Bioinformatics: LSCF Publications

  1. 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).
  2. 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).
  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. Gumpert N., Sagie S., Arnedo-Pac C., Babu T., Weller C., Gonzalez-Perez A., Wang Y., Michel Todó L., Levy R., Chen X., Greenberg P., Dayan-Rubinov M., Yakubovich E., Wasserman-Bartov T., Zerbib M., Gong J., Rebernick R. J., Oliveira Tercero A., Agundez Muriel L., 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 , 16 (2):OF1-OF20.
  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. 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).
  7. 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 , 188 (16):4350-4365.e22.
  8. 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 .
  9. 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 , 188 (16):4350-4365.e22.
  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. Ogran A., Green J., Hayat D., Sinha S., Avinoam O., Azuri I. & Dikstein R. (2025). Discovery of translation regulatory features and cross-UTR interactions through precise mapping of mRNA ends and machine learning.  . 2025, .
  12. 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).
  13. 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).
  14. 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).
  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. 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 .
  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. 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 .
  19. 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).
  20. 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).