Pan-genome Graph Algorithms and Data Integration

Project Information

PANGAIA

Grant agreement ID: 872539

DOI

10.3030/872539

EC signature date 4 October 2019

Start date 1 January 2020

End date 31 October 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 1 140 800,00

EU contribution

€ 1 140 800,00

Coordinated by

UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCA
Italy

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (2)

Communication and dissemination report

Report on dissemination strategies and activities of the network Monitoring and recording of individual dissemination activities

First progress report

First progress report on secondments and scientific and financial aspects of the project

Other (1)

Kick-off meeting report

Description of the overall planning for the Project development, as discussed and agreed during the Kick-Off meeting.

Publications

Peer reviewed articles (66)

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Author(s): Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
Published in: SIAM Journal on Computing, Issue 51/3, 2022, Page(s) 549-576, ISSN 0097-5397
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1368033

Simpler and Faster Development of Tumor Phylogeny Pipelines

Author(s): Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson
Published in: Journal of Computational Biology, Issue 28/11, 2021, Page(s) 1142-1155, ISSN 1066-5277
Publisher: Mary Ann Liebert Inc.
DOI: 10.1089/cmb.2021.0271

Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic-One Year Experience

Author(s): Diana Rusňáková, Tatiana Sedláčková, Peter Radvák, Miroslav Böhmer, Pavol Mišenko, Jaroslav Budiš, Silvia Bokorová, Nikola Lipková, Michaela Forgáčová-Jakúbková, Tomáš Sládeček, Jozef Sitarčík, Werner Krampl, Michaela Gažiová, Anna Kaliňáková, Edita Staroňová, Elena Tichá, Terézia Vrábľová, Lucia Ševčíková, Barbora Kotvasová, Lucia Maďarová, Soňa Feiková
Published in: Viruses, Issue 14/11, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14112432

Finding Maximal Exact Matches Using the r-Index

Author(s): Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Published in: Journal of Computational Biology, Issue 29/2, 2022, Page(s) 188-194, ISSN 1066-5277
Publisher: Mary Ann Liebert Inc.
DOI: 10.1089/cmb.2021.0445

RecGraph: recombination-aware alignment of sequences to variation graphs

Author(s): Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
Published in: Bioinformatics, Issue 40(5), 2024, Page(s) btae292, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btae292

Automated prediction of the clinical impact of structural copy number variations

Author(s): Michaela Gažiová, Tomáš Sládeček, Ondrej Pös, M. Števko, Werner Krampl, Zuzana Pös, Rastislav Hekel, M. Hlavačka, Marcel Kucharík, Jan Radvánszky, Jaroslav Budiš, Tomáš Szemes
Published in: Scientific Reports, Issue 12, 2022, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Comparing methods for constructing and representing human pangenome graphs

Author(s): Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi
Published in: Genome Biology, 2023, ISSN 1474-760X
Publisher: BioMed Central Ltd
DOI: 10.1186/s13059-023-03098-2

Elastic-degenerate string comparison

Author(s): Estéban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Published in: Information and Computation, Issue 304, 2025, Page(s) 105296, ISSN 0890-5401
Publisher: Academic Press
DOI: 10.1016/j.ic.2025.105296

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Author(s): Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Published in: BMC Bioinformatics, Issue 25, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-024-05958-5

MALVIRUS: an integrated application for viral variant analysis

Author(s): Simone Ciccolella; Luca Denti; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali
Published in: BMC Bioinformatics, Issue 22, 2021, Page(s) 625, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-04668-0

On recognizing graphs representing persistent perfect phylogenies

Author(s): Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez, Gabriella Trucco
Published in: Natural Computing, 2025, ISSN 1567-7818
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11047-025-10039-4

High-quality metagenome assembly from long accurate reads with metaMDBG

Author(s): Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
Published in: Nature Biotechnology, 2024, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01983-6

Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations

Author(s): Tomáš Sládeček, Michaela Gažiová, Marcel Kucharík, Andrea Zaťková, Zuzana Pös, Ondrej Pös, Werner Krampl, Erika Tomková, Michaela Hýblová, Gabriel Minárik, Ján Radvánszky, Jaroslav Budiš, Tomáš Szemes
Published in: Scientific Reports, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-37352-1

VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples

Author(s): Askar Gafurov, Andrej Baláž, Fabian Amman, Kristína Boršová, Viktória Čabanová, Boris Klempa, Andreas Bergthaler, Tomáš Vinař, Broňa Brejová
Published in: BMC Bioinformatics, Issue 23, 2022, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-022-05100-3

IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences

Author(s): Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts
Published in: BMC Bioinformatics, Issue 22, 2021, Page(s) 51, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-03983-2

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA

Author(s): Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Published in: Nature Computational Science, Issue 4, 2024, Page(s) 104–109, ISSN 2662-8457
Publisher: Nature Publishing Group
DOI: 10.1038/s43588-024-00596-6

Strainline: Full-length de novo viral haplotype reconstruction from noisy long reads

Author(s): Luo, Xiao; Kang, Xiangbin; Schönhuth, Alexander
Published in: Genome Biology, 2022, ISSN 1474-760X
Publisher: BioMed Central Ltd.
DOI: 10.1186/s13059-021-02587-6

Pangenome comparison via ED strings

Author(s): Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Published in: Frontiers in Bioinformatics, Issue 4, 2024, ISSN 2673-7647
Publisher: Frontiers Media SA
DOI: 10.3389/fbinf.2024.1397036

Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches

Author(s): Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Published in: Information Sciences, Issue 607, 2022, Page(s) 458-476, ISSN 0020-0255
Publisher: Elsevier BV
DOI: 10.1016/j.ins.2022.06.005

Shark: fishing relevant reads in an RNA-Seq sample

Author(s): Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
Published in: Bioinformatics, Issue 37/4, 2020, Page(s) 464-472, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa779

μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data

Author(s): Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
Published in: Bioinformatics, 2023, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad552

Nanopore base calling on the edge

Author(s): Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař
Published in: Bioinformatics, Issue 37/24, 2021, Page(s) 4661-4667, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab528

Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.

Author(s): Brona Brejova; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Askar Gafurov; Dominika Fricova; Martina Neboháčová; Tomas Vinar; Boris Klempa; Jozef Nosek
Published in: PLoS ONE, Issue 16, 2021, Page(s) e0259277, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0259277

Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels

Author(s): Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
Published in: Bioinformatics, Issue 37/2, 2020, Page(s) 178-184, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa676

Computing linkage disequilibrium aware genome embeddings using autoencoders

Author(s): Gizem Taş, Timo Westerdijk, Eric Postma, Project MinE ALS GWAS Consortium , Jan H Veldink, Alexander Schönhuth, Marleen Balvert
Published in: Bioinformatics, 2024, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btae326

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning

Author(s): Aniket Mane, Mahsa Faizrahnemoon, Tomáš Vinař, Broňa Brejová, Cedric Chauve
Published in: Bioinformatics, 2023, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad250

Repurposing non-invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome

Author(s): Natalia Forgacova, Juraj Gazdarica, Jaroslav Budiš, Jan Radvanszky, Tomáš Szemes
Published in: Oncology Letters, Issue 22/5, 2021, ISSN 1792-1074
Publisher: Spandidos Publications
DOI: 10.3892/ol.2021.13040

DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects

Author(s): Ondrej Pös, Jan Radvanszky, Gergely Buglyó, Zuzana Pös, Diana Rusnakova, Bálint Nagy, Tomas Szemes
Published in: Biomedical Journal, Issue 44/5, 2021, Page(s) 548-559, ISSN 2319-4170
Publisher: Medknow Publications and Media Pvt. Ltd
DOI: 10.1016/j.bj.2021.02.003

Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations

Author(s): Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Published in: BMC Genomics, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10267-5

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Author(s): Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
Published in: iScience, 2023, ISSN 2589-0042
Publisher: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2023.108057

Efficient mapping of accurate long reads in minimizer space with mapquik

Author(s): Barış Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Published in: Genome Research, 2023, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277679.123

WarpSTR: Determining tandem repeat lengths using raw nanopore signals

Author(s): Jozef Sitarčík; Tomáš Vinař; Broňa Brejová; Werner Krampl; Jaroslav Budiš; Ján Radvánszky; Mária Lucká
Published in: Bioinformatics, 2023, ISSN 1367-4803
Publisher: Oxford University Press

Insights into non-informative results from non-invasive prenatal screening through gestational age, maternal BMI, and age analyses

Author(s): Juraj Gazdarica, Natalia Forgacova, Tomas Sladecek, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Martina Sekelska, Andrej Gnip, Gabriel Minarik, Tomas Szemes
Published in: PLoS One, 2024, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0280858

Hybrid-hybrid correction of errors in long reads with HERO

Author(s): Xiongbin Kang, Jialu Xu, Xiao Luo, Alexander Schönhuth
Published in: Genome Biology, 2023, ISSN 1474-760X
Publisher: BioMed Central Ltd
DOI: 10.1186/s13059-023-03112-7

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Author(s): Luc Blassel, Paul Medvedev, Rayan Chikhi
Published in: iScience, Issue 25/11, 2022, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2022.105305

Clustering sequence graphs

Author(s): Haodi Zhong, Grigorios Loukides, Solon P. Pissis
Published in: Data & Knowledge Engineering, Issue 138, 2022, Page(s) 101981, ISSN 0169-023X
Publisher: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

Computational graph pangenomics: a tutorial on data structures and their applications

Author(s): Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
Published in: Natural Computing, Issue 21, 2022, Page(s) 81-108, ISSN 1567-7818
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s11047-022-09882-6

Bidirectional String Anchors for Improved Text Indexing and Top-K Similarity Search

Author(s): Grigorios Loukidis, Solon Pissis, Michelle Sweering
Published in: IEEE Transactions on Knowledge and Data Engineering, 2023, Page(s) 1-18, ISSN 1041-4347
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3231780

Internal shortest absent word queries in constant time and linear space

Author(s): Golnaz Badkobeh, Panagiotis Charalampopoulos, Dmitry Kosolobov, Solon P. Pissis
Published in: Theoretical Computer Science, Issue 922, 2020, Page(s) 271-282, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2022.04.029

All-pairs suffix/prefix in optimal time using Aho-Corasick space

Author(s): Grigorios Loukides, Solon P. Pissis
Published in: Information Processing Letters, Issue 178, 2022, Page(s) 106275, ISSN 0020-0190
Publisher: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

$$\textsc {McDag}$$: indexing maximal common subsequences for k strings

Author(s): Giovanni Buzzega, Alessio Conte, Roberto Grossi, Giulia Punzi
Published in: Algorithms for Molecular Biology, Issue 20, 2025, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-025-00271-z

ESKEMAP: exact sketch-based read mapping

Author(s): Tizian Schulz, Paul Medvedev
Published in: Algorithms for Molecular Biology, 2024, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-024-00261-7

Seedability: optimizing alignment parameters for sensitive sequence comparison

Author(s): Lorraine A. K. Ayad, Rayan Chikhi, Solon P. Pissis
Published in: Bioinformatics Advances, Issue 3, 2023, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbad108

Elastic-Degenerate String Matching with 1 Error or Mismatch

Author(s): Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Published in: Theory of Computing Systems, Issue 68, 2024, Page(s) 1442-1467, ISSN 1432-4350
Publisher: Springer Verlag
DOI: 10.1007/s00224-024-10194-8

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads

Author(s): Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Published in: Nature Methods, Issue 20, 2022, Page(s) 550-558, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01674-1

DeepNano-blitz: a fast base caller for MinION nanopore sequencers

Author(s): Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Published in: Bioinformatics, Issue 36/14, 2020, Page(s) 4191–4192, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa297

Accurate and fast clade assignment via deep learning and frequency chaos game representation

Author(s): Jorge Avila Cartes, Santosh Anand, Simone Ciccolella, Paola Bonizzoni, Gianluca Della Vedova
Published in: Gigascience, Issue 12, 2022, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giac119

phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

Author(s): Xiao Luo; Xiao Luo; Xiongbin Kang; Xiongbin Kang; Alexander Schönhuth; Alexander Schönhuth
Published in: Genome Biology, Issue 22, 2021, Page(s) 299, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-021-02512-x

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Author(s): Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Published in: Frontiers in Genetics, Issue 13, 2022, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Sequence-based pangenomic core detection

Author(s): Tizian Schulz, Roland Wittler, Jens Stoye
Published in: IScience, Issue 25/6, 2022, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2022.104413

StrainXpress: strain aware metagenome assembly from short reads

Author(s): Xiongbin Kang, Xiao Luo, Alexander Schönhuth
Published in: Nucleic Acids Research, Issue 50/17, 2022, Page(s) e101, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac543

Efficient Computation of Sequence Mappability

Author(s): Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Published in: Algorithmica, Issue 84, 2022, Page(s) 1418-1440, ISSN 0178-4617
Publisher: Springer Verlag
DOI: 10.1007/s00453-022-00934-y

Detecting High Scoring Local Alignments in Pangenome Graphs

Author(s): Tizian Schulz; Roland Wittler; Sven Rahmann; Faraz Hach; Faraz Hach; Jens Stoye
Published in: Bioinformatics, Issue 37, 2021, Page(s) 2266–2274, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1101/2020.09.03.280958

VeChat: correcting errors in long reads using variation graphs

Author(s): Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Published in: Nature Communications, Issue 13, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

Dynamic Pooling Improves Nanopore Base Calling Accuracy

Author(s): Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Issue 19/6, 2022, Page(s) 3416-3424, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2021.3128366

Computing the multi-string BWT and LCP array in external memory

Author(s): Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Published in: Theoretical Computer Science, Issue 862, 2021, Page(s) 42-58, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2020.11.041

plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph

Author(s): Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomáš Vinař, Cedric Chauve
Published in: Frontiers in Microbiology, 2023, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2023.1267695

Palidis: fast discovery of novel insertion sequences

Author(s): Victoria R. Carr, Solon P. Pissis​, Peter Mullany​, Saeed Shoaie​, David Gomez-Cabrero​, David L. Moyes
Published in: Microbial Genomics, Issue 9/3, 2023, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.000917

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison

Author(s): Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipović; Mauricio Soto Gomez
Published in: Algorithms, 2023, ISSN 1999-4893
Publisher: MDPI Open Access Publishing
DOI: 10.3390/a16070333

Text Indexing for Long Patterns: Anchors are All you Need

Author(s): Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Published in: Proceedings of the VLDB Endowment, Issue 16(9), 2023, Page(s) 2117-2131, ISSN 2150-8097
Publisher: Association for Computing Machinery (ACM)
DOI: 10.14778/3598581.3598586

Comparative genome analysis using sample-specific string detection in accurate long reads

Author(s): Parsoa Khorsand; Luca Denti; Paola Bonizzoni; Rayan Chikhi; Fereydoun Hormozdiari; Fereydoun Hormozdiari
Published in: Bioinformatics Advances, Issue 1, 2021, ISSN 2635-0041
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbab005

Markov chains improve the significance computation of overlapping genome annotations

Author(s): Askar Gafurov, Broňa Brejová, Paul Medvedev
Published in: Bioinformatics, Issue 38, 2022, Page(s) i203–i211, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac255

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

Author(s): Barış Ekim, Bonnie Berger, Rayan Chikhi
Published in: Cell Systems, Issue 12/10, 2021, Page(s) 958--968, ISSN 2405-4720
Publisher: Elsevier
DOI: 10.1016/j.cels.2021.08.009

Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks

Author(s): Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Published in: Nature Machine Intelligence, 2023, ISSN 2522-5839
Publisher: Springer
DOI: 10.1038/s42256-022-00604-2

Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook

Author(s): Jakub Styk, Zuzana Pös, Ondrej Pös, Jan Radvanszky, Evelina Hrckova Turnova, Gergely Buglyó, Daniela Klimova, Jaroslav Budis, Vanda Repiska, Bálint Nagy, Tomas Szemes
Published in: The EPMA Journal, 2023, ISSN 1878-5085
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/s13167-023-00312-w

A SARS-CoV-2 mutant from B.1.258 lineage with ∆H69/∆V70 deletion in the Spike protein circulating in Central Europe in the fall 2020.

Author(s): Broňa Brejová; Kristína Boršová; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Lenka Reizigová; Evan D. Paul; Pavol Čekan; Boris Klempa; Jozef Nosek; Tomáš Vinař
Published in: Virus Genes, Issue 57, 2021, Page(s) 556–560, ISSN 1572-994X
Publisher: Springer Science and Business Media LLC
DOI: 10.1007/s11262-021-01866-5

Conference proceedings (43)

Minimizing the Minimizers via Alphabet Reordering

Author(s): Hilde Verbeek, Lorraine A.K. Ayad, Grigorios Loukides, Solon P. Pissis
Published in: Combinatorial Pattern Matching (CPM 2024), 2024
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.28

Elastic-Degenerate String Matching with 1 Error

Author(s): Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Published in: Latin American Symposium on Theoretical Informatics (LATIN 2022), Issue 13568, 2022, Page(s) 20-37, ISBN 978-3-031-20623-8
Publisher: Springer
DOI: 10.1007/978-3-031-20624-5_2

Enhancing Generalized Compressed Suffix Trees, with Applications

Author(s): Sankardeep Chakraborty, Kunihiko Sadakane, Wiktor Zuba
Published in: International Symposium on Algorithms and Computation (ISAAC 2024), 2024, ISBN 978-3-95977-354-6
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2024.18

Utility-Oriented String Mining

Author(s): Giulia Bernardini, Huiping Chen, Alessio Conte, Roberto Grossi, Veronica Guerrini, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis
Published in: SIAM International Conference on Data Mining (SDM 2024), 2024, ISBN 978-1-61197-803-2
Publisher: Society for Industrial and Applied Mathematics
DOI: 10.1137/1.9781611978032.22

KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints

Author(s): Paola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
Published in: International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2022), 2022, ISBN 978-3-031-07801-9
Publisher: Springer
DOI: 10.1007/978-3-031-07802-6_37

Phasing Data from Genotype Queries via the μ-PBWT

Author(s): Davide Cozzi, Paola Bonizzoni, Christina Boucher, Ben Langmead, Yuri Pirola
Published in: The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday, 2025, ISBN 978-3-95977-390-4
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/oasics.manzini.10

Solving the Minimal Positional Substring Cover Problem in Sublinear Space

Author(s): Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola
Published in: Combinatorial Pattern Matching (CPM 2024), 2024, ISBN 978-3-95977-326-3
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.12

Faster Approximate Elastic-Degenerate String Matching - Part A

Author(s): Solon P. Pissis, Jakub Radoszewski, Wiktor Zuba
Published in: Combinatorial Pattern Matching (CPM 2025), 2025, ISBN 978-3-95977-369-0
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2025.28

On Strings Having the Same Length-k Substrings

Author(s): Giulia Bernardini, Alessio Conte, Esteban Gabory, Roberto Grossi, Grigorios Loukides, Solon P. Pissis, Giulia Punzi, Michelle Sweering
Published in: Combinatorial Pattern Matching (CPM 2022), Issue 223, 2022, Page(s) 16:1--16:17, ISBN 978-3-95977-234-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.16

Substring Complexity in Sublinear Space

Author(s): Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis
Published in: International Symposium on Algorithms and Computation (ISAAC 2023), 2023
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2023.12

Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?

Author(s): Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
Published in: Developments in Language Theory (DLT 2022), Issue 13257, 2022, Page(s) 3-12, ISBN 978-3-031-05578-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-031-05578-2_1

A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs

Author(s): Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, Nadia Pisanti
Published in: Algorithms in Bioinformatics (WABI 2024), 2024, ISBN 978-3-95977-340-9
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2024.14

U-Index: A Universal Indexing Framework for Matching Long Patterns

Author(s): Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, Solon P. Pissis
Published in: Symposium on Experimental Algorithms, 2025, ISBN 978-3-95977-375-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.sea.2025.4

Space-Efficient Indexes for Uncertain Strings

Author(s): Esteban Gabory, Chang Liu, Grigorios Loukides, Solon P. Pissis, Wiktor Zuba
Published in: 2024 IEEE 40th International Conference on Data Engineering (ICDE), 2024, ISBN 979-8-3503-1715-2
Publisher: IEEE
DOI: 10.1109/icde60146.2024.00367

The Rational Construction of a Wheeler DFA

Author(s): Giovanni Manzini, Alberto Policriti, Nicola Prezza, Brian Riccardi
Published in: Combinatorial Pattern Matching (CPM 2024), 2024, ISBN 978-3-95977-326-3
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.23

Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning

Author(s): Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Published in: Algorithms for Computational Biology (AlCoB 2021), 2021, Page(s) 16-28, ISBN 978-3-030-74432-8
Publisher: Springer
DOI: 10.1007/978-3-030-74432-8_2

Pangenome Graph Indexing via the Multidollar-BWT

Author(s): Davide Cozzi, Brian Riccardi, Luca Denti, Simone Ciccolella, Kunihiko Sadakane, Paola Bonizzoni
Published in: Symposium on Experimental Algorithms (SEA 2025), 2025, ISBN 978-3-95977-375-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.sea.2025.13

Faster Approximate Elastic-Degenerate String Matching - Part B

Author(s): Paweł Gawrychowski, Adam Górkiewicz, Pola Marciniak, Solon P. Pissis, Karol Pokorski
Published in: Combinatorial Pattern Matching (CPM 2025), 2025, ISBN 978-3-95977-369-0
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2025.29

McDag: Indexing Maximal Common Subsequences in Practice

Author(s): Giovanni Buzzega; Alessio Conte; Roberto Grossi; Giulia Punzi
Published in: Algorithms in Bioinformatics (WABI 2024), 2024, ISBN 978-3-95977-340-9
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2024.21

Pattern Masking for Dictionary Matching

Author(s): Panagiotis Charalampopoulos and Huiping Chen and Peter Christen and Grigorios Loukides and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski
Published in: International Symposium on Algorithms and Computation (ISAAC 2021), 2021, ISBN 978-3-95977-214-3
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2021.65

Approximate Circular Pattern Matching

Author(s): Panagiotis Charalampopoulos, Tomasz Kociumaka, Jakub Radoszewski, Solon P. Pissis, Wojciech Rytter, Tomasz Waleń, Wiktor Zuba
Published in: European Symposium on Algorithms (ESA 2022), Issue 244, 2022, Page(s) 35:1--35:19, ISBN 978-3-95977-247-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.35

On the Construction of Elastic Degenerate Strings

Author(s): Nicola Rizzo, Veli Mäkinen, Nadia Pisanti
Published in: From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday, 2025, ISBN 978-3-95977-391-1
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/oasics.grossi.2

Unary Words Have the Smallest Levenshtein k-Neighbourhoods

Author(s): Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski, Tomasz Waleń, Wiktor Zuba
Published in: Combinatorial Pattern Matching (CPM 2020), Issue 161, 2020, Page(s) 10:1--10:12, ISBN 978-3-95977-149-8
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2020.10

BWT for String Collections

Author(s): Davide Cenzato, Zsuzsanna Lipták, Nadia Pisanti, Giovanna Rosone, Marinella Sciortino
Published in: The Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday, 2025, ISBN 978-3-95977-390-4
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/oasics.manzini.3

Indexing Strings with Utilities

Author(s): Giulia Bernardini, Huiping Chen, Alessio Conte, Roberto Grossi, Veronica Guerrini, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis
Published in: 2025 IEEE 41st International Conference on Data Engineering (ICDE), 2025, Page(s) 2782-2795
Publisher: IEEE
DOI: 10.1109/icde65448.2025.00209

String Sanitization Under Edit Distance

Author(s): Giulia Bernardini, Grigorios Loukides, Solon P. Pissis, Michelle Sweering, Huiping Chen, Nadia Pisanti, Leen Stougie
Published in: Combinatorial Pattern Matching (CPM 2020), Issue 161, 2020, Page(s) 7:1--7:14, ISBN 978-3-95977-149-8
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2020.7

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

Author(s): Philip Bille, Inge Li Gørtz, Moshe Lewenstein, Solon P. Pissis, Eva Rotenberg, Teresa Anna Steiner
Published in: Symposium on Theoretical Aspects of Computer Science (STACS 2024), 2024, ISBN 978-3-95977-311-9
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.16

Approximate Circular Pattern Matching Under Edit Distance

Author(s): Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Tomasz Waleń, Wiktor Zuba
Published in: Symposium on Theoretical Aspects of Computer Science (STACS 2024), 2024, ISBN 978-3-95977-311-9
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.24

Exact Sketch-Based Read Mapping

Author(s): Tizian Schulz, Paul Medvedev
Published in: Algorithms in Bioinformatics (WABI 2023), 2023, ISBN 978-3-95977-294-5
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2023.14

Subsequence-Based Indices for Genome Sequence Analysis

Author(s): Giovanni Buzzega, Alessio Conte, Veronica Guerrini, Giulia Punzi, Giovanna Rosone, Lorenzo Tattini
Published in: From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday, 2025, ISBN 978-3-95977-391-1
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/oasics.grossi.20

Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications

Author(s): Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Published in: Combinatorial Pattern Matching (CPM 2023), Issue 259, 2023, Page(s) 11:1-11:20, ISBN 978-3-95977-276-1
Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.11

On String and Graph Sanitization

Author(s): Giulia Bernardini, Huiping Chen, Grigorios Loukides, Solon P. Pissis
Published in: From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday, 2025, ISBN 978-3-95977-391-1
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/oasics.grossi.9

Faster Algorithms for Longest Common Substring

Author(s): Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski
Published in: European Symposium on Algorithms (ESA 2021), Issue 204, 2021, Page(s) 30:1--30:17, ISBN 978-3-95977-204-4
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast Assessment of Eulerian Trails

Author(s): Alessio Conte, Roberto Grossi, Grigorios Loukidis, Nadia Pisanti, Solon P. Pissis, Giulia Punzi
Published in: Fundamentals of Computation Theory (FCT 2021), Issue 12867, 2021, Page(s) 162--175, ISBN 978-3-030-86593-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Suffix-Prefix Queries on a Dictionary

Author(s): Grigorios Loukides, Solon P. Pissis, Sharma V. Thankachan, Wiktor Zuba
Published in: Combinatorial Pattern Matching (CPM 2023), Issue 259, 2023, Page(s) 21:1-21:20, ISBN 978-3-95977-276-1
Publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Size-Constrained Weighted Ancestors with Applications

Author(s): Philip Bille, Yakov Nekrich, Solon P. Pissis
Published in: Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024), 2024, ISBN 978-3-95977-318-8
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.swat.2024.14

Making de Bruijn Graphs Eulerian

Author(s): Giulia Bernardini, Huiping Chen, Grigorios Loukides, Solon P. Pissis, Leen Stougie, Michelle Sweering
Published in: Combinatorial Pattern Matching (CPM 2022), Issue 223, 2022, Page(s) 12:1--12:18, ISBN 978-3-95977-234-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Author(s): Askar Gafurov, Tomáš Vinař, Broňa Brejová
Published in: Conference on Computability in Europe (CiE 2021), 2021, Page(s) 227-236, ISBN 978-3-030-80049-9
Publisher: Springer
DOI: 10.1007/978-3-030-80049-9_21

Sparse Suffix and LCP Array: Simple, Direct, Small, and Fast

Author(s): Lorraine A.K. Ayad, Grigorios Loukides, Solon P. Pissis, Hilde Verbeek
Published in: Latin American Symposium on Theoretical Informatics (LATIN 2024), 2024, ISBN 978-3-031-55597-8
Publisher: Springer
DOI: 10.1007/978-3-031-55598-5_11

Bidirectional String Anchors: A New String Sampling Mechanism

Author(s): Grigorios Loukides, Solon P. Pissis
Published in: European Symposium on Algorithms (ESA 2021), Issue 204, 2021, Page(s) 64:1--64:21, ISBN 978-3-95977-204-4
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts

Author(s): Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová
Published in: Research in Computational Molecular Biology (RECOMB 2024), 2024, ISBN 978-1-0716-3989-4
Publisher: Springer
DOI: 10.1007/978-1-0716-3989-4_3

Connecting de Bruijn Graphs

Author(s): Giulia Bernardini, Huiping Chen, Inge Li Gørtz, Christoffer Krogh, Grigorios Loukides, Solon P. Pissis, Leen Stougie, Michelle Sweering
Published in: Combinatorial Pattern Matching (CPM 2024), 2024
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.6

Longest Palindromic Substring in Sublinear Time

Author(s): Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski
Published in: Combinatorial Pattern Matching (CPM 2022), Issue 223, 2022, Page(s) 20:1--20:9, ISBN 978-3-95977-234-1
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.20