Publications

What we publish
Unveiling Our Latest findings
  1. Arar, Hala, et al. SOORENA: Self-lOOp containing or autoREgulatory Nodes in biological network Analysis. bioRxiv (2025): 2025-11.
  2. Zakeri, S., and  Jafari, M., Reducing Boolean Networks via Analysis of Dynamic Network Subgraph Behavior. bioRxiv (2026): 2026-07.
  3. Amir Ata Saei, Xueyao Wang, Konstantinos Fragkoulis et al. Deep proteomics profiling of the cell secretome by DeepSec, 21 July 2026, PREPRINT (Version 1) available at Research Square.
  4. Zandi et al. Integrative Host–Virus Network Analysis Reveals Coordinated Immune, Proteostatic, and Mitochondrial Responses during Rabies Virus Infection. Microbiology Spectrum, July 2026 (Submitted).
Selected publications
  1. Zangene, E., Gholizadeh, E., Vadadokhau, U., Ritz, D., Saei, A. A., and Jafari, M., . Sci Data (2026). 
  2. Zangene, E., Gholizadeh, E., Schwämmle, V., Saei, A. A., Wilhelm, M., Käll, L., and Jafari, M., Molecular & Cellular Proteomics (2026): 101603.
  3. Zangene, E., Schwämmle, V., and Jafari, M., . Comput Struct Biotechnol J., Volume 35, Issue 1 (2026).
  4. Malekpour, SA., Jafari, M., Sadeghi, M. Nucleic Acids Research, Volume 54, Issue 6, (2026).
  5. Gholizadeh, E., Zangene, E., Vadadokhau, U. et al. . Nat Commun 17, 2744, (2026).
  6. Vadadokhau, U., Soliman, M., Castillon, L. et al. . Sci Data 13, 287 (2026).
  7. Gholizadeh, E., et al. , Biomedicine & Pharmacotherapy, Volume 192, 118647, (2025).
  8. Nickchi, P., et al. . Proteomics, e202400238, (2025).
  9. Mirzaie, M., et al. Oncogenesis 13(1):11, (2024).
  10. Jafari, M., et al. . Nature Communications 13 (1): 2128, (2022).
  11. Jafari, M., et al. . Genome Biology 22 (1): 71, (2021).
  12. Gholizadeh, E., et al. . Molecular Pharmacology 99 (5): 308–18, (2021).
  13. Barneh, F., et al. Briefings in Bioinformatics 20 (2): 717–31, (2019).
  14. Wang, Z., et al.. Nature Communications 7 (1): 12846, (2016).
View all