Mattia Sgrò

PhD candidate in Computer Science at DISCo, University of Milano-Bicocca. I design data structures and algorithms for computational pangenomics, and I’m a photographer in my spare time.

Research

My thesis, Data Structures in Pangenomics, is supervised by Gianluca Della Vedova and Paola Bonizzoni (BIAS Lab).

PBWT at biobank scale. Sampled and parallel construction of the positional Burrows–Wheeler transform, which processes several columns at once with bit-level operations, and haplotype blocks with wildcards (missing data).
Pebbling. Compact representation of paths in pangenome variation graphs through dominator-based path traces.
Plasmid binning. Recovering plasmids from bacterial assemblies with pangenome and assembly graphs, via ILP and network flows.

Complete CV

Publications

Published

Bonizzoni P., Della Vedova G., Pirola Y., Rizzi R., Sgrò M. Multiallelic maximal perfect haplotype blocks with wildcards via PBWT. IWBBIO 2023, Springer, pp. 62–76.

In review

Sgrò M., Brejová B., Pirola Y., Vinař T., Bonizzoni P., Chauve C. Pangebin: improving plasmid binning in bacterial isolates using pangenome-assembly graphs. bioRxiv preprint
Sgrò M., Riccardi B., Ciccolella S., Cozzi D., Della Vedova G., Sadakane K., Bonizzoni P. On optimizing the positional Burrows–Wheeler transform via sampling. 2026.
Epain V., Mane A., Sgrò M., Della Vedova G., Bonizzoni P., Chauve C. A multi-flow approach for binning circular plasmids from short-reads assembly graphs. 2026.

Software

sp-pbwt: sampled and parallel PBWT. C.
Wild-pBWT: all maximal perfect haplotype blocks with wildcards. C++.
Pangebin: plasmid binning pipeline on top of nf-core/pangenome. Nextflow, Python.

Research visits

Oct 2025: Geneton, Comenius University in Bratislava, Slovakia. Host: Tomáš Szemes
Jun 2025: University of California, Santa Cruz, USA. Host: Benedict Paten
Feb–May 2025: The University of Tokyo, Japan. Host: Kunihiko Sadakane
Jul–Sep 2024: The University of Tokyo, Japan. Host: Kunihiko Sadakane
Jun 2024: Simon Fraser University, Vancouver, Canada. Host: Cedric Chauve
Aug–Oct 2023: Simon Fraser University, Vancouver, Canada. Host: Cedric Chauve
2019–2023: Graduate research fellow, BIAS Lab (formerly AlgoLab), University of Milano-Bicocca. Efficient algorithms for haplotype panel indexing.

Teaching

Mar–Jun 2026: Informatica Giuridica (Legal Informatics), School of Law. A course for first-year law students, inspired by CS50 for Lawyers: information, networks, cryptography, security, search engines, AI.
Apr–Oct 2024: Laboratorio di Supporto ai Percorsi di Tesi (thesis support lab), DISCo
Apr–May 2024: Laboratorio di Informatica I, Department of Physics

Tutoring

2024–2026: Teacher training programme for secondary-school teachers (60 CFU, class A41), DISCo. Three editions.
Oct 2025: Informatica ed elementi di machine learning, Department of Law
Oct 2025: Modelli e Computazione, DISCo
Apr–Oct 2024: Thesis support tutoring, DISCo
2022–2023: First-year students, Computer Science BSc and MSc, DISCo

I also co-supervised a BSc thesis on variation graph algorithms.

Talks

Sep 2024: Invited talk, MIGGS 2024, Lille. PangeBin: pangenome graphs improve bacterial plasmid binning in short-read assemblies
Jul 2024: Poster, ISMB 2024, Montréal
Mar 2024: Invited talk, DSB 2024, Montpellier. PangeBin: pangenome graphs improve bacterial plasmid binning in short-read assemblies
2023: Talk, IWBBIO 2023, Gran Canaria

Education

2023–now: PhD in Computer Science, University of Milano-Bicocca, XXXIX cycle
2020–2023: MSc in Computer Science, University of Milano-Bicocca, 110/110 cum laude. Thesis: Algorithms for the positional BWT with missing data and applications for haplotype analysis. Advisors: Paola Bonizzoni, Raffaella Rizzi
2017–2020: BSc in Computer Science, University of Milano-Bicocca. Thesis on PBWT extensions for haplotype matrices with gaps. Advisors: Paola Bonizzoni, Yuri Pirola

Service and outreach

Jun 2026: Outreach, “Studiare il DNA con Python” (PNRR), Milan
Jun 2025: Organizing committee, CPM 2025 (Combinatorial Pattern Matching), Milan
Nov 2024: Outreach, “Io e il Genoma” (PNRR), I.I.S. G.B. Vico, Corsico
Sep 2024: COPA 2024, PhD school on evolution in computational pangenomics
Nov 2023: ALPACA–PANGAIA annual workshop, CWI, Amsterdam

Download CV (PDF)

Other stuff

I take a lot of pictures, mostly with an Olympus OM-D E-M5 Mark III, and the ones I like end up on the Photos page. I also go bouldering, and hiking whenever I get the chance. I love a good board game night with friends, and I’m always up for trying a new craft beer.