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

Members:

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

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
  • 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