Pan-genome Graph Algorithms and Data Integration

Rezultaty

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.

Publikacje

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autorzy: Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, Giovanna Rosone
Opublikowane w: SIAM Journal on Computing, Numer 51/3, 2022, Strona(/y) 549-576, ISSN 0097-5397
Wydawca: Society for Industrial and Applied Mathematics
DOI: 10.1137/20m1368033

Simpler and Faster Development of Tumor Phylogeny Pipelines

Autorzy: Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, Murray Patterson
Opublikowane w: Journal of Computational Biology, Numer 28/11, 2021, Strona(/y) 1142-1155, ISSN 1066-5277
Wydawca: 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

Autorzy: 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
Opublikowane w: Viruses, Numer 14/11, 2022, ISSN 1999-4915
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14112432

Finding Maximal Exact Matches Using the r-Index

Autorzy: Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher
Opublikowane w: Journal of Computational Biology, Numer 29/2, 2022, Strona(/y) 188-194, ISSN 1066-5277
Wydawca: Mary Ann Liebert Inc.
DOI: 10.1089/cmb.2021.0445

Automated prediction of the clinical impact of structural copy number variations

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

MALVIRUS: an integrated application for viral variant analysis

Autorzy: Simone Ciccolella; Luca Denti; Paola Bonizzoni; Gianluca Della Vedova; Yuri Pirola; Marco Previtali
Opublikowane w: BMC Bioinformatics, Numer 22, 2021, Strona(/y) 625, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-022-04668-0

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

Autorzy: Askar Gafurov, Andrej Baláž, Fabian Amman, Kristína Boršová, Viktória Čabanová, Boris Klempa, Andreas Bergthaler, Tomáš Vinař, Broňa Brejová
Opublikowane w: BMC Bioinformatics, Numer 23, 2022, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-022-05100-3

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

Autorzy: Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts
Opublikowane w: BMC Bioinformatics, Numer 22, 2021, Strona(/y) 51, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-021-03983-2

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

Autorzy: Luo, Xiao; Kang, Xiangbin; Schönhuth, Alexander
Opublikowane w: Genome Biology, 2022, ISSN 1474-760X
Wydawca: BioMed Central Ltd.
DOI: 10.1186/s13059-021-02587-6

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

Autorzy: Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Opublikowane w: Information Sciences, Numer 607, 2022, Strona(/y) 458-476, ISSN 0020-0255
Wydawca: Elsevier BV
DOI: 10.1016/j.ins.2022.06.005

Shark: fishing relevant reads in an RNA-Seq sample

Autorzy: Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
Opublikowane w: Bioinformatics, Numer 37/4, 2020, Strona(/y) 464-472, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa779

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

Autorzy: Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
Opublikowane w: Bioinformatics, 2023, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btad552

Nanopore base calling on the edge

Autorzy: Peter Perešíni, Vladimír Boža, Broňa Brejová, Tomáš Vinař
Opublikowane w: Bioinformatics, Numer 37/24, 2021, Strona(/y) 4661-4667, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btab528

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

Autorzy: Brona Brejova; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Askar Gafurov; Dominika Fricova; Martina Neboháčová; Tomas Vinar; Boris Klempa; Jozef Nosek
Opublikowane w: PLoS ONE, Numer 16, 2021, Strona(/y) e0259277, ISSN 1932-6203
Wydawca: Public Library of Science
DOI: 10.1371/journal.pone.0259277

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

Autorzy: Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova
Opublikowane w: Bioinformatics, Numer 37/2, 2020, Strona(/y) 178-184, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa676

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

Autorzy: Natalia Forgacova, Juraj Gazdarica, Jaroslav Budiš, Jan Radvanszky, Tomáš Szemes
Opublikowane w: Oncology Letters, Numer 22/5, 2021, ISSN 1792-1074
Wydawca: Spandidos Publications
DOI: 10.3892/ol.2021.13040

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

Autorzy: Ondrej Pös, Jan Radvanszky, Gergely Buglyó, Zuzana Pös, Diana Rusnakova, Bálint Nagy, Tomas Szemes
Opublikowane w: Biomedical Journal, Numer 44/5, 2021, Strona(/y) 548-559, ISSN 2319-4170
Wydawca: Medknow Publications and Media Pvt. Ltd
DOI: 10.1016/j.bj.2021.02.003

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Autorzy: Luc Blassel, Paul Medvedev, Rayan Chikhi
Opublikowane w: iScience, Numer 25/11, 2022, ISSN 2589-0042
Wydawca: Cell Press
DOI: 10.1016/j.isci.2022.105305

Clustering sequence graphs

Autorzy: Haodi Zhong, Grigorios Loukides, Solon P. Pissis
Opublikowane w: Data & Knowledge Engineering, Numer 138, 2022, Strona(/y) 101981, ISSN 0169-023X
Wydawca: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

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

Autorzy: Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
Opublikowane w: Natural Computing, Numer 21, 2022, Strona(/y) 81-108, ISSN 1567-7818
Wydawca: Kluwer Academic Publishers
DOI: 10.1007/s11047-022-09882-6

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

Autorzy: Grigorios Loukidis, Solon Pissis, Michelle Sweering
Opublikowane w: IEEE Transactions on Knowledge and Data Engineering, 2023, Strona(/y) 1-18, ISSN 1041-4347
Wydawca: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3231780

Internal shortest absent word queries in constant time and linear space

Autorzy: Golnaz Badkobeh, Panagiotis Charalampopoulos, Dmitry Kosolobov, Solon P. Pissis
Opublikowane w: Theoretical Computer Science, Numer 922, 2020, Strona(/y) 271-282, ISSN 0304-3975
Wydawca: Elsevier BV
DOI: 10.1016/j.tcs.2022.04.029

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

Autorzy: Grigorios Loukides, Solon P. Pissis
Opublikowane w: Information Processing Letters, Numer 178, 2022, Strona(/y) 106275, ISSN 0020-0190
Wydawca: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

Seedability: optimizing alignment parameters for sensitive sequence comparison

Autorzy: Lorraine A. K. Ayad, Rayan Chikhi, Solon P. Pissis
Opublikowane w: Bioinformatics Advances, Numer 3, 2023, ISSN 2635-0041
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbad108

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

Autorzy: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Opublikowane w: Nature Methods, Numer 20, 2022, Strona(/y) 550-558, ISSN 1548-7091
Wydawca: Nature Publishing Group
DOI: 10.1038/s41592-022-01674-1

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

Autorzy: Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Opublikowane w: Bioinformatics, Numer 36/14, 2020, Strona(/y) 4191–4192, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa297

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

Autorzy: Jorge Avila Cartes, Santosh Anand, Simone Ciccolella, Paola Bonizzoni, Gianluca Della Vedova
Opublikowane w: Gigascience, Numer 12, 2022, ISSN 2047-217X
Wydawca: Oxford University Press
DOI: 10.1093/gigascience/giac119

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

Autorzy: Xiao Luo; Xiao Luo; Xiongbin Kang; Xiongbin Kang; Alexander Schönhuth; Alexander Schönhuth
Opublikowane w: Genome Biology, Numer 22, 2021, Strona(/y) 299, ISSN 1474-760X
Wydawca: BioMed Central
DOI: 10.1186/s13059-021-02512-x

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Autorzy: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Opublikowane w: Frontiers in Genetics, Numer 13, 2022, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Sequence-based pangenomic core detection

Autorzy: Tizian Schulz, Roland Wittler, Jens Stoye
Opublikowane w: IScience, Numer 25/6, 2022, ISSN 2589-0042
Wydawca: Cell Press
DOI: 10.1016/j.isci.2022.104413

StrainXpress: strain aware metagenome assembly from short reads

Autorzy: Xiongbin Kang, Xiao Luo, Alexander Schönhuth
Opublikowane w: Nucleic Acids Research, Numer 50/17, 2022, Strona(/y) e101, ISSN 0305-1048
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkac543

Efficient Computation of Sequence Mappability

Autorzy: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Opublikowane w: Algorithmica, Numer 84, 2022, Strona(/y) 1418-1440, ISSN 0178-4617
Wydawca: Springer Verlag
DOI: 10.1007/s00453-022-00934-y

Detecting High Scoring Local Alignments in Pangenome Graphs

Autorzy: Tizian Schulz; Roland Wittler; Sven Rahmann; Faraz Hach; Faraz Hach; Jens Stoye
Opublikowane w: Bioinformatics, Numer 37, 2021, Strona(/y) 2266–2274, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1101/2020.09.03.280958

VeChat: correcting errors in long reads using variation graphs

Autorzy: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Opublikowane w: Nature Communications, Numer 13, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

Dynamic Pooling Improves Nanopore Base Calling Accuracy

Autorzy: Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař
Opublikowane w: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numer 19/6, 2022, Strona(/y) 3416-3424, ISSN 1545-5963
Wydawca: IEEE Computer Society
DOI: 10.1109/tcbb.2021.3128366

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

Autorzy: Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi
Opublikowane w: Theoretical Computer Science, Numer 862, 2021, Strona(/y) 42-58, ISSN 0304-3975
Wydawca: Elsevier BV
DOI: 10.1016/j.tcs.2020.11.041

Palidis: fast discovery of novel insertion sequences

Autorzy: Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Opublikowane w: Microbial Genomics, Numer 9/3, 2023, ISSN 2057-5858
Wydawca: Microbiology Society
DOI: 10.1099/mgen.0.000917

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison

Autorzy: Simone Ciccolella; Gianluca Della Vedova; Vladimir Filipović; Mauricio Soto Gomez
Opublikowane w: Algorithms, 2023, ISSN 1999-4893
Wydawca: MDPI Open Access Publishing
DOI: 10.3390/a16070333

Text Indexing for Long Patterns: Anchors are All you Need

Autorzy: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Opublikowane w: Proceedings of the VLDB Endowment, Numer 16(9), 2023, Strona(/y) 2117-2131, ISSN 2150-8097
Wydawca: Association for Computing Machinery (ACM)
DOI: 10.14778/3598581.3598586

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

Autorzy: Parsoa Khorsand; Luca Denti; Paola Bonizzoni; Rayan Chikhi; Fereydoun Hormozdiari; Fereydoun Hormozdiari
Opublikowane w: Bioinformatics Advances, Numer 1, 2021, ISSN 2635-0041
Wydawca: Oxford University Press (OUP)
DOI: 10.1093/bioadv/vbab005

Markov chains improve the significance computation of overlapping genome annotations

Autorzy: Askar Gafurov, Broňa Brejová, Paul Medvedev
Opublikowane w: Bioinformatics, Numer 38, 2022, Strona(/y) i203–i211, ISSN 1367-4811
Wydawca: 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

Autorzy: Barış Ekim, Bonnie Berger, Rayan Chikhi
Opublikowane w: Cell Systems, Numer 12/10, 2021, Strona(/y) 958--968, ISSN 2405-4720
Wydawca: Elsevier
DOI: 10.1016/j.cels.2021.08.009

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

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

Autorzy: Broňa Brejová; Kristína Boršová; Kristína Boršová; Viktória Hodorová; Viktória Čabanová; Lenka Reizigová; Evan D. Paul; Pavol Čekan; Boris Klempa; Jozef Nosek; Tomáš Vinař
Opublikowane w: Virus Genes, Numer 57, 2021, Strona(/y) 556–560, ISSN 1572-994X
Wydawca: Springer Science and Business Media LLC
DOI: 10.1007/s11262-021-01866-5

Elastic-Degenerate String Matching with 1 Error

Autorzy: Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Opublikowane w: Latin American Symposium on Theoretical Informatics (LATIN 2022), Numer 13568, 2022, Strona(/y) 20-37, ISBN 978-3-031-20623-8
Wydawca: Springer
DOI: 10.1007/978-3-031-20624-5_2

KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints

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

On Strings Having the Same Length-k Substrings

Autorzy: Giulia Bernardini, Alessio Conte, Esteban Gabory, Roberto Grossi, Grigorios Loukides, Solon P. Pissis, Giulia Punzi, Michelle Sweering
Opublikowane w: Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 16:1--16:17, ISBN 978-3-95977-234-1
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.16

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

Autorzy: Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza
Opublikowane w: Developments in Language Theory (DLT 2022), Numer 13257, 2022, Strona(/y) 3-12, ISBN 978-3-031-05578-2
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-031-05578-2_1

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

Autorzy: Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza
Opublikowane w: Algorithms for Computational Biology (AlCoB 2021), 2021, Strona(/y) 16-28, ISBN 978-3-030-74432-8
Wydawca: Springer
DOI: 10.1007/978-3-030-74432-8_2

Approximate Circular Pattern Matching

Autorzy: Panagiotis Charalampopoulos, Tomasz Kociumaka, Jakub Radoszewski, Solon P. Pissis, Wojciech Rytter, Tomasz Waleń, Wiktor Zuba
Opublikowane w: European Symposium on Algorithms (ESA 2022), Numer 244, 2022, Strona(/y) 35:1--35:19, ISBN 978-3-95977-247-1
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.35

Unary Words Have the Smallest Levenshtein k-Neighbourhoods

Autorzy: Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski, Tomasz Waleń, Wiktor Zuba
Opublikowane w: Combinatorial Pattern Matching (CPM 2020), Numer 161, 2020, Strona(/y) 10:1--10:12, ISBN 978-3-95977-149-8
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2020.10

String Sanitization Under Edit Distance

Autorzy: Giulia Bernardini, Grigorios Loukides, Solon P. Pissis, Michelle Sweering, Huiping Chen, Nadia Pisanti, Leen Stougie
Opublikowane w: Combinatorial Pattern Matching (CPM 2020), Numer 161, 2020, Strona(/y) 7:1--7:14, ISBN 978-3-95977-149-8
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2020.7

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

Autorzy: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Opublikowane w: Combinatorial Pattern Matching (CPM 2023), Numer 259, 2023, Strona(/y) 11:1-11:20, ISBN 978-3-95977-276-1
Wydawca: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.11

Faster Algorithms for Longest Common Substring

Autorzy: Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski
Opublikowane w: European Symposium on Algorithms (ESA 2021), Numer 204, 2021, Strona(/y) 30:1--30:17, ISBN 978-3-95977-204-4
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast Assessment of Eulerian Trails

Autorzy: Alessio Conte, Roberto Grossi, Grigorios Loukidis, Nadia Pisanti, Solon P. Pissis, Giulia Punzi
Opublikowane w: Fundamentals of Computation Theory (FCT 2021), Numer 12867, 2021, Strona(/y) 162--175, ISBN 978-3-030-86593-1
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Suffix-Prefix Queries on a Dictionary

Autorzy: Grigorios Loukides, Solon P. Pissis, Sharma V. Thankachan, Wiktor Zuba
Opublikowane w: Combinatorial Pattern Matching (CPM 2023), Numer 259, 2023, Strona(/y) 21:1-21:20, ISBN 978-3-95977-276-1
Wydawca: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Making de Bruijn Graphs Eulerian

Autorzy: Giulia Bernardini, Huiping Chen, Grigorios Loukides, Solon P. Pissis, Leen Stougie, Michelle Sweering
Opublikowane w: Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 12:1--12:18, ISBN 978-3-95977-234-1
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Autorzy: Askar Gafurov, Tomáš Vinař, Broňa Brejová
Opublikowane w: Conference on Computability in Europe (CiE 2021), 2021, Strona(/y) 227-236, ISBN 978-3-030-80049-9
Wydawca: Springer
DOI: 10.1007/978-3-030-80049-9_21

Bidirectional String Anchors: A New String Sampling Mechanism

Autorzy: Grigorios Loukides, Solon P. Pissis
Opublikowane w: European Symposium on Algorithms (ESA 2021), Numer 204, 2021, Strona(/y) 64:1--64:21, ISBN 978-3-95977-204-4
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Longest Palindromic Substring in Sublinear Time

Autorzy: Panagiotis Charalampopoulos, Solon P. Pissis, Jakub Radoszewski
Opublikowane w: Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 20:1--20:9, ISBN 978-3-95977-234-1
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.20

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