Bioinformatics: LSCF Publications

  1. 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).
  2. 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).
  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. 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.
  5. 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).
  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. 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.
  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. 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).
  10. 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.
  11. 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 .
  12. Mayo R. P., Pewzner-Jung Y., Khan S., Solmesky L., Kozer N. K., Yona M., Zahradnik J., Unger T., Rotkopf R., Barr H., Goldman-Wohl D., Schreiber G., Yagel S., Beharier O., Kovo M., Avinoam O. & Neeman M. (2025). Neutralization and Assessment of the Binding Capacity of Maternal Sera Against Various Sars-cov-2 Variants.  Placenta. 2025 Nov , 171 :e281-e282.
  13. 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).
  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).