ALgorithms for PAngenome Computational Analysis

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Data Management Plan

Compilation of a data management plan.

Communications and public engagement report

Compilation of a report on communications and public engagement (WP5).

Final scientific advances report on WP1

Compilation of a report on the scientific advances of WP1 (Primary CPG)

Final scientific advances report on WP2

Compilation of a report on the scientific advances of WP2 (Evolutionary/Comparative CPG).

Final scientific advances report on WP3

Compilation of a report on the scientific advances of WP3 (Translational CPG).

Collective scientific advances report 3

Joint report of WP1-3 on their scientific advances

Report on training activities and career fair

Compilation of a report on training activities and career fair (WP4).

Scientific publications report

Compilation of a report on scientific publications (WP5).

Collective scientific advances report 1

Joint report of WP13 on their scientific advances

Collective scientific advances report 2

Joint report of WP1-3 on their scientific advances

Summer school 2

Title: Pan-genome applicationsPreliminary course topics: (i) Building and comparing recombination networks (P.Bonizzoni UNIMIB, 1 ECTS); (ii) Advanced Linear Programming (L.Stougie NWO-I, 1 ECTS); (iii) Cancer evolution (G.Della Vedova UNIMIB, 0.5 ECTS); (iv) Probabilistic and machine learning methods (T.Vinař UKBA, 0.5 ECTS); (v) Reproducible research (J.Köster, 0.5 ECTS); (vi) Innovation, entrepreneurship, and commercial exploitation (F.Perraudeau PENDULUM, 0.5 ECTS). The school will include a multi-session hackathon where groups of participants will analyze pan-genomic data sets provided by non-academic partners (analysis leaders Z.Iqbal EMBL, F.Perraudeau PENDULUM, P.Bonizzoni UNIMIB).

Summer school 1

Title: Algorithmic techniques in pan-genomicsPreliminary course topics: (i) Data structures for genomic variants (R.Durbin UCAM, T.Marschall UDUS, 0.5 ECTS), (ii) Pan-genome storage and search (J.Stoye UNIBI, 1 ECTS); (iii) Alignments of pan-genome graphs (V.Mäkinen UHEL, 1 ECTS); (iv) Research dissemination, open science and open access (T.Marschall UDUS, 0.5 ECTS); (v) Project management (J.Budiš GENETON, 0.5 ECTS); (vi) Scientific writing and research dissemination (A.Schönhuth UNIBI, 0.5 ECTS). The school will include a multi-session hackathon where groups of participants will analyze pan-genomic data sets provided by non- academic partners (analysis leaders B.Brejová UK BA, J.Budiš GENETON, T.Marschall UDUS)

Winter wet lab

Title: Collaborating with wet-lab biologistsThe winter school will give participants hands-on laboratory experience, allowing them to better understand wet-lab possibilities and limitations and become more effective collaborators with wet-lab biologists. Preliminary topics include: (i) Basic laboratory techniques, DNA extraction (UK BA, 0.5 ECTS); (ii) Sequencing with Oxford Nanopore devices: from DNA sample to sequences (XXX ONT, 1 ECTS), (iii) Illumina sequencing for clinical diagnostics (J.Budiš GENETON, 1 ECTS), (iv) Data analysis challenges (T.Vinař UK BA, 0.5 ECTS), (v) Soft-skills: Efficient interdisciplinary communication (Z.Iqbal EMBL, 0.5 ECTS), (vi) Soft-skills: Intellectual Property: Management and issues (W.Pirovano BC, 0.5 ECTS).

Annual workshop 2

Title: Pan-genome sequencing and analysisThree half-days will be dedicated to scientific courses, one half-day to the soft-skills course. Other activities will include business meeting (afternoon of day 1), hackathon (afternoon of day 3), and problem sessions (evenings). The preliminary topics of the courses: (i) Metagenome assembly and analysis (R.Chikhi IP, 1 ECTS); (ii) Latest pan-genome research trends (seminars by advisory board members, 0.5 ECTS); (iii) Soft-skills: Improving research impact with social media presence (P. Peterlongo INRIA, 0.5 ECTS), (iv) Peer Community in bioinformatics: a new approach to reviewing and publishing (C. Scornavacca, CNRS, 0.5).

Supervisory Board of the network

Appoint a supervisory board of the ITN

Annual workshop 3

Title: Large-scale pan-genomicsThree half-days will be dedicated to scientific courses, one half-day to the soft-skills course. Other activities will include business meeting (afternoon of day 1), hackathon (afternoon of day 3), and problem sessions (evenings). The preliminary topics of the courses: (i) Pan-genome data structure based AI/Machine Learning. (A.Schönhuth UNIBI, 1 ECTS); (ii) Distributed processing of large genomic data (K.Heljanko UHEL, 0.5 ECTS); (iii) Soft-skills: Communication techniques for research dissemination (L.Stougie NWO-I, 0.5 ECTS).

Annual Workshop 1

Title Challenges of computational pangenomicsThree halfdays will be dedicated to scientific courses one halfday to the softskills course Other activities will include business meeting afternoon of day 1 hackathon afternoon of day 3 and problem sessions evenings The preliminary topics of the coursesi Overview of existing methods and tools for pangenomics SPissis NWOI E Rivals CNRS JStoye UNIBI 1 ECTS ii Overview of open challenges for pangenomics ASchonhuth UNIBI RDurbin UCAM TMarschall UDUS 05 ECTS iii Softskills Ethics in research research integrity Gender and Diversity Issues NPisanti UNIPI PBonizzoni UNIMIB 05 ECTS

Pubblicazioni

Substring Complexity in Sublinear Space

Autori: Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis
Pubblicato in: Leibniz International Proceedings in Informatics (LIPIcs), Numero 283, 2023, Pagina/e 12:1-12:19, ISBN 978-3-95977-289-1
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2023.12

Periodicity of Degenerate Strings

Autori: Estéban Gabory and Eric Rivals and Michelle Sweering and Hilde Verbeek and Pengfei Wang
Pubblicato in: Proceedings of the Prague Stringology Conference 2023, 2023, Pagina/e 42-56, ISBN 978-80-01-07206-6
Editore: Prague Stringology Club

Pattern Masking for Dictionary Matching

Autori: Panagiotis Charalampopoulos and Huiping Chen and Peter Christen and Grigorios Loukides and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski
Pubblicato in: 32nd International Symposium on Algorithms and Computation (ISAAC 2021), Numero 212, 2021, Pagina/e 65:1--65:19, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2021.65

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Autori: Park, Sangsoo; Park, Sung Gwan; Cazaux, Bastien; Park, Kunsoo; Rivals, Eric
Pubblicato in: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numero 191, 2021, Pagina/e 22:1--22:9, ISBN 978-3-95977-186-3
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.22

On Strings Having the Same Length- k Substrings

Autori: Bernardini, Giulia and Conte, Alessio and Gabory, Esteban and Grossi, Roberto and Loukides, Grigorios and Pissis, Solon P. and Punzi, Giulia and Sweering, Michelle
Pubblicato in: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numero 223, 2022, Pagina/e 16:1--16:17, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.16

Approximate Suffix-Prefix Dictionary Queries

Autori: Wiktor Zuba and Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan
Pubblicato in: 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024), Numero Vol 306, 2024, Pagina/e 85:1–85:18
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.mfcs.2024.85

Space-Efficient Indexes for Uncertain Strings

Autori: Esteban Gabory, Chang Liu, Grigorios Loukides, Solon P. Pissis, Wiktor Zuba
Pubblicato in: 2024 IEEE 40th International Conference on Data Engineering (ICDE), 2024, Pagina/e 4828-4842
Editore: IEEE
DOI: 10.1109/icde60146.2024.00367

Linear Time Construction of Indexable Elastic Founder Graphs

Autori: Nicola Rizzo and Veli Mäkinen
Pubblicato in: International Workshop on Combinatorial Algorithms: Combinatorial Algorithms, Numero 13270, 2022, Pagina/e 480--493, ISBN 978-3-031-06678-8
Editore: Springer International Publishing
DOI: 10.1007/978-3-031-06678-8_35

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

Autori: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis, Hilde Verbeek
Pubblicato in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Pagina/e 162-177
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_11

Utility-Oriented String Mining

Autori: Giulia Bernardini, Huiping Chen, Alessio Conte, Roberto Grossi, Veronica Guerrini, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis
Pubblicato in: Proceedings of the 2024 SIAM International Conference on Data Mining (SDM), 2024, Pagina/e 190-198
Editore: Society for Industrial and Applied Mathematics
DOI: 10.1137/1.9781611978032.22

Faster Algorithms for Longest Common Substring

Autori: Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski
Pubblicato in: 29th Annual European Symposium on Algorithms (ESA 2021), Numero 204, 2021, Pagina/e 30:1--30:17, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast assessment of Eulerian Trails

Autori: Conte, Alessio; Grossi, Roberto; Loukides, Grigorios; Pisanti, Nadia; Pissis, Solon P.; Punzi, Giulia; Bampis, Evripidis; Pagourtzis, Aris
Pubblicato in: Fundamentals of Computation Theory, 23rd International Symposium (FCT), Numero 12867, 2021, Pagina/e 162--175, ISBN 978-3-030-86593-1
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Indexable Elastic Founder Graphs of Minimum Height

Autori: Nicola Rizzo and Veli Mäkinen
Pubblicato in: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numero 223, 2022, Pagina/e 480--493, ISBN 978-3-031-06678-8
Editore: Springer International Publishing
DOI: 10.4230/lipics.cpm.2022.19

Size-Constrained Weighted Ancestors with Applications

Autori: Philip Bille and Yakov Nekrich and Solon P. Pissis
Pubblicato in: 19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024), Numero Vol 294, 2024, Pagina/e 14:1–14:12
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.swat.2024.14

Longest Palindromic Substring in Sublinear Time

Autori: Charalampopoulos, Panagiotis; Pissis, Solon P.; Radoszewski, Jakub; Bannai, Hideo; Holub, Jan
Pubblicato in: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numero 223, 2022, Pagina/e 20:1--20:9, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.20

A new string sampling mechanism

Autori: Loukides, Grigorios; Pissis, Solon P.; Mutzel, Petra; Pagh, Rasmus; Herman, Grzegorz
Pubblicato in: 29th Annual European Symposium on Algorithms (ESA 2021) . , 64 , Leibniz International Proceedings in Informatics, LIPIcs , vol. 204 , Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing , pp. 1-21 , 29th Annual European Symposium on Algorithms, ESA 2021 , Vitual, Lisbon , Portugal , 6/09/21 . https://doi.org/10.4230/LIPIcs.ESA.2021.64, Numero 204, 2021, Pagina/e 64:1--64:21, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Convergence of the Number of Period Sets in Strings

Autori: Eric Rivals, Michelle Sweering, and Pengfei Wang
Pubblicato in: Leibniz International Proceedings in Informatics (LIPIcs), Numero 261, 2023, Pagina/e 100:1--100:14, ISBN 978-3-95977-278-5
Editore: Schloss Dagstuhl –- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.icalp.2023.100

Optimal Sequence Alignment to ED-Strings

Autori: Njagi Moses Mwaniki and Nadia Pisanti
Pubblicato in: ISBRA 2022: Bioinformatics Research and Applications, Numero 13760, 2023, Pagina/e 204–216, ISSN 0302-9743
Editore: Springer Verlag
DOI: 10.1007/978-3-031-23198-8_19

A BWT-Based Algorithm for Random de Bruijn Sequence Construction

Autori: Zsuzsanna Lipták, Luca Parmigiani
Pubblicato in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Pagina/e 130-145
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_9

Making de Bruijn Graphs Eulerian

Autori: Bernardini, Giulia; Chen, Huiping; Loukides, Grigorios; Pissis, Solon P.; Stougie, Leen; Sweering, Michelle; Bannai, Hideo; Holub, Jan
Pubblicato in: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numero 223, 2022, Pagina/e 12:1-12:18, ISBN 978-3-95977-234-1
Editore: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Suffix-prefix queries on a dictionary

Autori: Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan and Wiktor Zuba
Pubblicato in: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numero Vol 259, 2023, Pagina/e 21:1--21:20, ISBN 978-3-95977-276-1
Editore: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Wheeler Maps

Autori: Andrej Baláž, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Pubblicato in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Pagina/e 178-192
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_12

Faster Maximal Exact Matches with Lazy LCP Evaluation

Autori: Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Pubblicato in: 2024 Data Compression Conference (DCC), 2024, Pagina/e 123-132
Editore: IEEE
DOI: 10.1109/dcc58796.2024.00020

Fast Exact String to D-Texts Alignments

Autori: Njagi Mwaniki, Erik Garrison, Nadia Pisanti
Pubblicato in: Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024, Pagina/e 70-79
Editore: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0011666900003414

Elastic-Degenerate String Matching with 1 Error

Autori: Giulia Bernardini; Esteban Gabory; Solon P. Pissis; Leen Stougie; Michelle Sweering; Wiktor Zuba
Pubblicato in: Latin American Symposium on Theoretical Informatics, Numero 13568, 2022, Pagina/e 20–37, ISBN 978-3-031-20624-5
Editore: Springer International Publishing
DOI: 10.48550/arxiv.2209.01095

On-Line Pattern Matching on D-Texts

Autori: Nadia Pisanti
Pubblicato in: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numero 191, 2021, Pagina/e 3:1--3:2, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.3

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

Autori: Philip Bille and Inge Li Gørtz and Moshe Lewenstein and Solon P. Pissis and Eva Rotenberg and Teresa Anna Steiner
Pubblicato in: 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024), Numero Vol 289, 2024, Pagina/e 16:1–16:21
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.16

Approximate Circular Pattern Matching

Autori: Panagiotis Charalampopoulos and Tomasz Kociumaka and Jakub Radoszewski and Solon P. Pissis and Wojciech Rytter and Tomasz Waleń and Wiktor Zuba
Pubblicato in: 30th Annual European Symposium on Algorithms (ESA 2022), Numero 244, 2022, Pagina/e 35:1--35:19, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.35

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Autori: Askar Gafurov, Tomáš Vinař, Broňa Brejová
Pubblicato in: Lecture Notes in Computer Science, Connecting with Computability, 2021, Pagina/e 227-236
Editore: Springer International Publishing
DOI: 10.1007/978-3-030-80049-9_21

Prefix-free graphs and suffix array construction in sublinear space

Autori: Baláž, Andrej; Petescia, Alessia
Pubblicato in: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numero 1, 2023, Pagina/e 232-241
Editore: CEUR Workshop Proceedings
DOI: 10.48550/arxiv.2306.14689

Chaining of Maximal Exact Matches in Graphs

Autori: Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Pubblicato in: Lecture Notes in Computer Science, String Processing and Information Retrieval, 2023, Pagina/e 353-366
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-43980-3_29

Comparing elastic-degenerate strings: Algorithms, lower bounds, and applications

Autori: Esteban Gabory and Moses Njagi Mwaniki and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski and Michelle Sweering and Wiktor Zuba
Pubblicato in: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numero Vol 259, 2023, Pagina/e 11:1--11:20, ISBN 978-3-95977-276-1
Editore: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.11

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Autori: Konstantinn Bonnet and Tobias Marschall and Daniel Doerr
Pubblicato in: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numero 242, 2022, Pagina/e 6:1--6:23, ISSN 1868-8969
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.6

Prefix-free parsing for building large tunnelled Wheeler graphs

Autori: Adrián Goga and Andrej Baláž
Pubblicato in: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numero Vol 242, 2022, Pagina/e 18:1--18:12, ISBN 978-3-95977-243-3
Editore: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.18

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

Autori: Rocco Ascone and Giulia Bernardini and Alessio Conte and Massimo Equi and Esteban Gabory and Roberto Grossi and Nadia Pisanti
Pubblicato in: 24th International Workshop on Algorithms in Bioinformatics (WABI 2024), Numero Vol 312, 2024, Pagina/e 14:1–14:21
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2024.14

Identifying Clusters in Graph Representations of Genomes

Autori: Eva Herencsárová, Broňa Brejová
Pubblicato in: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numero 1, 2023, Pagina/e 232-241
Editore: CEUR Workshop Proceedings
DOI: 10.1101/2023.07.20.549917v1

Approximate Circular Pattern Matching Under Edit Distance

Autori: Panagiotis Charalampopoulos and Solon P. Pissis and Jakub Radoszewski and Wojciech Rytter and Tomasz Waleń and Wiktor Zuba
Pubblicato in: 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024), Numero Vol 289, 2024, Pagina/e 24:1–24:22
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.24

Minimizing the Minimizers via Alphabet Reordering

Autori: Verbeek, Hilde and Ayad, Lorraine A.K. and Loukides, Grigorios and Pissis, Solon P.
Pubblicato in: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Numero Vol 296, 2024, Pagina/e 28:1--28:13
Editore: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.28

Finding Maximal Exact Matches in Graphs

Autori: Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen
Pubblicato in: Leibniz International Proceedings in Informatics (LIPIcs), Numero 273, 2023, Pagina/e 10:1--10:17, ISBN 978-3-95977-294-5
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2023.10

Connecting de Bruijn Graphs

Autori: Giulia Bernardini and Huiping Chen and Inge Li Gørtz and Christoffer Krogh and Grigorios Loukides and Solon P. Pissis and Leen Stougie and Michelle Sweering
Pubblicato in: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Numero Vol 296, 2024, Pagina/e 6:1–6:16
Editore: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.6

Text Indexing for Long Patterns: Anchors are All you Need

Autori: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Pubblicato in: Proceedings of the VLDB Endowment, Numero 16, 2023, Pagina/e 2117-2131, ISSN 2150-8097
Editore: Proceedings VLDB Endowment
DOI: 10.14778/3598581.3598586

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Autori: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Pubblicato in: Frontiers in Genetics, Numero 13, 2022, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Identification of transposable element families from pangenome polymorphisms

Autori: Pío Sierra, Richard Durbin
Pubblicato in: Mobile DNA, Numero 15, 2024, ISSN 1759-8753
Editore: BioMed Central
DOI: 10.1186/s13100-024-00323-y

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

Autori: Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Pubblicato in: BMC Genomics, Numero 25, 2024, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-024-10267-5

Panacus: fast and exact pangenome growth and core size estimation

Autori: Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
Pubblicato in: Bioinformatics, Numero 40, 2024, ISSN 1367-4811
Editore: Bioinformatics
DOI: 10.1093/bioinformatics/btae720

EPIK: precise and scalable evolutionary placement with informativek-mers

Autori: Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals
Pubblicato in: Bioinformatics, Numero 39, 2024, ISSN 1367-4811
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btad692

Palidis: fast discovery of novel insertion sequences

Autori: Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Pubblicato in: Microbial Genomics, Numero 9, 2023, ISSN 2057-5858
Editore: Microbial Genomics
DOI: 10.1099/mgen.0.000917

Computing linkage disequilibrium aware genome embeddings using autoencoders

Autori: Gizem Taş, Timo Westerdijk, Eric Postma, null null, Wouter van Rheenen, Mark K Bakker, Kristel R van Eijk, Maarten Kooyman, Ahmad Al Khleifat, Alfredo Iacoangeli, Nicola Ticozzi, Johnathan Cooper-Knock, Marta Gromicho, Siddharthan Chandran, Karen E Morrison, Pamela J Shaw, John Hardy, Michael Sendtner, Thomas Meyer, Nazli Başak, Isabella Fogh, Adriano Chiò, Andrea Calvo, Elisabetta Pupillo, Gia
Pubblicato in: Bioinformatics, Numero 40, 2024, ISSN 1367-4811
Editore: Bioinformatics
DOI: 10.1093/bioinformatics/btae326

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Autori: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Pubblicato in: BMC Bioinformatics, Numero 25, 2024, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-024-05958-5

kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections

Autori: Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo
Pubblicato in: Bioinformatics Advances, Numero 2, 2022, ISSN 2635-0041
Editore: Oxford University Press
DOI: 10.1093/bioadv/vbac029

Efficient computation of sequence mappability

Autori: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Pubblicato in: Algorithmica, Numero 84, 2022, Pagina/e 1418–1440, ISSN 1432-0541
Editore: Springer Science
DOI: 10.48550/arxiv.1807.11702

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

Autori: Grigorios Loukides, Solon P. Pissis, Michelle Sweering
Pubblicato in: IEEE Transactions on Knowledge and Data Engineering, Numero 35, 2023, Pagina/e 11093-11111, ISSN 1041-4347
Editore: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3231780

Internal shortest absent word queries in constant time and linear space

Autori: Golnaz Badkobeh and Panagiotis Charalampopoulos and Dmitry Kosolobov and Solon P. Pissis
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High-quality metagenome assembly from long accurate reads with metaMDBG

Autori: Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
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FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species

Autori: Sauer, Lena,; Cánovas, Rodrigo; Roche, Daniel,; Shams-Eldin, Hosam; Ravel, Patrice; Colinge, Jacques; Schwarz, Ralph T.; Mamoun, Choukri Ben; Rivals, Eric; Cornillot, Emmanuel
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Maximal degenerate palindromes with gaps and mismatches

Autori: Mai Alzamel, Christopher Hampson, Costas S. Iliopoulos, Zara Lim, Solon Pissis, Dimitrios Vlachakis, Steven Watts
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WarpSTR: determining tandem repeat lengths using raw nanopore signals

Autori: Jozef Sitarčík, Tomáš Vinař, Broňa Brejová, Werner Krampl, Jaroslav Budiš, Ján Radvánszky, Mária Lucká
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Efficient mapping of accurate long reads in minimizer space with mapquik

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Hybrids of RNA viruses and viroid-like elements replicate in fungi

Autori: Marco Forgia, Beatriz Navarro, Stefania Daghino, Amelia Cervera, Andreas Gisel, Silvia Perotto, Dilzara N. Aghayeva, Mary F. Akinyuwa, Emanuela Gobbi, Ivan N. Zheludev, Robert C. Edgar, Rayan Chikhi, Massimo Turina, Artem Babaian, Francesco Di Serio, Marcos de la Peña
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Revisiting pangenome openness with k-mers

Autori: Luca Parmigiani, Roland Wittler, Jens Stoye
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Comparing methods for constructing and representing human pangenome graphs

Autori: Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi
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A tutorial on data structures and their applications

Autori: Baaijens, Jasmijn A.; Bonizzoni, Paola; Boucher, Christina; Della Vedova, Gianluca; Pirola, Yuri; Rizzi, Raffaella; Sirén, Jouni
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Pattern Masking for Dictionary Matching: Theory and Practice

Autori: Panagiotis Charalampopoulos, Huiping Chen, Peter Christen, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski
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RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape

Autori: Nico Cillari, Giuseppe Neri, Nadia Pisanti, Paolo Milazzo, Ugo Borello
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Comparative genome analysis using sample-specific string detection in accurate long reads

Autori: Parsoa Khorsand, Luca Denti, null null, Paola Bonizzoni, Rayan Chikhi, Fereydoun Hormozdiari
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Maximum-scoring path sets on pangenome graphs of constant treewidth

Autori: Broňa Brejová, Travis Gagie, Eva Herencsárová, Tomáš Vinař
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μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data

Autori: Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
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Autori: Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi
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Elastic founder graphs improved and enhanced

Autori: Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
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kmdiff, large-scale and user-friendly differential k-mer analyses

Autori: Téo Lemane; Rayan Chikhi; Pierre Peterlongo
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Critical Assessment of Metagenome Interpretation: the second round of challenges

Autori: Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluç, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas,
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Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Autori: Stefano Porrelli, Michèle Gerbault-Seureau, Roberto Rozzi, Rayan Chikhi, Manon Curaudeau, Anne Ropiquet, Alexandre Hassanin
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Automated prediction of the clinical impact of structural copy number variations

Autori: M. Gažiová and T. Sládeček and O. Pös and M. Števko and W. Krampl and Z. Pös and R. Hekel and M. Hlavačka and M. Kucharík and J. Radvánszky and J. Budiš and T. Szemes
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Applying rearrangement distances to enable plasmid epidemiology with pling

Autori: Daria Frolova, Leandro Lima, Leah Wendy Roberts, Leonard Bohnenkämper, Roland Wittler, Jens Stoye, Zamin Iqbal
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Predicting the prevalence of complex genetic diseases from individual genotype profiles using capsule networks

Autori: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
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Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation

Autori: Antonella Teramo and Andrea Binatti and Elena Ciabatti and Gianluca Schiavoni and Giulia Tarrini and Gregorio Baril`a and Giulia Calabretto and Cristina Vicenzetto and Vanessa Rebecca Gasparini and Monica Facco and Iacopo Petrini and Roberto Grossi and Nadia Pisanti and Stefania Bortoluzzi and Brunangelo Falini and Enrico Tiacci and Sara Galimberti and Gianpietro Semenzato and Renato Zambello
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HyLight: Strain aware assembly of low coverage metagenomes

Autori: Xiongbin Kang, Wenhai Zhang, Yichen Li, Xiao Luo, Alexander Schönhuth
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StrainXpress: strain aware metagenome assembly from short reads

Autori: Xiongbin Kang and Xiao Luo and Alexander Schönhuth
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The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

Autori: Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi
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Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations

Autori: 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
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VeChat: correcting errors in long reads using variation graphs

Autori: Xiao Luo and Xiongbin Kang and Alexander Schönhuth
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Finding maximal exact matches in graphs

Autori: Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Pubblicato in: Algorithms for Molecular Biology, Numero 19, 2024, ISSN 1748-7188
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aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

Autori: Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
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Gaps and complex structurally variant loci in phased genome assemblies

Autori: David Porubsky, Mitchell R. Vollger, William T. Harvey, Allison N. Rozanski, Peter Ebert, Glenn Hickey, Patrick Hasenfeld, Ashley D. Sanders, Catherine Stober, null null, Jan O. Korbel, Benedict Paten, Tobias Marschall, Evan E. Eichler
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Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

Autori: Jorge Avila Cartes; Santosh Anand; Simone Ciccolella; Paola Bonizzoni; Gianluca Della Vedova
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All-pairs suffix/prefix in optimal time using Aho-Corasick space

Autori: Solon Pissis; Grigorios Loukides
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Constructing founder sets under allelic and non-allelic homologous recombination

Autori: Konstantinn Bonnet, Tobias Marschall, Daniel Doerr
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Strainline: full-length de novo viral haplotype reconstruction from noisy long reads

Autori: Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander
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Hide and Mine in Strings: Hardness, Algorithms, and Experiments

Autori: Giulia Bernardini, Alessio Conte, Garance Gourdel, Roberto Grossi, Grigorios Loukides, Nadia Pisanti, Solon Pissis, Giulia Punzi, Leen Stougie, Michelle Sweering
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Clustering sequence graphs

Autori: Haodi Zhong; Grigorios Loukides; Solon P. Pissis
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Considerations in the search for epistasis

Autori: Marleen Balvert, Johnathan Cooper-Knock, Julian Stamp, Ross P. Byrne, Soufiane Mourragui, Juami van Gils, Stefania Benonisdottir, Johannes Schlüter, Kevin Kenna, Sanne Abeln, Alfredo Iacoangeli, Joséphine T. Daub, Brian L. Browning, Gizem Taş, Jiajing Hu, Yan Wang, Elham Alhathli, Calum Harvey, Luna Pianesi, Sara C. Schulte, Jorge González-Domínguez, Erik Garrisson, null null, Ammar Al-Chalab
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A draft human pangenome reference

Autori: Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, Jordan M. Eizenga, Xiaowen Feng, Christian Fischer, Robert S. Fulton, Shilpa Garg, Cristian Groza, Andrea Guarracino, William T. Harvey, Simon Heumos, Kerstin Howe, Miten Jain, Tsun
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DOI: 10.1038/s41586-023-05896-x

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

Autori: Beatriz Willink, Kalle Tunström, Sofie Nilén, Rayan Chikhi, Téo Lemane, Michihiko Takahashi, Yuma Takahashi, Erik I. Svensson, Christopher West Wheat
Pubblicato in: Nature Ecology & Evolution, Numero 8, 2024, Pagina/e 83-97, ISSN 2397-334X
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DOI: 10.1038/s41559-023-02243-1

RecGraph: recombination-aware alignment of sequences to variation graphs

Autori: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
Pubblicato in: Bioinformatics, Numero 40, 2024, ISSN 1367-4811
Editore: Oxford University Press (OUP)
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Computing Phylo-k-Mers

Autori: Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi
Pubblicato in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numero 20, 2024, Pagina/e 2889-2897, ISSN 1545-5963
Editore: IEEE Computer Society
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Seedability: optimizing alignment parameters for sensitive sequence comparison

Autori: Lorraine A K Ayad, Rayan Chikhi, Solon P Pissis
Pubblicato in: Bioinformatics Advances, Numero 3, 2023, ISSN 2635-0041
Editore: Oxford University Press
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SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads

Autori: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
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Hybrid-hybrid correction of errors in long reads with HERO

Autori: Xiongbin Kang, Jialu Xu, Xiao Luo, Alexander Schönhuth
Pubblicato in: Genome Biology, Numero 24, 2023, ISSN 1474-760X
Editore: BioMed Central
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phasebook: haplotype-aware de novo assembly of diploid genomes from long reads

Autori: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Pubblicato in: Genome Biology, Numero 22, 2021, Pagina/e 1--26, ISSN 1474-760X
Editore: BioMed Central (BMC)
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dipwmsearch: a Python package for searching di-PWM motifs

Autori: Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals
Pubblicato in: Bioinformatics, Numero 39, 2023, ISSN 1367-4811
Editore: Bioinformatics
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Pangenome comparison via ED strings

Autori: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Pubblicato in: Frontiers in Bioinformatics, Numero 4, 2024, ISSN 2673-7647
Editore: Frontiers in Bioinformatics
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Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA

Autori: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Pubblicato in: Nature Computational Science, Numero 4, 2024, Pagina/e 104-109, ISSN 2662-8457
Editore: Nature Computational Science
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Mapping-friendly sequence reductions: Going beyond homopolymer compression

Autori: Luc Blassel and Paul Medvedev and Rayan Chikhi
Pubblicato in: iScience, Numero 25 (11), 2022, Pagina/e 105305, ISSN 2589-0042
Editore: Cell Press
DOI: 10.1016/j.isci.2022.105305

Elastic-Degenerate String Matching with 1 Error or Mismatch

Autori: Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Pubblicato in: Theory of Computing Systems, Numero 68, 2024, Pagina/e 1442-1467, ISSN 1432-4350
Editore: Springer Verlag
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Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autori: Giulia Bernardini and Paweł Gawrychowski and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone
Pubblicato in: SIAM Journal on Computing, Numero 51 (3), 2022, Pagina/e 549--576, ISSN 1095-7111
Editore: Society for Industrial & Applied Mathematics (SIAM)
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Constructing phylogenetic networks via cherry picking and machine learning

Autori: Giulia Bernardini, Leo van Iersel, Esther Julien, Leen Stougie
Pubblicato in: Algorithms for Molecular Biology, Numero 18, 2024, ISSN 1748-7188
Editore: BioMed Central
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Generating Synthetic Genotypes using Diffusion Models

Autori: Philip Kenneweg, Raghuram Dandinasivara, Xiao Luo, Barbara Hammer, Alexander Schönhuth
Pubblicato in: 2025
Editore: Cornell University
DOI: 10.48550/arxiv.2412.03278

PanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs

Autori: Wenhai Zhang, Yuansheng Liu, Jialu Xu, Enlian Chen, Alexander Schönhuth, Xiao Luo
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.15.623887

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Autori: Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
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On-Line Pattern Matching on D-Texts (Invited Talk)

Autori: Pisanti, Nadia
Pubblicato in: Leibniz International Proceedings in Informatics (LIPIcs), vol 191, Numero 1, 2021, Pagina/e 3:1--3:2, ISBN 978-3-95977-186-3
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MCHelper automatically curates transposable element libraries across eukaryotic species

Autori: Simon Orozco-Arias, Pío Sierra, Richard Durbin, Josefa González
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.10.17.562682

Incremental computation of the set of period sets

Autori: Eric Rivals
Pubblicato in: 2024
Editore: Cornell University
DOI: 10.48550/arxiv.2410.12077

ChoruMM: a versatile multi-components mixed model for bacterial-GWAS

Autori: Arthur Frouin, Fabien Laporte, Lukas Hafner, Mylene Maury, Zachary R. McCaw, Hanna Julienne, Léo Henches, Rayan Chikhi, Marc Lecuit, Hugues Aschard
Pubblicato in: 2023
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.03.28.534531

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

Autori: Miguel Vasconcelos Almeida, Moritz Blumer, Chengwei Ulrika Yuan, Pío Sierra, Jonathan L. Price, Fu Xiang Quah, Aleksandr Friman, Alexandra Dallaire, Grégoire Vernaz, Audrey L. K. Putman, Alan M. Smith, Domino A. Joyce, Falk Butter, Astrid D. Haase, Richard Durbin, M. Emília Santos, Eric A. Miska
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.01.587621

DiVerG: Scalable Distance Index for Validation of Paired-End Alignments in Sequence Graphs

Autori: Ali Ghaffaari, Alexander Schönhuth, Tobias Marschall
Pubblicato in: 2025
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.12.637964

Cdbgtricks: Strategies to update a compacted de Bruijn graph

Autori: Khodor Hannoush, Camille Marchet, Pierre Peterlongo
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.05.24.595676

Counting overlapping pairs of strings

Autori: Eric Rivals, Pengfei Wang
Pubblicato in: 2024
Editore: Cornell University
DOI: 10.48550/arxiv.2405.09393

kmindex and ORA: indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets

Autori: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.31.543043

Unlocking the microblogging potential for science and medicine

Autori: Aditya Sarkar, Augustin Giros, Louis Mockly, Jaden Moore, Andrew Moore, Anish Nagareddy, Boyang Fu, Andrada Fiscutean, Karishma Chhugani, Nicholas Darci-Maher, Yesha M. Patel, Varuni Sarwal, Yutong Chang, Srishti Ginjala, Lana X. Garmire, Riyue Bao, Sriram Sankararaman, Rayan Chikhi, Serghei Mangul
Pubblicato in: 2022
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.04.22.488804

Petascale Homology Search for Structure Prediction

Autori: Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger
Pubblicato in: 2023
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.10.548308

Methods for Pangenomic Core Detection

Autori: Tizian Schulz, Luca Parmigiani, Andreas Rempel, Jens Stoye
Pubblicato in: Methods in Molecular Biology, Comparative Genomics, 2024, Pagina/e 73-106
Editore: Springer US
DOI: 10.1007/978-1-0716-3838-5_4

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