Department of
Environmental Sciences, Informatics and Statistics

Computational Biology, Bioinformatics and Complex Systems

The laboratory’s research activities are focused on the following topics:

  • Algorithms and data structures. The goal is to design efficient algorithmic techniques to store and process large quantities of genomic data (e.g. genomes, pan-genomes).  This includes compressed data structures for aligning sequences to pan-genomes and compression techniques for storing large quantities of DNA sequences.
  • Systems biology. Development of approaches to model, analyze, simulate, and compare biological (e.g., metabolic networks, protein interaction networks, etc.) or ecological systems (e.g., food networks, ecosystem services networks);
  • Protein mutation analysis. Development of computational approaches to detect or predict deleterious mutations of a protein under consideration. The aim is to quickly obtain, through computational techniques,  a first selection of genetic variants to submit to a more in-depth analysis, but expensive in terms of time and resources;
  • Development, automatic calibration and analysis of models of complex systems (biological, chemical, physical, social) and high-performance simulation using unconventional architectures (e.g., GPUs, TPUs, NPUs, neuromorphic chips);
  • Automatic development of clinical decision support systems based on interpretable artificial intelligence, exploiting computational intelligence techniques (e.g., fuzzy reasoning, evolutionary computation, swarm intelligence, machine learning).
Research group

Collaborators

  • Chiara Gallese (Università di Torino)
  • Luca Manzoni (Università di Trieste)
  • Leone Bacciu (Research fellow at DAIS)
  • Matteo Grazioso (Research fellow at DAIS)
  • Camilla Torlasco (Istituto Auxologico Italiano)
  • Daniela Besozzi (Università Milano-Bicocca)
  • Paolo Cazzaniga (Università di Bergamo)
  • Mohsen Abbaspour Onari, PhD Student at the Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
  • Daniele M. Papetti, PhD Student at the Università degli Studi di Milano-Bicocca, Milano, Italia
  • Vasco Coelho, PhD Student at the Università degli Studi di Milano-Bicocca, Milano, Italia
  • Elisa Perinot, PhD Student at the Konrad Lorenz Institute of Ethology, University of VeterinaryMedicine, Wien, Austria
  • Nicola Cotumaccio, PhD Student at GSSI, L’Aquila, Italy and Dalhousie university, Nova Scotia, Canada

Collaborations

Publications

  • Nicola Cotumaccio, Giovanna D’Agostino, Alberto Policriti, Nicola Prezza. Co-lexicographically Ordering Automata and Regular Languages - Part I. J ournal of the ACM (JACM), https://dl.acm.org/doi/10.1145/3607471
  • Tomasz Kociumaka, Gonzalo Navarro, Nicola Prezza, Towards a Definitive Compressibility Measure for Repetitive Sequences, in IEEE Transactions on Information Theory, https://doi.org/10.1109/TIT.2022.3224382
  • Ruben Becker, Sung-Hwan Kim, Nicola Prezza, Carlo Tosoni. Indexing Finite-State Automata Using Forward-Stable Partitions. SPIRE 2024, https://doi.org/10.1007/978-3-031-72200-4_3
  • Davide Cenzato, Francisco Olivares, Nicola Prezza. On Computing the Smallest Suffixient Set. SPIRE 2024, https://doi.org/10.1007/978-3-031-72200-4_6
  • Giovanni Manzini, Alberto Policriti, Nicola Prezza, Brian Riccardi. The Rational Construction of a Wheeler DFA. CPM 2024, https://doi.org/10.4230/LIPIcs.CPM.2024.23
  • Ruben Becker, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Riccardo Maso, Nicola Prezza. Random Wheeler Automata. CPM 2024, https://doi.org/10.4230/LIPIcs.CPM.2024.5
  • Jarno N. Alanko, Davide Cenzato, Nicola Cotumaccio, Sung-Hwan Kim, Giovanni Manzini, Nicola Prezza. Computing the LCP Array of a Labeled Graph. CPM 2024, https://doi.org/10.4230/LIPIcs.CPM.2024.1
  • Patrick Dinklage, Johnnes Fischer, and Nicola Prezza. Top-k Frequent Patterns in Streams and Parameterized-Space LZ Compression. In 22nd International Symposium on Experimental Algorithms (SEA 2024), https://doi.org/10.4230/LIPIcs.SEA.2024.9
  • Ruben Becker, Matteo Canton, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, and Nicola Prezza. Sketching and Streaming for Dictionary Compression. DCC 2024, https://doi.org/10.1109/DCC58796.2024.00029
  • Ruben Becker, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Alberto Policriti and Nicola Prezza. Optimal Wheeler Language Recognition. SPIRE 2023, https://doi.org/10.1007/978-3-031-43980-3_6
  • Nicola Cotumaccio, Travis Gagie, Dominik Koeppl and Nicola Prezza. Space-time Trade-offs for the LCP Array of Wheeler DFAs. SPIRE 2023, https://doi.org/10.1007/978-3-031-43980-3_12
  • Ruben Becker, Manuel Cáceres, Davide Cenzato, Sung-Hwan Kim, Bojana Kodric, Francisco Olivares, Nicola Prezza. Sorting Finite Automata via Partition Refinement. ESA 2023, https://doi.org/10.4230/LIPIcs.ESA.2023.15
  • Alessio Conte, Nicola Cotumaccio, Travis Gagie, Giovanni Manzini, Nicola Prezza, Marinella Sciortino. Computing matching statistics on Wheeler DFAs. DCC 2023, https://doi.org/10.1109/DCC55655.2023.00023
  • Sung-Hwan Kim, Francisco Olivares, Nicola Prezza. Faster Prefix-Sorting Algorithms for Deterministic Finite Automata. CPM 2023, https://doi.org/10.4230/LIPIcs.CPM.2023.16
  • Jarno Alanko, Nicola Cotumaccio, Nicola Prezza. Linear-time Minimization of Wheeler DFAs. DCC 2022, https://doi.org/10.1109/DCC52660.2022.00013
  • Travis Gagie, Gonzalo Navarro, and Nicola Prezza. Fully functional suffix trees and optimal text searching in BWT-runs bounded space. Journal of the ACM (JACM). 2020 Jan 15;67(1):1-54. https://doi.org/10.1145/3375890
  • Nobile M.S., Nisoli E., Vlachou T., Spolaor S., Cazzaniga P., Mauri G., P.G. Pelicci, D. Besozzi: cuProCell: GPU-accelerated analysis of cell proliferation with flow cytometry data, IEEE Journal of Biomedical and Health Informatics, 24(11):3173–3181, 2020. https://doi.org/10.1109/JBHI.2020.3005423
  • Toffano, Alberto A.; Chiarot, Giacomo; Zamuner, Stefano; Marchi, Margherita; Salvi, Erika; Waxman, Stephen G.; Faber, Catharina G.; Lauria, Giuseppe; Giacometti, Achille; Simeoni, Marta Computational pipeline to probe NaV1.7 gain-of-function variants in neuropathic painful syndromes in SCIENTIFIC REPORTS, vol. 10 (ISSN 2045-2322), 2020.
  • Ankrah NYD, Chouaia B, Douglas AE, The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes. mBio. 2018 Sep-Oct; 9(5): e01433-18. https://doi.org/10.1128/mBio.01433-18
  • Giulio Ermanno Pibiri, "Sparse and skew hashing of k-mers", Bioinformatics, Volume 38, Issue Supplement_1, July 2022, pp. i185–i194, https://doi.org/10.1093/bioinformatics/btac245
  • Fan, Jason, Jamshed Khan, Giulio Ermanno Pibiri, and Rob Patro. "Spectrum preserving tilings enable sparse and modular reference indexing." In International Conference on Research in Computational Molecular Biology, 2023, pp. 21-40, https://doi.org/10.1007/978-3-031-29119-7_2

Awards

  • Marco S. Nobile, Daniela Besozzi, Camilla Torlasco, Daniele Papetti: “Shark Tank” award at CMR 2024 (the Global Cardiac Magnetic Resonance conference), London, UK for the talk “Optimizing Inversion Time Prediction for Late Gadolinium Enhancement Imaging with Artificial Intelligence” (2024)
  • Marco S. Nobile, Daniela Besozzi, Camilla Torlasco, Daniele Papetti: Best abstract award at the 83th Congress of the Italian Cardiology Society (SIC) for the paper “Techniques of Artificial Intelligence for the determination of the optimal inversion time: the Thaiti project” (2022)
  • Best Paper Award at the 2019 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2019) for the paper: Nobile M.S., Vlachou T., Spolaor S., Cazzaniga P., Mauri G., Pelicci P.G., Besozzi D.: ProCell: Investigating cell proliferation with Swarm Intelligence
  • Best Paper Award at the 2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2022) for the paper: Gallese C., Fuchs C., Riva S.G., Foglia E., Schettini F., Ferrario L., Falletti E., and Nobile M.S.: Predicting and characterizing legal claims of hospitals with Computational Intelligence: the legal and ethical implications
  • Best publication of the year 2014 in the field of environmental microbiology from the Italian Society of Agro-food and environmental microbiology for the paper Chouaia et al. 2014, Genome Biol Evol. 6: 912-920

Equipment

  • One DELL Precision 5820 Tower XCTO Base workstation (8 cores, 128 GiB RAM DDR4, 256 GiB SSD, 1 TiB hard disk)

Research projects

  • REGINDEX ("Compressed Indexes for Regular Languages with Applications to Pangenomics Research"). ERC Starting grant. Period: 1/9/2022 - 1/9/2027 (https://www.unive.it/regindex)
  • DAIS Project - IRIDE "Reconstructing and comparing metabolic networks" assigned to Marta Simeoni, 2020
  • DAIS Project - IRIDE(B) "Automatic feature transformation for interpretable AI systems" assigned to Marco S. Nobile, 2022
  • DAIS Project - IRIDE (B) "Modular de Bruijn Graph Indexes", assigned to Giulio Ermanno Pibiri, 2023

Last update: 22/09/2025