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. 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 .
  3. 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.
  4. 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).
  5. 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).
  6. 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).
  7. Griess O., Furth N., Harpaz N., Di Bernardo N., Salame T. M., Dassa B., Karagiannidis I., Isshiki Y., Gross M., Melnick A. M., Béguelin W., Ron G. & Shema E. (2025). Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma.  PLoS Biology. 2025 Jun , 23 (6 ).
  8. 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).
  9. 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 Feb 17 , 44 (4):1007-1038.
  10. 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.
  11. 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. (2025). pH variations enable guanine crystal formation within iridosomes.  Nature Chemical Biology. 2025 Sept 2 , 22 (1):19-27.
  12. Haddad M., Trzebanski S., Bossardi Ramos R., Ordonez Moreno L. A., Rahtes A., Khatib-Massalha E., Chakrabarti P., Petrovich-Kopitman E., Wigoda N., Biram A., Poller W. C., Aroca-Crevillén A., Hidalgo A., Fredman G., Swirski F. K., Egeblad M., Markus R. P., Schlegel M., Jung S., Lapidot T., Adrover J. M. & Kollet O. (2025). Diurnally-Regulated Corticosterone and Melatonin Inversely Control Endotoxin-Induced Acute Immune Responses.  European Journal of Immunology. 2025 Nov , 55 (11).
  13. 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. (2025). Recurrent Immunogenic Neoantigens and Their Cognate T-cell Receptors in Treatment-Resistant Metastatic Prostate Cancer.  Cancer Discovery. 2025 Dec 10 , :OF1-OF20.
  14. Zilkha N., Hamade R., Chuartzman S. G., Sofer Y., Kashash Y., Meir R., Fishman R., Biton I. E., Ben-Dor S. & Kimchi T. (2025). Distinct oxytocin populations support seismic social communication and militant behaviors in a naturally solitary wild rodent.  iScience. 2025 Dec 19 , 28 (12).
  15. 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 Feb 17 , 44 (4):1007-1038.
  16. Aylon Y., Furth N., Pirona A. C., Lavie A., Fedorova O., Hassin O., Padrão N., Steinmetz M., Sarusi-Potuguez A., Fellus-Alyagor L., Shimoni I., Dassa B., Zwart W., Shema E. & Oren M. (2025). p53 regulates the expression of histone modifiers to restrict stemness and maintain differentiated luminal identity in breast cancer.  Proceedings of the National Academy of Sciences - PNAS. 2025 Nov 4 , 122 (44).
  17. Kotli P., Morgenstern D., Ben-Dor S., Kolska Horwitz L. & Boaretto E. (2025). Sex Identification and Species Confirmation in Modern and Archeological Caprine Enamel.  Journal of Proteome Research. 2025 Sept 5 , 24 (9):4403-4416.
  18. Gelman S., Rosenhek-Goldian I., Kampf N., Patocka M., Rios M., Penedo M., Fantner G., Beker A., Cohen S. R. & Azuri I. (2025). Deep learning for enhancement of low-resolution and noisy scanning probe microscopy images.  Beilstein Journal of Nanotechnology. 2025 Jul 16 , 16 :1129-1140.
  19. Marom S., Lifshits Dayan I., Narasimha Kadali V., Giurgiu-Kraljič M., Koifman G., Hakeny K., Chaurasia M., Benamozig O., Nevo R., Azuri I., Ryvkin J., Rotkopf R., Stelzer G., Oniashvili N., Mardoukh J., Pollock S., Iremadze N., Shipony Z., Kupervaser M., Wigoda N., Leshkowitz D., Elazar Z., Berko E., Henssen A. G. & Shoshani O. (2025). Aberrant inheritance of extrachromosomal DNA amplifications promotes cancer evolution.  BioRxiv. 2025 Sept 21 , .
  20. Marom S., Lifshits Dayan I., Narasimha Kadali V., Giurgiu-Kraljič M., Koifman G., Hakeny K., Chaurasia M., Benamozig O., Nevo R., Azuri I., Ryvkin J., Rotkopf R., Stelzer G., Oniashvili N., Mardoukh J., Pollock S., Iremadze N., Shipony Z., Kupervaser M., Wigoda N., Leshkowitz D., Elazar Z., Berko E., Henssen A. G. & Shoshani O. (2025). Aberrant inheritance of extrachromosomal DNA amplifications promotes cancer evolution.  BioRxiv. 2025 Sept 21 , .