Bioinformatics: LSCF Publications

  1. Abou Karam P., Kiper E., Ziv T., Yadid S., Kozela E., Zharoni N., Nevo R., Alfandari D., Otesh H., Cruz Camacho A., Lubelsky Y., Rotkopf R., Weizman E., Cossin M., Rosenhek-Goldian I., Petrovich-Kopitman E., Porat Z., Shoshani O., Ulitsky I., Levy C., Melamed Z. & Regev-Rudzki N. (2026). Nuclear import of malaria RNA rewires splicing in host immune cells.  Cell Reports. 2026 Feb 24 , 45 (2).
  2. Lebon S., Habshush Menachem A., Davidzohn N., Katz A., Wigoda N., Braun T., Yahalomi D., Rotkopf R., Holiar V., Dadosh T., Levin-Zaidman S., Dezorella N., Goliand I., Kupervaser M., Leebhoff S., Blumberger N., Hoffman D., Grunewald M., Levin Y., Haberman Y., Hofree M. & Biton M. (2026). An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection.  Nature Immunology. 2026 May 12 , .
  3. Tishler H., Ziman S., Cheng K., Wang K., Sanghvi N., Adler L., Stelzer G., Maniriho H., Dassa B., Bab-Dinitz E., Levi M., Galai S., Goldman O., Ariav Y., Darzi N., Ezagouri S., Nimni N., Rosenfeld N., Rotkopf R., Brandis A., Mehlman T., Oren R., Zerbib M., Kuznetsov Y., Donzelli S., Blandino G., Seger R., Ruppin E. & Erez A. (2026). Inhibition of Tumor Microenvironment-Driven JAK-STAT Signaling Enhances Response to Arginine Deprivation Therapy in Triple-Negative Breast Cancer.  Cells. 2026 Jan , 15 (1).
  4. Alon T., Ross M., Spirer J., Silva P. D. S., Rosov A., Lifshitz L., Kra G., Gershoni M., Malitsky S., Itkin M., Rotkopf R. & Moallem U. (2026). Lipidomics of allantoic fluid collected by allantocentesis indicates a possible mechanism underlying partial litter loss in multifetal pregnancies of ewes.  Scientific Reports. 2026 Mar 18 , 16 .
  5. Tishler H., Ziman S., Cheng K., Wang K., Sanghvi N., Adler L., Stelzer G., Maniriho H., Dassa B., Bab-Dinitz E., Levi M., Galai S., Goldman O., Ariav Y., Darzi N., Ezagouri S., Nimni N., Rosenfeld N., Rotkopf R., Brandis A., Mehlman T., Oren R., Zerbib M., Kuznetsov Y., Donzelli S., Blandino G., Seger R., Ruppin E. & Erez A. (2026). Inhibition of Tumor Microenvironment-Driven JAK-STAT Signaling Enhances Response to Arginine Deprivation Therapy in Triple-Negative Breast Cancer.  Cells. 2026 Jan , 15 (1).
  6. Lebon S., Habshush Menachem A., Davidzohn N., Katz A., Wigoda N., Braun T., Yahalomi D., Rotkopf R., Holiar V., Dadosh T., Levin-Zaidman S., Dezorella N., Goliand I., Kupervaser M., Leebhoff S., Blumberger N., Hoffman D., Grunewald M., Levin Y., Haberman Y., Hofree M. & Biton M. (2026). An inflammasome-driven differentiation program in intestinal stem cells protects against Salmonella infection.  Nature Immunology. 2026 May 12 , .
  7. Sadeh M., Schatz D., Ben-Dor S., Mizrachi A., Graff van Creveld S., Zafrin A. & Vardi A. (2026). Metacaspases contribute to the cellular response to heat stress in a marine diatom.  New Phytologist. 2026 Feb 22 , .
  8. Gumpert N., Sagie S., Arnedo-Pac C., Babu T., Weller C., Gonzalez-Perez A., Wang Y., Todó L. M., Levy R., Chen X., Greenberg P., Dayan-Rubinov M., Yakubovich E., Wasserman-Bartov T., Zerbib M., Gong J., Rebernick R. J., Tercero A. O., Muriel L. A., Benedek G., Kedmi M., Oren R., Ben-Dor S., Levin Y., Troyanskaya O. G., Munzur A. D., Wyatt A. W., Cieslik M. P., Quigley D. A., Van Allen E. M., Anandasabapathy N., Mateo J., Yang X., Martínez-Jiménez F., Lopez-Bigas N. & Samuels Y. (2026). Recurrent Immunogenic Neoantigens and Their Cognate T-cell Receptors in Treatment-Resistant Metastatic Prostate Cancer.  Cancer Discovery. 2026 Feb 6 , 16 (2):250-269.
  9. Tishler H., Ziman S., Cheng K., Wang K., Sanghvi N., Adler L., Stelzer G., Maniriho H., Dassa B., Bab-Dinitz E., Levi M., Galai S., Goldman O., Ariav Y., Darzi N., Ezagouri S., Nimni N., Rosenfeld N., Rotkopf R., Brandis A., Mehlman T., Oren R., Zerbib M., Kuznetsov Y., Donzelli S., Blandino G., Seger R., Ruppin E. & Erez A. (2026). Inhibition of Tumor Microenvironment-Driven JAK-STAT Signaling Enhances Response to Arginine Deprivation Therapy in Triple-Negative Breast Cancer.  Cells. 2026 Jan , 15 (1).
  10. Eyal Z., Deis R., Gorelick-Ashkenazi A., Barzilay Y., Broder Y., Kellum A. P., Varsano N., Hartstein M., Sorrentino A., Rotkopf R., Kaplan-Ashiri I., Rechav K., Metzler R., Houben L., Kronik L., Rez P. & Gur D. (2026). pH variations enable guanine crystal formation within iridosomes.  Nature Chemical Biology. 2026 Jan , 22 (1):19-27.
  11. Zoler E., Miodownik I., Ben-Dor S., Harari D., Zahradnik J., Afek A. & Schreiber G. (2026). IRF1 is a context-dependent homeostatic gatekeeper of basal immunity and antiviral readiness.  Journal of Biological Chemistry. 2026 Feb , 302 (2).
  12. Lebow M., Rotkopf R., Malik E., Amitai M., Weizman A., Krieger O., Geyshin A., Israel A., Merzon E., Magen E., Vinker S., Nuttman-Shwartz O. & Chen A. (2026). Intensity and exposure proximity as determinants of differential stress-related health outcomes.  Molecular Psychiatry. 2026 Mar 6 , .
  13. 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.
  14. 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).
  15. 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).
  16. 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 Dec , 26 (1).
  17. Haque R., Setty H., Lorenzo R., Stelzer G., Rotkopf R., Salzberg Y., Goldman G., Kumar S., Halber S. N., Leifer A. M., Schneidman E., Laurent P. & Oren-Suissa M. (2025). Decoding sexual dimorphism of the sex-shared nervous system at single-neuron resolution.  Science advances. 2025 Jul 11 , 11 (28).
  18. Mestre B., Zelnik I. D., Izrailov S., Dingjan T., Lvovsky G., Fidel L., Ben-Dor S. & Futerman A. H. (2025). An anomalous abundance of tryptophan residues in ceramide synthases based on analysis of all membrane proteins in the Swiss-Prot database.  Journal of Biological Chemistry. 2025 Jan , 301 (1).
  19. 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 May 12 , 43 (5):823-840.e18.
  20. 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).