• Elastic-Degenerate String Comparison.
  Gabory, E., Mwaniki, M. N., Pisanti, N., Pissis, S. P., Radoszewski, J., Sweering, M., & Zuba, W. (2025).
  Information and Computation, 105296.
• Differential analysis of alternative splicing events in gene regions using residual neural networks.
  Ciccolella, S., Denti, L., Avila Cartes, J., Della Vedova, G., Pirola, Y., Rizzi, R., & Bonizzoni, P. (2025).
  Neural Computing and Applications, 1-11.
• Differential quantification of alternative splicing events on spliced pangenome graphs.
  Ciccolella, S., Cozzi, D., Della Vedova, G., Kuria, S. N., Bonizzoni, P., & Denti, L. (2024).
  PLOS Computational Biology, 20(12), e1012665.
• PangeBlocks: customized construction of pangenome graphs via maximal blocks.
  Avila Cartes, J., Bonizzoni, P., Ciccolella, S., Della Vedova, G., & Denti, L. (2024).
  BMC bioinformatics, 25(1), 344.
• RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape.
  Cillari, N., Neri, G., Pisanti, N., Milazzo, P., & Borello, U. (2024).
  Database, 2024, baae109.
• Pattern masking for dictionary matching: theory and practice.
  Charalampopoulos, P., Chen, H., Christen, P., Loukides, G., Pisanti, N., Pissis, S. P., & Radoszewski, J. (2024).
  Algorithmica, 86(6), 1948-1978.
• RecGraph: recombination-aware alignment of sequences to variation graphs.
  Avila Cartes, J., Bonizzoni, P., Ciccolella, S., Della Vedova, G., Denti, L., Didelot, X., Monti D. C. & Pirola, Y. (2024)
  Bioinformatics, 40(5), btae292.
• r-indexing the eBWT.
  Boucher, C., Cenzato, D., Lipták, Z., Rossi, M., & Sciortino, M. (2024).
  Information and Computation, 298, 105155.
• New string attractor-based complexities for infinite words.
  Cassaigne, J., Gheeraert, F., Restivo, A., Romana, G., Sciortino, M., & Stipulanti, M. (2024).
  Journal of Combinatorial Theory, Series A, 208, 105936.
• Pangenome comparison via ED strings.
  Gabory, E., Mwaniki, M. N., Pisanti, N., Pissis, S. P., Radoszewski, J., Sweering, M., & Zuba, W. (2024).
  Frontiers in Bioinformatics, 4, 1397036.

---

• Utility-Oriented String Mining.
  Bernardini, G., Chen, H., Conte, A., Grossi, R., Guerrini, V., Loukides, G., Pisanti, N. & Pissis, S. P. (2024).
  In Proceedings of the 2024 SIAM International Conference on Data Mining (SDM) (pp. 190-198). Society for Industrial and Applied Mathematics.
• The rational construction of a Wheeler DFA.
  Manzini, G., Policriti, A., Prezza, N., & Riccardi, B. (2024).
  LEIBNIZ INTERNATIONAL PROCEEDINGS IN INFORMATICS, 296.
• A unifying taxonomy of pattern matching in degenerate strings and founder graphs.
  Ascone, R., Bernardini, G., Conte, A., Equi, M., Gabory, E., Grossi, R., & Pisanti, N. (2024, September).
  In WABI 2024-Workshop on Algorithms in BioInformatics. Schloss Dagstuhl–Leibniz-Zentrum für Informatik.
• Unveiling the connection between the Lyndon factorization and the Canonical Inverse Lyndon factorization via a border property.
  Bonizzoni, P., De Felice, C., Riccardi, B., Zaccagnino, R., & Zizza, R. (2024).
  In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024) (pp. 31:1–31:14). Schloss Dagstuhl – Leibniz-Zentrum fur Informatik.
• Solving the Minimal Positional Substring Cover Problem in Sublinear Space.
  Bonizzoni, P., Boucher, C., Cozzi, D., Gagie, T., & Pirola, Y. (2024, June).
  In 35th Annual Symposium on Combinatorial Pattern Matching (p. 1).
• Generalization of Repetitiveness Measures for Two-Dimensional Strings.
  Carfagna, L., Manzini, G., Romana, G., Sciortino, M., & Urbina, C. (2024, September).
  In International Symposium on String Processing and Information Retrieval (pp. 57-72). Cham: Springer Nature Switzerland.

---

Recent works on ArXiv

• Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development.
  Mahadevaraju, S., Pal, S., Bhaskar, P., McDonald, B. D., Benner, L., Denti, L., Cozzi, D., Bonizzoni, P., Przytycka, T. M., & Oliver, B. (2024).
  bioRxiv : the preprint server for biology, 2024.08.12.607556.
• Faster run-length compressed suffix arrays.
  Brown, N. K., Gagie, T., Manzini, G., Navarro, G., & Sciortino, M. (2024).
  arXiv e-prints, arXiv-2408.
• Exploring repetitiveness measures for two-dimensional strings.
  Romana, G., Sciortino, M., & Urbina, C. (2024).
  arXiv preprint arXiv:2404.07030.
• Movelet Trees. 
  Gagie, T., Manzini, G., Navarro, G., & Sciortino, M. (2024).
  arXiv e-prints, arXiv-2408.
• Elastic-Degenerate String Comparison. 
  Gabory, E., Mwaniki, M. N., Pisanti, N., Pissis, S. P., Radoszewski, J., Sweering, M., & Zuba, W. (2024).
  arXiv preprint arXiv:2411.07782.
• Popping Bubbles in Pangenome Graphs.
  Mwaniki, N., Garrison, E., & Pisanti, N. (2024).
  arXiv preprint arXiv:2410.20932.
• From the Lyndon factorization to the Canonical Inverse Lyndon factorization: back and forth.
  Bonizzoni, P., De Felice, C., Zaccagnino, R., & Zizza, R. (2024).
  arXiv preprint arXiv:2404.17969.