Pan-genome Graph Algorithms and Data Integration

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Kick-off meeting report

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

Publicaciones

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autores: Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
Publicado en: SIAM Journal on Computing, Edición 51/3, 2022, Página(s) 549-576, ISSN 0097-5397
Editor: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1368033

Simpler and Faster Development of Tumor Phylogeny Pipelines

Autores: Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson
Publicado en: Journal of Computational Biology, Edición 28/11, 2021, Página(s) 1142-1155, ISSN 1066-5277
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 14/11, 2022, ISSN 1999-4915
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14112432

Finding Maximal Exact Matches Using the r-Index

Autores: Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Publicado en: Journal of Computational Biology, Edición 29/2, 2022, Página(s) 188-194, ISSN 1066-5277
Editor: Mary Ann Liebert Inc.
DOI: 10.1089/cmb.2021.0445

RecGraph: recombination-aware alignment of sequences to variation graphs

Autores: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
Publicado en: Bioinformatics, Edición 40(5), 2024, Página(s) btae292, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btae292

Automated prediction of the clinical impact of structural copy number variations

Autores: Michaela Gažiová, Tomáš Sládeček, Ondrej Pös, M. Števko, Werner Krampl, Zuzana Pös, Rastislav Hekel, M. Hlavačka, Marcel Kucharík, Jan Radvánszky, Jaroslav Budiš, Tomáš Szemes
Publicado en: Scientific Reports, Edición 12, 2022, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Comparing methods for constructing and representing human pangenome graphs

Autores: Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi
Publicado en: Genome Biology, 2023, ISSN 1474-760X
Editor: BioMed Central Ltd
DOI: 10.1186/s13059-023-03098-2

Elastic-degenerate string comparison

Autores: Estéban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Publicado en: Information and Computation, Edición 304, 2025, Página(s) 105296, ISSN 0890-5401
Editor: Academic Press
DOI: 10.1016/j.ic.2025.105296

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Autores: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Publicado en: BMC Bioinformatics, Edición 25, 2024, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-024-05958-5

MALVIRUS: an integrated application for viral variant analysis

Autores: Simone Ciccolella; Luca Denti; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali
Publicado en: BMC Bioinformatics, Edición 22, 2021, Página(s) 625, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-022-04668-0

On recognizing graphs representing persistent perfect phylogenies

Autores: Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez, Gabriella Trucco
Publicado en: Natural Computing, 2025, ISSN 1567-7818
Editor: Kluwer Academic Publishers
DOI: 10.1007/s11047-025-10039-4

High-quality metagenome assembly from long accurate reads with metaMDBG

Autores: Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
Publicado en: Nature Biotechnology, 2024, ISSN 1087-0156
Editor: 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

Autores: 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
Publicado en: Scientific Reports, 2023, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-023-37352-1

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

Autores: Askar Gafurov, Andrej Baláž, Fabian Amman, Kristína Boršová, Viktória Čabanová, Boris Klempa, Andreas Bergthaler, Tomáš Vinař, Broňa Brejová
Publicado en: BMC Bioinformatics, Edición 23, 2022, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859-022-05100-3

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

Autores: Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts
Publicado en: BMC Bioinformatics, Edición 22, 2021, Página(s) 51, ISSN 1471-2105
Editor: 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

Autores: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Publicado en: Nature Computational Science, Edición 4, 2024, Página(s) 104–109, ISSN 2662-8457
Editor: Nature Publishing Group
DOI: 10.1038/s43588-024-00596-6

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

Autores: Luo, Xiao; Kang, Xiangbin; Schönhuth, Alexander
Publicado en: Genome Biology, 2022, ISSN 1474-760X
Editor: BioMed Central Ltd.
DOI: 10.1186/s13059-021-02587-6

Pangenome comparison via ED strings

Autores: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Publicado en: Frontiers in Bioinformatics, Edición 4, 2024, ISSN 2673-7647
Editor: Frontiers Media SA
DOI: 10.3389/fbinf.2024.1397036

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

Autores: Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Publicado en: Information Sciences, Edición 607, 2022, Página(s) 458-476, ISSN 0020-0255
Editor: Elsevier BV
DOI: 10.1016/j.ins.2022.06.005

Shark: fishing relevant reads in an RNA-Seq sample

Autores: Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
Publicado en: Bioinformatics, Edición 37/4, 2020, Página(s) 464-472, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa779

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

Autores: Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
Publicado en: Bioinformatics, 2023, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btad552

Nanopore base calling on the edge

Autores: Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař
Publicado en: Bioinformatics, Edición 37/24, 2021, Página(s) 4661-4667, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btab528

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

Autores: Brona Brejova; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Askar Gafurov; Dominika Fricova; Martina Neboháčová; Tomas Vinar; Boris Klempa; Jozef Nosek
Publicado en: PLoS ONE, Edición 16, 2021, Página(s) e0259277, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0259277

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

Autores: Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
Publicado en: Bioinformatics, Edición 37/2, 2020, Página(s) 178-184, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa676

Computing linkage disequilibrium aware genome embeddings using autoencoders

Autores: Gizem Taş, Timo Westerdijk, Eric Postma, Project MinE ALS GWAS Consortium , Jan H Veldink, Alexander Schönhuth, Marleen Balvert
Publicado en: Bioinformatics, 2024, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btae326

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

Autores: Aniket Mane, Mahsa Faizrahnemoon, Tomáš Vinař, Broňa Brejová, Cedric Chauve
Publicado en: Bioinformatics, 2023, ISSN 1367-4803
Editor: 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

Autores: Natalia Forgacova, Juraj Gazdarica, Jaroslav Budiš, Jan Radvanszky, Tomáš Szemes
Publicado en: Oncology Letters, Edición 22/5, 2021, ISSN 1792-1074
Editor: Spandidos Publications
DOI: 10.3892/ol.2021.13040

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

Autores: Ondrej Pös, Jan Radvanszky, Gergely Buglyó, Zuzana Pös, Diana Rusnakova, Bálint Nagy, Tomas Szemes
Publicado en: Biomedical Journal, Edición 44/5, 2021, Página(s) 548-559, ISSN 2319-4170
Editor: 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

Autores: Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Publicado en: BMC Genomics, 2024, ISSN 1471-2164
Editor: BioMed Central
DOI: 10.1186/s12864-024-10267-5

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

Autores: Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
Publicado en: iScience, 2023, ISSN 2589-0042
Editor: Cell Press Elsevier Inc.
DOI: 10.1016/j.isci.2023.108057

Efficient mapping of accurate long reads in minimizer space with mapquik

Autores: Barış Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Publicado en: Genome Research, 2023, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277679.123

WarpSTR: Determining tandem repeat lengths using raw nanopore signals

Autores: Jozef Sitarčík; Tomáš Vinař; Broňa Brejová; Werner Krampl; Jaroslav Budiš; Ján Radvánszky; Mária Lucká
Publicado en: Bioinformatics, 2023, ISSN 1367-4803
Editor: Oxford University Press

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

Autores: Juraj Gazdarica, Natalia Forgacova, Tomas Sladecek, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Martina Sekelska, Andrej Gnip, Gabriel Minarik, Tomas Szemes
Publicado en: PLoS One, 2024, ISSN 1932-6203
Editor: Public Library of Science
DOI: 10.1371/journal.pone.0280858

Hybrid-hybrid correction of errors in long reads with HERO

Autores: Xiongbin Kang, Jialu Xu, Xiao Luo, Alexander Schönhuth
Publicado en: Genome Biology, 2023, ISSN 1474-760X
Editor: BioMed Central Ltd
DOI: 10.1186/s13059-023-03112-7

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Autores: Luc Blassel, Paul Medvedev, Rayan Chikhi
Publicado en: iScience, Edición 25/11, 2022, ISSN 2589-0042
Editor: Cell Press
DOI: 10.1016/j.isci.2022.105305

Clustering sequence graphs

Autores: Haodi Zhong, Grigorios Loukides, Solon P. Pissis
Publicado en: Data & Knowledge Engineering, Edición 138, 2022, Página(s) 101981, ISSN 0169-023X
Editor: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

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

Autores: Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
Publicado en: Natural Computing, Edición 21, 2022, Página(s) 81-108, ISSN 1567-7818
Editor: Kluwer Academic Publishers
DOI: 10.1007/s11047-022-09882-6

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

Autores: Grigorios Loukidis, Solon Pissis, Michelle Sweering
Publicado en: IEEE Transactions on Knowledge and Data Engineering, 2023, Página(s) 1-18, ISSN 1041-4347
Editor: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3231780

Internal shortest absent word queries in constant time and linear space

Autores: Golnaz Badkobeh, Panagiotis Charalampopoulos, Dmitry Kosolobov, Solon P. Pissis
Publicado en: Theoretical Computer Science, Edición 922, 2020, Página(s) 271-282, ISSN 0304-3975
Editor: Elsevier BV
DOI: 10.1016/j.tcs.2022.04.029

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

Autores: Grigorios Loukides, Solon P. Pissis
Publicado en: Information Processing Letters, Edición 178, 2022, Página(s) 106275, ISSN 0020-0190
Editor: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

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

Autores: Giovanni Buzzega, Alessio Conte, Roberto Grossi, Giulia Punzi
Publicado en: Algorithms for Molecular Biology, Edición 20, 2025, ISSN 1748-7188
Editor: BioMed Central
DOI: 10.1186/s13015-025-00271-z

ESKEMAP: exact sketch-based read mapping

Autores: Tizian Schulz, Paul Medvedev
Publicado en: Algorithms for Molecular Biology, 2024, ISSN 1748-7188
Editor: BioMed Central
DOI: 10.1186/s13015-024-00261-7

Seedability: optimizing alignment parameters for sensitive sequence comparison

Autores: Lorraine A. K. Ayad, Rayan Chikhi, Solon P. Pissis
Publicado en: Bioinformatics Advances, Edición 3, 2023, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbad108

Elastic-Degenerate String Matching with 1 Error or Mismatch

Autores: Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Publicado en: Theory of Computing Systems, Edición 68, 2024, Página(s) 1442-1467, ISSN 1432-4350
Editor: 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

Autores: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Publicado en: Nature Methods, Edición 20, 2022, Página(s) 550-558, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/s41592-022-01674-1

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

Autores: Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Publicado en: Bioinformatics, Edición 36/14, 2020, Página(s) 4191–4192, ISSN 1367-4811
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa297

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

Autores: Jorge Avila Cartes, Santosh Anand, Simone Ciccolella, Paola Bonizzoni, Gianluca Della Vedova
Publicado en: Gigascience, Edición 12, 2022, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1093/gigascience/giac119

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

Autores: Xiao Luo; Xiao Luo; Xiongbin Kang; Xiongbin Kang; Alexander Schönhuth; Alexander Schönhuth
Publicado en: Genome Biology, Edición 22, 2021, Página(s) 299, ISSN 1474-760X
Editor: BioMed Central
DOI: 10.1186/s13059-021-02512-x

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Autores: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publicado en: Frontiers in Genetics, Edición 13, 2022, ISSN 1664-8021
Editor: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Sequence-based pangenomic core detection

Autores: Tizian Schulz, Roland Wittler, Jens Stoye
Publicado en: IScience, Edición 25/6, 2022, ISSN 2589-0042
Editor: Cell Press
DOI: 10.1016/j.isci.2022.104413

StrainXpress: strain aware metagenome assembly from short reads

Autores: Xiongbin Kang, Xiao Luo, Alexander Schönhuth
Publicado en: Nucleic Acids Research, Edición 50/17, 2022, Página(s) e101, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkac543

Efficient Computation of Sequence Mappability

Autores: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Publicado en: Algorithmica, Edición 84, 2022, Página(s) 1418-1440, ISSN 0178-4617
Editor: Springer Verlag
DOI: 10.1007/s00453-022-00934-y

Detecting High Scoring Local Alignments in Pangenome Graphs

Autores: Tizian Schulz; Roland Wittler; Sven Rahmann; Faraz Hach; Faraz Hach; Jens Stoye
Publicado en: Bioinformatics, Edición 37, 2021, Página(s) 2266–2274, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1101/2020.09.03.280958

VeChat: correcting errors in long reads using variation graphs

Autores: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publicado en: Nature Communications, Edición 13, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

Dynamic Pooling Improves Nanopore Base Calling Accuracy

Autores: Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Publicado en: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Edición 19/6, 2022, Página(s) 3416-3424, ISSN 1545-5963
Editor: IEEE Computer Society
DOI: 10.1109/tcbb.2021.3128366

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

Autores: Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Publicado en: Theoretical Computer Science, Edición 862, 2021, Página(s) 42-58, ISSN 0304-3975
Editor: Elsevier BV
DOI: 10.1016/j.tcs.2020.11.041

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

Autores: Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomáš Vinař, Cedric Chauve
Publicado en: Frontiers in Microbiology, 2023, ISSN 1664-302X
Editor: Frontiers Media
DOI: 10.3389/fmicb.2023.1267695

Palidis: fast discovery of novel insertion sequences

Autores: Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Publicado en: Microbial Genomics, Edición 9/3, 2023, ISSN 2057-5858
Editor: Microbiology Society
DOI: 10.1099/mgen.0.000917

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison

Autores: Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipović; Mauricio Soto Gomez
Publicado en: Algorithms, 2023, ISSN 1999-4893
Editor: MDPI Open Access Publishing
DOI: 10.3390/a16070333

Text Indexing for Long Patterns: Anchors are All you Need

Autores: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Publicado en: Proceedings of the VLDB Endowment, Edición 16(9), 2023, Página(s) 2117-2131, ISSN 2150-8097
Editor: Association for Computing Machinery (ACM)
DOI: 10.14778/3598581.3598586

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

Autores: Parsoa Khorsand; Luca Denti; Paola Bonizzoni; Rayan Chikhi; Fereydoun Hormozdiari; Fereydoun Hormozdiari
Publicado en: Bioinformatics Advances, Edición 1, 2021, ISSN 2635-0041
Editor: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbab005

Markov chains improve the significance computation of overlapping genome annotations

Autores: Askar Gafurov, Broňa Brejová, Paul Medvedev
Publicado en: Bioinformatics, Edición 38, 2022, Página(s) i203–i211, ISSN 1367-4811
Editor: 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

Autores: Barış Ekim, Bonnie Berger, Rayan Chikhi
Publicado en: Cell Systems, Edición 12/10, 2021, Página(s) 958--968, ISSN 2405-4720
Editor: Elsevier
DOI: 10.1016/j.cels.2021.08.009

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

Autores: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publicado en: Nature Machine Intelligence, 2023, ISSN 2522-5839
Editor: Springer
DOI: 10.1038/s42256-022-00604-2

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

Autores: Jakub Styk, Zuzana Pös, Ondrej Pös, Jan Radvanszky, Evelina Hrckova Turnova, Gergely Buglyó, Daniela Klimova, Jaroslav Budis, Vanda Repiska, Bálint Nagy, Tomas Szemes
Publicado en: The EPMA Journal, 2023, ISSN 1878-5085
Editor: 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.

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

Minimizing the Minimizers via Alphabet Reordering

Autores: Hilde Verbeek, Lorraine A.K. Ayad, Grigorios Loukides, Solon P. Pissis
Publicado en: Combinatorial Pattern Matching (CPM 2024), 2024
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.28

Elastic-Degenerate String Matching with 1 Error

Autores: Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Publicado en: Latin American Symposium on Theoretical Informatics (LATIN 2022), Edición 13568, 2022, Página(s) 20-37, ISBN 978-3-031-20623-8
Editor: Springer
DOI: 10.1007/978-3-031-20624-5_2

Enhancing Generalized Compressed Suffix Trees, with Applications

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

Utility-Oriented String Mining

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

KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints

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

Phasing Data from Genotype Queries via the μ-PBWT

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

Solving the Minimal Positional Substring Cover Problem in Sublinear Space

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

Faster Approximate Elastic-Degenerate String Matching - Part A

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

On Strings Having the Same Length-k Substrings

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

Substring Complexity in Sublinear Space

Autores: Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis
Publicado en: International Symposium on Algorithms and Computation (ISAAC 2023), 2023
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2023.12

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

Autores: Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
Publicado en: Developments in Language Theory (DLT 2022), Edición 13257, 2022, Página(s) 3-12, ISBN 978-3-031-05578-2
Editor: Springer International Publishing
DOI: 10.1007/978-3-031-05578-2_1

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

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

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

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

Space-Efficient Indexes for Uncertain Strings

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

The Rational Construction of a Wheeler DFA

Autores: Giovanni Manzini, Alberto Policriti, Nicola Prezza, Brian Riccardi
Publicado en: Combinatorial Pattern Matching (CPM 2024), 2024, ISBN 978-3-95977-326-3
Editor: 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

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

Pangenome Graph Indexing via the Multidollar-BWT

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

Faster Approximate Elastic-Degenerate String Matching - Part B

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

McDag: Indexing Maximal Common Subsequences in Practice

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

Pattern Masking for Dictionary Matching

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

Approximate Circular Pattern Matching

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

On the Construction of Elastic Degenerate Strings

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

Unary Words Have the Smallest Levenshtein k-Neighbourhoods

Autores: Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski, Tomasz Waleń, Wiktor Zuba
Publicado en: Combinatorial Pattern Matching (CPM 2020), Edición 161, 2020, Página(s) 10:1--10:12, ISBN 978-3-95977-149-8
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2020.10

BWT for String Collections

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

Indexing Strings with Utilities

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

String Sanitization Under Edit Distance

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

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

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

Approximate Circular Pattern Matching Under Edit Distance

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

Exact Sketch-Based Read Mapping

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

Subsequence-Based Indices for Genome Sequence Analysis

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

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

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

On String and Graph Sanitization

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

Faster Algorithms for Longest Common Substring

Autores: Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski
Publicado en: European Symposium on Algorithms (ESA 2021), Edición 204, 2021, Página(s) 30:1--30:17, ISBN 978-3-95977-204-4
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast Assessment of Eulerian Trails

Autores: Alessio Conte, Roberto Grossi, Grigorios Loukidis, Nadia Pisanti, Solon P. Pissis, Giulia Punzi
Publicado en: Fundamentals of Computation Theory (FCT 2021), Edición 12867, 2021, Página(s) 162--175, ISBN 978-3-030-86593-1
Editor: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Suffix-Prefix Queries on a Dictionary

Autores: Grigorios Loukides, Solon P. Pissis, Sharma V. Thankachan, Wiktor Zuba
Publicado en: Combinatorial Pattern Matching (CPM 2023), Edición 259, 2023, Página(s) 21:1-21:20, ISBN 978-3-95977-276-1
Editor: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Size-Constrained Weighted Ancestors with Applications

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

Making de Bruijn Graphs Eulerian

Autores: Giulia Bernardini, Huiping Chen, Grigorios Loukides, Solon P. Pissis, Leen Stougie, Michelle Sweering
Publicado en: Combinatorial Pattern Matching (CPM 2022), Edición 223, 2022, Página(s) 12:1--12:18, ISBN 978-3-95977-234-1
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Autores: Askar Gafurov, Tomáš Vinař, Broňa Brejová
Publicado en: Conference on Computability in Europe (CiE 2021), 2021, Página(s) 227-236, ISBN 978-3-030-80049-9
Editor: Springer
DOI: 10.1007/978-3-030-80049-9_21

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

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

Bidirectional String Anchors: A New String Sampling Mechanism

Autores: Grigorios Loukides, Solon P. Pissis
Publicado en: European Symposium on Algorithms (ESA 2021), Edición 204, 2021, Página(s) 64:1--64:21, ISBN 978-3-95977-204-4
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts

Autores: Askar Gafurov, Tomáš Vinař, Paul Medvedev, Broňa Brejová
Publicado en: Research in Computational Molecular Biology (RECOMB 2024), 2024, ISBN 978-1-0716-3989-4
Editor: Springer
DOI: 10.1007/978-1-0716-3989-4_3

Connecting de Bruijn Graphs

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

Longest Palindromic Substring in Sublinear Time

Autores: Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski
Publicado en: Combinatorial Pattern Matching (CPM 2022), Edición 223, 2022, Página(s) 20:1--20:9, ISBN 978-3-95977-234-1
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.20

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