Journal articles

2024

• Insights into non-informative results from non-invasive prenatal screening through gestational age, maternal BMI, and age analyses.
  J. Gazdarica, N. Forgacova, T. Sladecek, M. Kucharik, J. Budis, M. Hyblova, M. Sekelska, A. Gnip, G. Minarik, T. Szemes.
  PLoS One, 2024.
  DOI: https://doi.org/10.1371/journal.pone.0280858
• Computing linkage disequilibrium aware genome embeddings using autoencoders.
  G. Taş, T. Westerdijk, E. Postma, Project MinE ALS GWAS Consortium , J.H. Veldink, A. Schönhuth, M. Balvert.
  Bioinformatics, 2024.
  DOI: https://doi.org/10.1093/bioinformatics/btae326
• ESKEMAP: exact sketch-based read mapping.
  T. Schulz, P. Medvedev.
  Algorithms for Molecular Biology, 2024.
  DOI: https://doi.org/10.1186/s13015-024-00261-7
• Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations.
  Z. Holesova, O. Pös, J. Gazdarica, M. Kucharik, J. Budis, M. Hyblova, G. Minarik, T. Szemes.
  BMC Genomics, 2024.
  DOI: https://doi.org/10.1186/s12864-024-10267-5
• High-quality metagenome assembly from long accurate reads with metaMDBG.
  G. Benoit, S. Raguideau, R. James, A.M. Phillippy, R. Chikhi, C. Quince.
  Nature Biotechnology, 2024.
  DOI: https://doi.org/10.1038/s41587-023-01983-6
  OA Accepted version: https://www.biorxiv.org/content/10.1101/2023.07.07.548136v1
• Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.
  T. Lemane, N. Lezzoche, J. Lecubin, E. Pelletier, M. Lescot, R. Chikhi, P. Peterlongo.
  Nature Computational Science, 2024.
  DOI: https://doi.org/10.1038/s43588-024-00596-6
  OA Accepted version: https://www.biorxiv.org/content/10.1101/2023.05.31.543043v4
• RecGraph: recombination-aware alignment of sequences to variation graphs.
  J. Avila Cartes, P. Bonizzoni, S. Ciccolella, G. Della Vedova, L. Denti, X. Didelot, D.C. Monti, Y. Pirola.
  Bioinformatics, 2024.
  DOI: https://doi.org/10.1093/bioinformatics/btae292

2023

• Hybrid-hybrid correction of errors in long reads with HERO.
  X. Kang, J. Xu, X. Luo, A. Schönhuth.
  Genome Biology, 2023.
  DOI: https://doi.org/10.1186/s13059-023-03112-7
• Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks.
  X. Luo, X. Kang, A. Schönhuth.
  Nature Machine Intelligence, 2023.
  DOI: https://doi.org/10.1038/s42256-022-00604-2
• WarpSTR: Determining tandem repeat lengths using raw nanopore signals.
  J. Sitarčík, T. Vinař, B. Brejová, W. Krampl, J. Budiš, J. Radvánszky, M. Lucká.
  Bioinformatics, 2023.
  DOI: https://doi.org/10.1093/bioinformatics/btad388
• Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations.
  T. Sládeček, M. Gažiová, M. Kucharík, A. Zaťková, Z. Pös, O. Pös, W. Krampl, E. Tomková, M. Hýblová, G. Minárik, J. Radvánszky, J. Budiš, T. Szemes.
  Scientific Reports, 2023.
  DOI: https://doi.org/10.1038/s41598-023-37352-1
• PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.
  A. Mane, M. Faizrahnemoon, T. Vinař, B. Brejová, C. Chauve.
  Bioinformatics, 2023.
  DOI: https://doi.org/10.1093/bioinformatics/btad250
• plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.
  J. Sielemann, K. Sielemann, B. Brejová, T. Vinař, C. Chauve.
  Frontiers in Microbiology, 2023.
  DOI: https://doi.org/10.3389/fmicb.2023.1267695
• Efficient mapping of accurate long reads in minimizer space with mapquik.
  B. Ekim, K. Sahlin, P. Medvedev, B. Berger, R. Chikhi.
  Genome Research, 2023.
  DOI: https://doi.org/10.1101/gr.277679.123
• Comparing methods for constructing and representing human pangenome graphs.
  F. Andreace, P. Lechat, Y. Dufresne, R. Chikhi.
  Genome Biology, 2023.
  DOI: https://doi.org/10.1186/s13059-023-03098-2
• aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.
  C.D. González, S. Rangavittal, R. Vicedomini, R. Chikhi, H. Richard.
  iScience, 2023.
  DOI: https://doi.org/10.1016/j.isci.2023.108057
• μ-PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data.
  D. Cozzi, M. Rossi, S. Rubinacci, T. Gagie, D. Köppl, C. Boucher, P. Bonizzoni.
  Bioinformatics, 2023.
  DOI: https://doi.org/10.1093/bioinformatics/btad552
• Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison.
  S. Ciccolella, G. Della Vedova, V. Filipovic, M. Soto Gomez.
  Algorithms, 2023.
  DOI: https://doi.org/10.3390/a16070333
• Seedability: optimizing alignment parameters for sensitive sequence comparison.
  L.A.K. Ayad, R. Chikhi, S.P. Pissis.
  Bioinformatics Advances, 2023.
  DOI: https://doi.org/10.1093/bioadv/vbad108
• Text Indexing for Long Patterns: Anchors are All you Need.
  L.A.K. Ayad, G. Loukidis, S.P. Pissis.
  Proceedings of the VLDB Endowment, 2023.
  DOI: https://doi.org/10.14778/3598581.3598586
  OA Accepted version: https://bura.brunel.ac.uk/handle/2438/26881
• Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook.
  J. Styk, Z. Pös, O. Pös, J. Radvanszky, E.H. Turnova, G. Buglyó, D. Klimova, J. Budis, V. Repiska, B. Nagy, T. Szemes.
  The EPMA Journal, 2023.
  DOI: https://doi.org/10.1007/s13167-023-00312-w
• Palidis: fast discovery of novel insertion sequences.
  V.R. Carr, S.P. Pissis​, P. Mullany​, S. Shoaie​, D. Gomez-Cabrero​, D.L. Moyes.
  Microbial genomics, 2023.
  DOI: https://doi.org/10.1099/mgen.0.000917
• Bidirectional String Anchors for Improved Text Indexing and Top-K Similarity Search.
  G. Loukidis, S.P. Pissis, M. Sweering.
  IEEE Transactions on Knowledge and Data Engineering, 2023.
  DOI: https://doi.org/10.1109/TKDE.2022.3231780
  OA Accepted version: https://kclpure.kcl.ac.uk/portal/files/195931388/Bidirectional_String_Anchors_4.pdf
• Accurate and fast clade assignment via deep learning and frequency chaos game representation.
  J.A. Cartes, S. Anand, S. Ciccolella, P. Bonizzoni, G. Della Vedova
  Gigascience, 2023.
  DOI: https://doi.org/10.1093/gigascience/giac119

2022

• SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.
  L. Denti, P. Khorsand, P. Bonizzoni, F. Hormozdiari, R. Chikhi.
  Nature Methods, 2022.
  DOI: https://doi.org/10.1038/s41592-022-01674-1
  OA Accepted version: https://hdl.handle.net/10281/400015
• VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.
  A. Gafurov, A. Baláž, F. Amman, K. Boršová, V. Čabanová, B. Klempa, A. Bergthaler, T. Vinař, B. Brejová.
  BMC Bioinformatics, 2022.
  DOI: https://doi.org/10.1186/s12859-022-05100-3
• Markov chains improve the significance computation of overlapping genome annotations.
  A. Gafurov, B. Brejová, P. Medvedev.
  Bioinformatics, 2022.
  DOI: https://doi.org/10.1093/bioinformatics/btac255
• VeChat: correcting errors in long reads using variation graphs.
  X. Luo, X. Kang, A. Schönhuth.
  Nature Communications, 2022.
  DOI: https://doi.org/10.1038/s41467-022-34381-8
• Automated prediction of the clinical impact of structural copy number variations.
  M. Gažiová, T. Sládeček, O. Pös, M. Števko, W. Krampl, Z. Pös, R. Hekel, M. Hlavačka, M. Kucharík, J. Radvánszky, J. Budiš, T. Szemes.
  Scientific Reports, 2022.
  DOI: https://doi.org/10.1038/s41598-021-04505-z
• Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic-One Year Experience.
  D. Rusňáková et al.
  Viruses, 2022.
  DOI: https://doi.org/10.3390/v14112432
• StrainXpress: strain aware metagenome assembly from short reads.
  X. Kang, X. Luo, A. Schönhuth.
  Nucleic Acids Research, 2022.
  DOI: https://doi.org/10.1093/nar/gkac543
• Internal shortest absent word queries in constant time and linear space.
  G. Badkobeh, P. Charalampopoulos, D. Kosolobov, S.P. Pissis.
  Theoretical Computer Science, 2022.
  DOI: https://doi.org/10.1016/j.tcs.2022.04.029
  OA Accepted version: https://arxiv.org/abs/2106.01763
• Elastic-Degenerate String Matching via Fast Matrix Multiplication.
  G. Bernardini, P. Gawrychowski, N. Pisanti, S.P. Pissis, G. Rosone.
  SIAM Journal on Computing, 2022.
  DOI: https://doi.org/10.1137/20M1368033
  OA Accepted version: https://arxiv.org/abs/1905.02298
• MALVIRUS: an integrated application for viral variant analysis.
  S. Ciccolella, L. Denti, P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali.
  BMC Bioinformatics, 2022.
  DOI: https://doi.org/10.1186/s12859-022-04668-0
• Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches.
  P. Bonizzoni, M. Costantini, C. De Felice, A. Petescia, Y. Pirola, M. Previtali, R. Rizzi, J. Stoye, R. Zaccagnino, R. Zizza.
  Information Sciences, 2022.
  DOI: https://doi.org/10.1016/j.ins.2022.06.005
  OA Accepted version: https://doi.org/10.48550/arXiv.2202.13884
• Enhancing Long-Read-Based Strain-Aware Metagenome Assembly.
  X. Luo, X. Kang, A. Schönhuth.
  Frontiers in Genetics, 2022.
  DOI: https://doi.org/10.3389/fgene.2022.868280
• Computational graph pangenomics: a tutorial on data structures and their applications.
  J.A. Baaijens, P. Bonizzoni, C. Boucher, G. Della Vedova, Y. Pirola, R. Rizzi, J. Sirén.
  Natural Computing, 2022.
  DOI: https://doi.org/10.1007/s11047-022-09882-6
• Sequence-based pangenomic core detection.
  T. Schulz, R. Wittler, J. Stoye.
  IScience, 2022.
  DOI: https://doi.org/10.1016/j.isci.2022.104413
• All-pairs suffix/prefix in optimal time using Aho-Corasick space.
  G. Loukides, S.P. Pissis.
  Information Processing Letters, 2022.
  DOI: https://doi.org/10.1016/j.ipl.2022.106275
• Strainline: full-length de novo viral haplotype reconstruction from noisy long reads.
  X. Luo, X. Kang, A. Schönhuth.
  Genome Biology, 2022.
  DOI: https://doi.org/10.1186/s13059-021-02587-6
• Clustering sequence graphs.
  H. Zhong, G. Loukides, S. P. Pissis.
  Data & Knowledge Engineering, 2022.
  DOI: https://doi.org/10.1016/j.datak.2022.101981
• Finding Maximal Exact Matches Using the r-Index.
  M. Rossi, M. Oliva, P. Bonizzoni, B. Langmead, T. Gagie, C. Boucher.
  Journal of Computational Biology, 2022.
  DOI: https://doi.org/10.1089/cmb.2021.0445
  OA version: https://europepmc.org/article/MED/35041518
• Efficient Computation of Sequence Mappability.
  P. Charalampopoulos, C.S. Iliopoulos, T. Kociumaka, S.P. Pissis, J. Radoszewski, J. Straszyński.
  Algorithmica, 2022.
  DOI: https://doi.org/10.1007/s00453-022-00934-y
• Mapping-friendly sequence reductions: Going beyond homopolymer compression.
  L. Blassel, P. Medvedev, R. Chikhi.
  iScience, 2022.
  DOI: https://doi.org/10.1016/j.isci.2022.105305

2021

• Repurposing non‑invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome.
  N. Forgacova, J. Gazdarica, J. Budiš, J. Radvanszky, T. Szemes.
  Oncology Letters, 2021.
  DOI: https://doi.org/10.3892/ol.2021.13040
• DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects.
  O. Pös, J. Radvanszky, G. Buglyó, Z. Pös, D. Rusnakova, B. Nagy, T. Szemes.
  Biomedical Journal, 2021.
  DOI: https://doi.org/10.1016/j.bj.2021.02.003
• Simpler and Faster Development of Tumor Phylogeny Pipelines.
  S. Ali, S. Ciccolella, L. Lucarella, G. Della Vedova, M. Patterson.
  Journal of Computational Biology, 2021.
  DOI: https://doi.org/10.1089/cmb.2021.0271
  OA Accepted version: https://hdl.handle.net/10281/352768
• Dynamic Pooling Improves Nanopore Base Calling Accuracy.
  V. Boža, P. Perešíni, B. Brejová, T. Vinař.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021.
  DOI: https://doi.org/10.1109/TCBB.2021.3128366
• Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tiling amplicon protocols.
  B. Brejová, K. Boršová, V. Hodorová, V. Čabanová, A. Gafurov, D. Fričová, M. Neboháčová, T. Vinař, B. Klempa, J. Nosek.
  PLoS One, 2021.
  DOI: https://doi.org/10.1371/journal.pone.0259277
• Comparative genome analysis using sample-specific string detection in accurate long reads.
  P. Khorsand, L. Denti, Human Genome Structural Variant Consortium, P. Bonizzoni, R. Chikhi, F. Hormozdiari.
  Bioinformatics Advances, 2021.
  DOI: https://doi.org/10.1093/bioadv/vbab005
• phasebook: haplotype-aware de novo assembly of diploid genomes from long reads.
  X. Luo, X. Kang, A. Schönhuth.
  Genome Biology, 2021.
  DOI: https://doi.org/10.1186/s13059-021-02512-x
• Nanopore base calling on the edge.
  P. Perešíni, V. Boža, B. Brejová, T. Vinař.
  Bioinformatics, 2021.
  DOI: https://doi.org/10.1093/bioinformatics/btab528
• Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.
  B. Ekim, B. Berger, R. Chikhi.
  Cells Systems, 2021.
  DOI: https://doi.org/10.1016/j.cels.2021.08.009
• 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.
  B. Brejová, K. Boršová, V. Hodorová, V. Čabanová, L. Reizigová, E.D. Paul, P. Čekan, B. Klempa, J. Nosek, T. Vinař.
  Virus Genes, 2021.
  DOI: https://doi.org/10.1007/s11262-021-01866-5
• Detecting high scoring local alignments in pangenome graphs.
  T. Schulz, R. Wittler, S. Rahmann, F. Hach, J. Stoye.
  Bioinformatics, 2021.
  DOI: https://doi.org/10.1093/bioinformatics/btab077
• IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences.
  H. Alamro, M. Alzamel, C.S. Iliopoulos, S.P. Pissis, S. Watts.
  BMC Bioinformatics, 2021.
  DOI: https://doi.org/10.1186/s12859-021-03983-2

2020

• DeepNano-blitz: a fast base caller for MinION nanopore sequencers.
  V. Boža, P. Perešíni, B. Brejová, T. Vinař.
  Bioinformatics, 2020.
  DOI: https://doi.org/10.1093/bioinformatics/btaa297
• Computing the multi-string BWT and LCP array in external memory.
  P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali, R. Rizzi.
  Theoretical Computer Science, 2020.
  DOI: https://doi.org/10.1016/j.tcs.2020.11.041
  OA Accepted version: arXiv:1705.07756 [cs.DS]
• Shark: fishing relevant reads in an RNA-Seq sample.
  L. Denti, Y. Pirola, M. Previtali, T. Ceccato, G. Della Vedova, R. Rizzi, P. Bonizzoni.
  Bioinformatics, 2020.
  DOI: https://doi.org/10.1093/bioinformatics/btaa779
• Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels.
  S. Ciccolella, G. Bernardini, L. Denti, P. Bonizzoni, M. Previtali, G. Della Vedova.
  Bioinformatics, 2020.
  DOI: https://doi.org/10.1093/bioinformatics/btaa676

Conference proceedings

2024

• Space-Efficient Indexes for Uncertain Strings.
  E. Gabory, C. Liu, G. Loukides, S.P. Pissis, W. Zuba.
  ICDE 2024: International Conference on Data Engineering 2024.
  DOI: https://doi.org/10.1109/icde60146.2024.00367
  OA Accepted version: https://doi.org/10.48550/arXiv.2403.14256
• Utility-Oriented String Mining.
  G. Bernardini, H. Chen, A. Conte, R. Grossi, V. Guerrini, G. Loukides, N. Pisanti, S.P. Pissis.
  SDM 2024: SIAM International Conference on Data Mining 2024.
  DOI: https://doi.org/10.1137/1.9781611978032.22
  OA Accepted version: https://kclpure.kcl.ac.uk/portal/en/publications/utility-oriented-string-mining
• Size-Constrained Weighted Ancestors with Applications.
  P. Bille, Y. Nekrich, S.P. Pissis.
  SWAT 2024: Scandinavian Symposium and Workshops on Algorithm Theory 2024.
  DOI: https://doi.org/10.4230/LIPIcs.SWAT.2024.14
• Approximate Circular Pattern Matching Under Edit Distance.
  P. Charalampopoulos, S.P. Pissis, J. Radoszewski, W. Rytter, T. Waleń, W. Zuba.
  STACS 2024: Symposium on Theoretical Aspects of Computer Science 2024.
  DOI: https://doi.org/10.4230/LIPIcs.STACS.2024.23
• Gapped String Indexing in Subquadratic Space and Sublinear Query Time.
  P. Bille, I.L. Gørtz, M. Lewenstein, S.P. Pissis, E. Rotenberg, T.A. Steiner.
  STACS 2024: Symposium on Theoretical Aspects of Computer Science 2024.
  DOI: https://doi.org/10.4230/LIPIcs.STACS.2024.16
• Sparse Suffix and LCP Array: Simple, Direct, Small, and Fast.
  L.A.K. Ayad, G. Loukides, S.P. Pissis, H. Verbeek.
  LATIN 2024: Latin American Symposium on Theoretical Informatics 2024.
  DOI: https://doi.org/10.1007/978-3-031-55598-5_11
  OA Accepted version: https://arxiv.org/pdf/2310.09023
• Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts.
  A. Gafurov, T. Vinař, P. Medvedev, B. Brejová.
  RECOMB 2024: Research in Computational Molecular Biology 2024.
  DOI: https://doi.org/10.1007/978-1-0716-3989-4_3
  OA Accepted version: https://doi.org/10.1101/2023.11.22.568259
• Solving the Minimal Positional Substring Cover Problem in Sublinear Space.
  P. Bonizzoni, C. Boucher, D. Cozzi, T. Gagie, Y. Pirola.
  CPM 2024: Combinatorial Pattern Matching 2024.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2024.12
• The Rational Construction of a Wheeler DFA.
  G. Manzini, A. Policriti, N. Prezza, B. Riccardi.
  CPM 2024: Combinatorial Pattern Matching 2024.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2024.23
• Connecting de Bruijn Graphs.
  G. Bernardini, H. Chen, I.L. Gørtz, C. Krogh, G. Loukides, S.P. Pissis, L. Stougie, M. Sweering.
  CPM 2024: Combinatorial Pattern Matching 2024.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2024.6
• Minimizing the Minimizers via Alphabet Reordering.
  H. Verbeek, L.A.K. Ayad, G. Loukides, S.P. Pissis.
  CPM 2024: Combinatorial Pattern Matching 2024.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2024.28

2023

• Substring Complexity in Sublinear Space.
  G. Bernardini, G. Fici, P. Gawrychowski, S.P. Pissis.
  ISAAC 2023: International Symposium on Algorithms and Computation 2023.
  DOI: https://doi.org/10.4230/LIPIcs.ISAAC.2023.12
• Exact Sketch-Based Read Mapping.
  T. Schulz, P. Medvedev.
  WABI 2023: Algorithms in Bioinformatics 2023.
  DOI: https://doi.org/10.4230/LIPIcs.WABI.2023.14
• Suffix-Prefix Queries on a Dictionary.
  G. Loukides, S.P. Pissis, S.V. Thankachan, W. Zuba.
  CPM 2023: Combinatorial Pattern Matching 2023.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2023.21
• Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications.
  E. Gabory, M.N. Mwaniki, N. Pisanti, S.P. Pissis, J. Radoszewski, M. Sweering, W. Zuba.
  CPM 2023: Combinatorial Pattern Matching 2023.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2023.11

2022

• Elastic-Degenerate String Matching with 1 Error.
  G. Bernardini, E. Gabory, S.P. Pissis, L. Stougie, M. Sweering, W. Zuba.
  LATIN 2022: Latin American Symposium on Theoretical Informatics 2022.
  DOI: https://doi.org/10.1007/978-3-031-20624-5_2
  OA Accepted version: https://doi.org/10.48550/arXiv.2209.01095
• Approximate Circular Pattern Matching.
  P. Charalampopoulos, T. Kociumaka, J. Radoszewski, S.P. Pissis, W. Rytter, T. Waleń, W. Zuba.
  ESA 2022: European Symposium on Algorithms 2022.
  DOI: https://doi.org/10.4230/LIPIcs.ESA.2022.35
• Longest Palindromic Substring in Sublinear Time.
  P. Charalampopoulos, S.P. Pissis, J. Radoszewski.
  CPM 2022: Combinatorial Pattern Matching 2022.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2022.20
• On Strings Having the Same Length-k Substrings.
  G. Bernardini, A. Conte, E. Gabory, R. Grossi, G. Loukides, S.P. Pissis, G. Punzi, M. Sweering.
  CPM 2022: Combinatorial Pattern Matching 2022.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2022.16
• Making de Bruijn Graphs Eulerian.
  G. Bernardini, H. Chen, G. Loukides, S.P. Pissis, L. Stougie, M. Sweering.
  CPM 2022: Combinatorial Pattern Matching 2022.
  DOI: https://doi.org/10.4230/LIPIcs.CPM.2022.12
• KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints.
  P. Bonizzoni, A. Petescia, Y. Pirola, R. Rizzi, R. Zaccagnino, R. Zizza.
  IWBBIO 2022: International Work-Conference on Bioinformatics and Biomedical Engineering 2022.
  DOI: https://doi.org/10.1007/978-3-031-07802-6_37
  OA Accepted version: https://hdl.handle.net/10281/388145
• Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes?
  P. Bonizzoni, C. De Felice, Y. Pirola, R. Rizzi, R. Zaccagnino, R. Zizza.
  DLT 2022: Developments in Language Theory 2022.
  DOI: https://doi.org/10.1007/978-3-031-05578-2_1
  OA Accepted version: https://boa.unimib.it/handle/10281/378700

2021

• Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning.
  P. Bonizzoni, C. De Felice, A. Petescia, Y. Pirola, R. Rizzi, J. Stoye, R. Zaccagnino, R. Zizza.
  AlCoB 2021: Algorithms for Computational Biology 2021.
  DOI: https://doi.org/10.1007/978-3-030-74432-8_2
  OA Accepted version: https://hdl.handle.net/10281/315998
• Probabilistic Models of k-mer Frequencies.
  A. Gafurov, T. Vinař, B. Brejová.
  CiE 2021: Connecting with Computability 2021.
  DOI: https://doi.org/10.1007/978-3-030-80049-9_21
  OA Accepted version: arXiv:2112.15107 [q-bio.QM]
• Beyond the BEST Theorem: Fast Assessment of Eulerian Trails.
  A. Conte, R. Grossi, G. Loukides, N. Pisanti, S.P. Pissis, G. Punzi.
  FCT 2021: Fundamentals of Computation Theory 2021.
  DOI: https://doi.org/10.1007/978-3-030-86593-1_11
  OA Accepted version: https://kclpure.kcl.ac.uk/portal/files/137497875/Fast_Assessment_Eulerian_Trails_TR.pdf
• Bidirectional String Anchors: A New String Sampling Mechanism.
  G. Loukides, S.P. Pissis.
  ESA 2021: European Symposium on Algorithms 2021.
  DOI: https://doi.org/10.4230/lipics.esa.2021.64
• Faster Algorithms for Longest Common Substring.
  P. Charalampopoulos, T. Kociumaka, S.P. Pissis, J. Radoszewski.
  ESA 2021: European Symposium on Algorithms 2021.
  DOI: https://doi.org/10.4230/lipics.esa.2021.30

2020

• Unary Words Have the Smallest Levenshtein k-Neighbourhoods.
  P. Charalampopoulos, S.P. Pissis, J. Radoszewski, T. Waleń, W. Zuba.
  CPM 2020: Combinatorial Pattern Matching 2020.
  DOI: https://doi.org/10.4230/lipics.cpm.2020.10
• String Sanitization Under Edit Distance.
  G. Bernardini, G. Loukides, S.P. Pissis, M. Sweering, H. Chen, N. Pisanti, L. Stougie.
  CPM 2020: Combinatorial Pattern Matching 2020.
  DOI: https://doi.org/10.4230/lipics.cpm.2020.7

Conference presentations

• MALVIRUS: an integrated web application for viral variant calling.
  S. Ciccolella, L. Denti, P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali.
  BBCC 2020.
  DOI (presentation): https://doi.org/10.7490/f1000research.1118377.1
• MALVIRUS: viral variant calling made easy.
  S. Ciccolella, L. Denti, P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali.
  BOSC 2020.
  Material: video

Preprints

• Markov chains improve the significance computation of overlapping genome annotations.
  A. Gafurov, B. Brejová, P. Medvedev.
  bioRxiv 2022.04.07.487119.
  DOI: https://doi.org/10.1101/2022.04.07.487119
• VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples.
  A. Gafurov, A. Baláž, F. Amman, K. Boršová, V. Čabanová, B. Klempa, A. Bergthaler, T. Vinař, B. Brejová.
  medRxiv 2022.06.21.22276717
  DOI: https://doi.org/10.1101/2022.06.21.22276717
• WarpSTR: Determining tandem repeat lengths using raw nanopore signals.
  J. Sitarčík, T. Vinař, B. Brejová, W. Krampl, J. Budiš, J. Radvánszky, M. Lucká.
  bioRxiv 2022.11.05.515275
  DOI: https://doi.org/10.1101/2022.11.05.515275
• Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols.
  B. Brejová, K. Boršová, V. Hodorová, V. Čabanová, A. Gafurov, D. Fričová, M. Neboháčová, T. Vinař, B. Klempa, J. Nosek.
  medRxiv 2021.05.12.21256693
  DOI: https://doi.org/10.1101/2021.05.12.21256693
• Dynamic Pooling Improves Nanopore Base Calling Accuracy.
  V. Boža, P. Perešíni, B. Brejová, T. Vinař.
  arXiv: 2105.07520 [cs.LG, q-bio.GN]
• B.1.258Δ, a SARS-CoV-2 variant with ΔH69/ΔV70 in the Spike protein circulating in the Czech Republic and Slovakia.
  B. Brejová, V. Hodorová, K. Boršová, V. Čabanová, L. Reizigová, E.D. Paul, P. Čekan, B. Klempa, J. Nosek, T. Vinař.
  arXiv: 2102.04689 [q-bio.OT]
• PHERI – Phage Host Exploration pipeline.
  A. Baláž, M. Kajsík, J. Budiš, T. Szemeš, J. Turňa.
  bioRxiv 2020.05.13.093773
  DOI: https://doi.org/10.1101/2020.05.13.093773
• Nanopore Base Calling on the Edge.
  P. Perešíni, V. Boža, B. Brejová, T. Vinař.
  arXiv: 2011.04312 [cs.LG, q-bio.GN]
• MALVIRUS: an integrated web application for viral variant calling.
  S. Ciccolella, L. Denti, P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali.
  bioRxiv 2020.05.05.076992
  DOI: https://doi.org/10.1101/2020.05.05.076992

Posters

• Scalable variant detection in pangenome models.
  F. Porto, F. Villani, A. Guarracino, C. Fischer, H. Chen, R.W. Williams, V. Colonna, G. Della Vedova, E. Garrison, P. Prins.
  T2T HPRC 2020.