Pan-genome Graph Algorithms and Data Integration

Deliverables

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.

Publications

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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