Where and when

DSB 2025 will take place at the Department of Computer Science, University of Pisa, Italy on March 5-6, 2025.

How to participate

Abstract submission deadline: February 1st, 2025 AoE. Expired.

Registration deadline: February 15th, 2025 AoE. Expired.

As in previous editions, there will be no formal review process. While we aim to provide everyone with an opportunity to present, the organizers reserve the right to select talks from the submissions to ensure a diverse and engaging program.

Program


Wednesday, 5 March

   
8:30 - 8:40 Registration
8:40 - 8:45 Opening
Session 1: Sampling, sketching and compression ( Chair: Veronica Guerrini )
8:45 - 9:10 Roland Faure, Jean-François Flot, Dominique Lavenier. A new sketching method for accurate long reads: a genome assembly example
9:10 - 9:35 Groot Koerkamp Ragnar. Practical and optimal sampling schemes
9:35 - 10:00 Lore Depuydt, Omar Ahmed, Jan Fostier, Ben Langmead, Travis Gagie. Run-length compressed metagenomic read classification with SMEM-finding and tagging
10:00 - 10:25 Léo Ackermann, Pierre Peterlongo, Karel Břinda. Towards space-efficient data structures for large genome-distance matrices with quick retrieval
10:25 - 10:55 Break
Session 2: Compression Techniques ( Chair: Ruben Becker )
10:55 - 11:20 Alix Regnier, Pierre Peterlongo. Compression of Binary k-mer Matrices
11:20 - 11:45 Alessio Campanelli, Giulio Ermanno Pibiri. Where the patterns are: repetition-aware compression for colored the Bruijn graphs
11:45 - 12:10 Mathilde Girard, Lea Vandamme, Bastien Cazaux, Antoine Limasset. OReO: Optimizing Read Order for practical compression
12:10 - 12:35 Stefan Böttcher. Extending grammar-based graph compression by negative hyperedges
12:35 - 14:00 Lunch
Session 3: Pangenomes graphs ( Chair: Lore Depuydt )
14:00 - 14:25 Peter Heringer, Luca Parmigiani, Daniel Doerr. Panacus: fast statistics for pangenome graphs
14:25 - 14:50 Leonard Bohnenkämper. CARP - A General Framework for Quantifying the Structural Complexity of Pangenomes
14:50 - 15:15 Carlo Tosoni, Ruben Becker, Sung-Hwan Kim, Nicola Prezza. Efficient indexes for pangenomic graphs through BWT-based data structures
15:15 - 15:35 Break
Session 4: Degenerate Strings ( Chair: Lucas Robidou )
15:35 - 16:00 Luca Parmigiani. Degeneratigs: minimal representation of k-mers as degenerate strings is NP-hard
16:00 - 16:25 Lapo Cioni, Veronica Guerrini, Giovanna Rosone. The Burrows-Wheeler transform of an elastic-degenerate string
16:25 - 16:45 Break
Session 5: Graphs ( Chair: Florian Ingels )
16:45 - 17:10 Daniel Puttini. A near-optimal time algorithm for Wheelerization problem
17:10 - 17:35 Bastien Degardins, Charles Paperman, Camille Marchet. Vizitig – Multi-sample sequencing data visualization


Thursday, 6 March

   
Session 6: Data Structures & Optimization Techniques ( Chair: Diego Diaz )
9:00 - 9:25 Johanna Schmitz, Jens Zentgraf, Sven Rahmann. Better Cuckoo Filters
9:25 - 9:50 Jens Zentgraf, Johanna Schmitz, Sven Rahmann. Blocked Bloom Filters with Choices
9:50 - 10:15 Angelo Savino, Rossano Venturini, Florian Kurpicz. Faster Wavelet Tree Queries
10:15 - 10:40 Davide Cenzato, Lore Depuydt, Travis Gagie, Sung-Hwan Kim, Giovanni Manzini, Francisco Olivares, Nicola Prezza. On a novel Suffix Array compression technique based on Suffixient sets
10:40 - 11:10 Break
Session 7: Burrows-Wheeler Transform and Related Topics ( Chair: TBD )
11:10 - 11:35 Sabrina Mantaci, Pierfrancesco Martinello, Giuseppe Romana, Giovanna Rosone, Marinella Sciortino. Computation of the XBWT-based Distance Measures for Labeled Trees
11:35 - 12:00 Diego Diaz. Efficient $r$-index implementation via dynamic partitioning of the BWT
12:00 - 12:25 Jarno N. Alanko, Elena Biagi, Joel Mackenzie, Simon J. Puglisi. Batched k-mer lookup on the Spectral Burrows-Wheeler Transform
12:25 - 13:50 Lunch
13:50 - 14:00 Presentation of DSB 2026
Session 8: Genomes Analysis ( Chair: Giulia Bernardini )
14:00 - 14:25 Nicola Rizzo. Practical colinear chaining on sequences revisited
14:25 - 14:50 Felix Wiegand, Johannes Köster. Uncertainty aware haplotype based genomic variant effect prediction
14:50 - 15:15 Simone Lucà, Zsuzsanna Lipták, Francesco Masillo. Measuring Genomic Data with PFP
15:15 - 15:40 Francesca Brunetti, Karel Břinda. Optimized K-mer Matching For Million-Genome Collections On Laptops
15:40 - 16:10 Break
Session 9: k-mer Compression & Representation ( Chair: Davide Cenzato )
16:10 - 16:35 Igor Martayan, Lucas Robidou, Yoshihiro Shibuya, Antoine Limasset. Hyper-k-mers: efficient streaming k-mers representation
16:35 - 17:00 Florian Ingels, Camille Marchet, Mikaël Salson. Imbalance in minimizer-based partitions of k-mers: a theoretical approach
17:00 - 17:25 Victor Levallois, Yoshihiro Shibuya, Pierre Peterlongo, Giulio Ermanno Pibiri. Kaminari: a resource-frugal index for approximate colored k-mer queries
17:25 - 17:50 Ondřej Sladký, Pavel Veselý, Karel Břinda. Masked superstrings as a compact, indexable, and dynamic representation of unconstrained k-mer sets
17:50 - 18:00 Closing
20:00 - Social dinner

Confirmed participants

  • Ackermann Léo, Univ. Rennes, Inria, CNRS, IRISA
  • Alfredo Carmona Tabja Gabriel, University of Pisa
  • Ascone Rocco, University of Trieste
  • Becker Ruben, Ca’ Foscari University of Venice
  • Bernardini Giulia, University of Milan
  • Biagi Elena, University of Helsinki
  • Bohnenkämper Leonard, Bielefeld University
  • Bohuslavova Dominika, Czech Technical University in Prague
  • Bonizzoni Paola, Università di Milano Bicocca
  • Böttcher Stefan, Paderborn University
  • Brinda Karel, Inria Rennes, France
  • Brunetti Francesca, Sapienza University of Rome
  • Campanelli Alessio, Ca’ Foscari University of Venice
  • Carfagna Lorenzo, University of Pisa
  • Cenzato Davide, Ca’ Foscari University of Venice
  • Cioni Lapo, Università degli Studi di Firenze
  • Cozzi Davide, University of Milano-Bicocca
  • Degardins Bastien, CRIStAL, Bonsaï Team - University of Lille
  • Depuydt Lore, Ghent University - imec
  • Diaz Diego, University of Helsinki
  • Elena Schmitz Johanna, Saarland University
  • Faure Roland, Institut Pasteur (Paris)
  • Flege Patrick, Wageningen University & Research
  • Gabory Estéban, University of Palermo
  • Gao Younan, University of Milano-Bicocca
  • Gargiulo Francesco, Università di Pisa
  • Girard Mathilde, University of Lille
  • Groot Koerkamp Ragnar, ETH Zurich
  • Grossi Roberto, Università di Pisa
  • Guerrini Veronica, University of Pisa
  • Heringer Peter, German Diabetes Center (DDZ)
  • Ingels Florian, Université de Lille
  • Kim Sung-Hwan, Ca’ Foscari University of Venice
  • Lari Filippo, Università di Pisa
  • Levallois Victor, Inria Rennes
  • Lipták Zsuzsanna, University of Verona
  • Lucà Simone, University of Verona
  • Manzini Giovanni, University of Pisa
  • Martinello Pierfrancesco, Università degli Studi di Palermo
  • Mbianda Turenne Bagoup, Fondation Hope For Humanity
  • Mwaniki Njagi, University of Pisa
  • Parmigiani Luca, Bielefeld University
  • Pibiri Giulio Ermanno, Ca’ Foscari University of Venice
  • Pisanti Nadia, University of Pisa
  • Prezza Nicola, Ca’ Foscari University of Venice
  • Punzi Giulia, University of Pisa
  • Puttini Daniel, Ca’ Foscari University of Venice
  • Regnier Alix, Inria - GenScale
  • Rivals Eric, LIRMM (CNRS) & Univ. Montpellier
  • Rizzo Nicola, University of Helsinki
  • Robidou Lucas, Bielefeld University, Germany
  • Romana Giuseppe, University of Palermo
  • Rosone Giovanna, University of Pisa - Italy
  • Rouzé Timothé, Institut Pasteur Paris
  • Savino Angelo, Università di Pisa
  • Sciortino Marinella, University of Palermo
  • Sena Francisco, University of Helsinki
  • Stoye Jens, Bielefeld University
  • Tosoni Carlo, Ca’ Foscari University
  • Venturini Rossano, University of Pisa
  • Vinciguerra Giorgio, University of Pisa
  • Wiegand Felix, Bioinformatics and Computational Oncology (Kösterlab), University Duisburg-Essen
  • Zentgraf Jens, Saarland University

Organizers

  • Nadia Pisanti, University of Pisa
  • Giorgio Vinciguerra, University of Pisa
  • Veronica Guerrini, University of Pisa
  • Njagi Mwaniki, University of Pisa
  • Giovanni Buzzega, University of Pisa
  • Giovanna Rosone, University of Pisa

For any questions about DSB 2025, please reach out to nadia.pisanti@unipi.it.

Sponsors

Lots of thanks for the financial support of:

  1. Department of Computer Science, University of Pisa
  2. PINC Pangenome INformatiCs
  3. ALPACA ALgorithms for PAngenome Computational Analysis
  4. THE Tuscany Health Ecosystem, Spoke 6

Funded by the European Union Ministero dell'Università e della Rircerca ItaliaDomani PNRR University of Pisa

PINC ALPACA THE

Information about Pisa

Travel. Pisa is conveniently served by Galileo Galilei International Airport. For additional travel options, the nearest alternative airport is Florence’s Amerigo Vespucci Airport. From there, you can take tram line T2 to the main train station, Firenze Santa Maria Novella. From this station, regular regional trains run directly to Pisa, with a travel time of about one hour.

Getting Around Pisa. Pisa is a compact and pedestrian-friendly city, with most attractions and key locations within easy walking distance. Buses are also readily available: you can easily find directions using Google Maps and buy tickets on board using contactless payment options.

Tourism. For information on local attractions, historical sites, guided tours, and more, please visit the official tourism website of Pisa: turismo.pisa.it. You’ll find everything you need to explore the city’s rich history, enjoy its vibrant culture, and discover hidden gems beyond the famous Leaning Tower.

Aerial picture of Piazza dei Miracoli by Guglielmo Giambartolomei.