Bioinformatics: LSCF Publications

  1. 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 Aug 7 , 188 (16):4350-4365.e22.
  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 Dec , 26 (1).
  3. 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).
  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 Dec , 26 (1).
  5. 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).
  6. 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.
  7. 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).
  8. 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).
  9. 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).
  10. 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 June).
  11. 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).
  12. 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.
  13. 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 , .
  14. 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 , .
  15. 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 , .
  16. 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 , .
  17. 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.
  18. 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).
  19. 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.
  20. 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).