarty S., Donahue R. J., Sahoo P. K., Ben-Dor S., Feldmesser E., Ryvkin J., Leshkowitz D., Perry R. B. T., Cheng Y., Farber E., Abraham O., Samra N., Okladnikov N., Alber S., Albus C. A., Rishal I., Ulitsky I., Tuszynski M. H., Twiss J. L., He Z., Burlingame A. L. & Fainzilber M. (2025). Repeat-element RNAs integrate a neuronal growth circuit.  Cell. 2025 May 16 , .
  12. Shpitzen S., Rosen H., Ben-Zvi A., Meir K., Levin G., Gudgold A., Ben Dor S., Haffner R., Zwas D. R., Leibowitz D., Slaugenhaupt S. A., Banin E., Mizrachi R., Obolensky A., Levine R. A., Gilon D., Leitersdorf E., Tessler I., Reshef N. & Durst R. (2025). Characterization of LTBP2 mutation causing mitral valve prolapse.  European Heart Journal Open. 2025 Jan 1 , 5 (1).
  13. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  14. Zahavi E. E., Koppel I., Kawaguchi R., Oses-Prieto J. A., Briner A., Monavarfeshani A., Dalla Costa I., van Niekerk E., Lee J., Matoo S., Hegarty S., Donahue R. J., Sahoo P. K., Ben-Dor S., Feldmesser E., Ryvkin J., Leshkowitz D., Perry R. B. T., Cheng Y., Farber E., Abraham O., Samra N., Okladnikov N., Alber S., Albus C. A., Rishal I., Ulitsky I., Tuszynski M. H., Twiss J. L., He Z., Burlingame A. L. & Fainzilber M. (2025). Repeat-element RNAs integrate a neuronal growth circuit.  Cell. 2025 May 16 , .
  15. Leushkin Y., Morgenstern D., Ben-Dor S., Haffner-Krausz R., Zittlau K., Ben-Nissan G. & Sharon M. (2025). Molecular insights into the unique properties of the blood-circulating proteasome.  Journal of Extracellular Biology. 2025 Jan , 4 (1).
  16. Kiper E., Ben Hur D., Alfandari D., Camacho A. C., Wani N. A., Efrat G. D., Morandi M. I., Goldsmith M., Rotkopf R., Kamyshinsky R., Deshmukh A., Binte Zulkifli N. E., Asmari N., Penedo M., Fantner G., Porat Z., Azuri I., Rosenhek-Goldian I., Chitnis C. E., Shai Y. & Regev-Rudzki N. (2025). Antimicrobial peptides selectively target malaria parasites by a cholesterol-dependent mechanism.  Journal of Biological Chemistry. 2025 Apr , 301 (4).
  17. Alfandari D., Rosenhek-Goldian I., Kozela E., Nevo R., Senprún M. B., Moisieiev A., Sogauker N., Azuri I., Gelman S., Kiper E., Ben Hur D., Dharan R., Sorkin R., Porat Z., Morandi M. I. & Regev-Rudzki N. (2025). Host Immune Cell Membrane Deformability Governs the Uptake Route of Malaria-Derived Extracellular Vesicles.  ACS Nano. 2025 Mar 18 , 19 (10):9760-9778.
  18. Kiper E., Ben Hur D., Alfandari D., Camacho A. C., Wani N. A., Efrat G. D., Morandi M. I., Goldsmith M., Rotkopf R., Kamyshinsky R., Deshmukh A., Binte Zulkifli N. E., Asmari N., Penedo M., Fantner G., Porat Z., Azuri I., Rosenhek-Goldian I., Chitnis C. E., Shai Y. & Regev-Rudzki N. (2025). Antimicrobial peptides selectively target malaria parasites by a cholesterol-dependent mechanism.  Journal of Biological Chemistry. 2025 Apr , 301 (4).
  19. Lindner J., Dassa B., Wigoda N., Stelzer G., Feldmesser E., Prilusky J. & Leshkowitz D. (2025). UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.  BMC Bioinformatics. 2025 Mar 7 , 26 .
  20. Shvefel S. C., Pai J. A., Cao Y., Pal L. R., Bartok O., Levy R., Zemanek M. J., Weller C., Herzog E., Yao W., Hiam-Galvez K. J., Cheng K., Yin Y., Du P. P., Raposo C. J., Gumpert N., Welti M., Martínez Gómez J. M., Sella F., Yakubovich E., Orr I., Ben-Dor S., Oren R., Fellus-Alyagor L., Golani O., Brenner O. J., Salame T. M., Zerbib M., Goliand I., Ranmar D., Savchenko I., Ketrarou N., Schäffer A. A., Dahan R., Levesque M. P., Ruppin E., Satpathy A. T. & Samuels Y. (2025). Temporal Genomic Analysis of Homogeneous Tumor Models Reveals Key Regulators of Immune Evasion in Melanoma.  Cancer Discovery. 2025 Mar 1 , 15 (3):553-577.