Davide Cozzi | Computer Scientist
in computational pangenomics
Efficient algorithms and compressed data structures for genomic data, from the PBWT to pangenome graph indexing.
About
My research focuses on the design and implementation of efficient algorithms and data structures for bioinformatics and computational biology, optimizing for both time and memory. I work at the intersection of theoretical results, such as succinct and compressed data structures and pattern-matching algorithms, and practical, large-scale genomic data.
During my Ph.D. at the BIAS research laboratory (Università degli Studi di Milano-Bicocca), I developed the μ-PBWT, a lightweight r-index for haplotype panels enabling maximal-match queries in sublinear space on datasets like the UK Biobank. I extended this work to genotype phasing, the Minimal Positional Substring Cover problem, and pangenome graph indexing with gindex.
I've collaborated internationally with research groups at Dalhousie University, the University of Florida, Johns Hopkins, the University of Tokyo, the University of Cambridge, Illumina, and the Institute for Molecular Medicine Finland, including secondments in Tokyo, Cambridge and Helsinki as part of the EU Horizon 2020 PANGAIA project.
Background
Post-Doc at BIAS Lab current
Ph.D. in Computer Science
M.Sc. in Computer Science
B.Sc. in Computer Science
Software
Open-source implementations of my research, built for real-world genomic datasets.
◇μ-PBWT09/23
Lightweight r-index of the PBWT for storing and querying UK Biobank-scale haplotype panels in sublinear space. ~3K BioConda downloads.
View repository →◇gindex07/25
Pangenome graph index for exact string-to-graph matching, based on the multidollar-BWT.
View repository →◇pantas12/24
First tool for alternative splicing detection and quantification on pangenome graphs.
View repository →◇μ-PBWT · extensions06/24–07/25
Branches of μ-PBWT for genotype phasing and k-mismatch maximal matches.
View branches →◇ESGq06/23
Graph-based model for alternative splicing quantification on a linear reference.
View repository →Publications
For the complete and up-to-date list, see my Google Scholar profile ↗
Journal Publications
μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data
Oxford BioinformaticsDifferential quantification of alternative splicing events on spliced pangenome graphs
PLOS Computational BiologyConference Proceedings & Special Issues
Optimal-Time Mapping in Run-Length Compressed PBWT
CPM 2026, Proc. 37th Annual Symposium on Combinatorial Pattern MatchingPangenome Graph Indexing via the Multidollar-BWT
SEA 2025, Proc. 23rd Int'l Symposium on Experimental AlgorithmsPhasing data from genotype queries via the μ-PBWT
The Expanding World of Compressed Data, Festschrift for Giovanni Manzini's 60th BirthdaySolving the Minimal Positional Substring Cover problem in sublinear space
CPM 2024, Proc. 35th Annual Symposium on Combinatorial Pattern MatchingTeaching & service
Teaching
- Bioinformatics, M.Sc. (2025–26)
- Theory of Computation, M.Sc. (2022–23)
- Algorithms Design, B.Sc. (2022–23)
Tutoring
- Algorithms Design, B.Sc. (2024–25)
- Theory of Computation, M.Sc. (2021–22)
Other activities
- Organizing Committee, CPM 2025, Milan
- Program Committee, WBCB 2025, part of ITAT
- Reviewer for RECOMB, CPM, SEA, WABI, others
- Social media manager, EU PANGAIA project