ALgorithms for PAngenome Computational Analysis

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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

Publications

Substring Complexity in Sublinear Space

Author(s): Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis
Published in: Leibniz International Proceedings in Informatics (LIPIcs), Issue 283, 2023, Page(s) 12:1-12:19, ISBN 978-3-95977-289-1
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2023.12

Periodicity of Degenerate Strings

Author(s): Estéban Gabory and Eric Rivals and Michelle Sweering and Hilde Verbeek and Pengfei Wang
Published in: Proceedings of the Prague Stringology Conference 2023, 2023, Page(s) 42-56, ISBN 978-80-01-07206-6
Publisher: Prague Stringology Club

Pattern Masking for Dictionary Matching

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

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

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

On Strings Having the Same Length- k Substrings

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

Approximate Suffix-Prefix Dictionary Queries

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

Space-Efficient Indexes for Uncertain Strings

Author(s): Esteban Gabory, Chang Liu, Grigorios Loukides, Solon P. Pissis, Wiktor Zuba
Published in: 2024 IEEE 40th International Conference on Data Engineering (ICDE), 2024, Page(s) 4828-4842
Publisher: IEEE
DOI: 10.1109/icde60146.2024.00367

Linear Time Construction of Indexable Elastic Founder Graphs

Author(s): Nicola Rizzo and Veli Mäkinen
Published in: International Workshop on Combinatorial Algorithms: Combinatorial Algorithms, Issue 13270, 2022, Page(s) 480--493, ISBN 978-3-031-06678-8
Publisher: Springer International Publishing
DOI: 10.1007/978-3-031-06678-8_35

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

Author(s): Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis, Hilde Verbeek
Published in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Page(s) 162-177
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_11

Utility-Oriented String Mining

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

Faster Algorithms for Longest Common Substring

Author(s): Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski
Published in: 29th Annual European Symposium on Algorithms (ESA 2021), Issue 204, 2021, Page(s) 30:1--30:17, ISSN 1868-8969
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): Conte, Alessio; Grossi, Roberto; Loukides, Grigorios; Pisanti, Nadia; Pissis, Solon P.; Punzi, Giulia; Bampis, Evripidis; Pagourtzis, Aris
Published in: Fundamentals of Computation Theory, 23rd International Symposium (FCT), 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

Indexable Elastic Founder Graphs of Minimum Height

Author(s): Nicola Rizzo and Veli Mäkinen
Published in: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Issue 223, 2022, Page(s) 480--493, ISBN 978-3-031-06678-8
Publisher: Springer International Publishing
DOI: 10.4230/lipics.cpm.2022.19

Size-Constrained Weighted Ancestors with Applications

Author(s): Philip Bille and Yakov Nekrich and Solon P. Pissis
Published in: 19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024), Issue Vol 294, 2024, Page(s) 14:1–14:12
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.swat.2024.14

Longest Palindromic Substring in Sublinear Time

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

A new string sampling mechanism

Author(s): Loukides, Grigorios; Pissis, Solon P.; Mutzel, Petra; Pagh, Rasmus; Herman, Grzegorz
Published 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, Issue 204, 2021, Page(s) 64:1--64:21, ISSN 1868-8969
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Convergence of the Number of Period Sets in Strings

Author(s): Eric Rivals, Michelle Sweering, and Pengfei Wang
Published in: Leibniz International Proceedings in Informatics (LIPIcs), Issue 261, 2023, Page(s) 100:1--100:14, ISBN 978-3-95977-278-5
Publisher: Schloss Dagstuhl –- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.icalp.2023.100

Optimal Sequence Alignment to ED-Strings

Author(s): Njagi Moses Mwaniki and Nadia Pisanti
Published in: ISBRA 2022: Bioinformatics Research and Applications, Issue 13760, 2023, Page(s) 204–216, ISSN 0302-9743
Publisher: Springer Verlag
DOI: 10.1007/978-3-031-23198-8_19

A BWT-Based Algorithm for Random de Bruijn Sequence Construction

Author(s): Zsuzsanna Lipták, Luca Parmigiani
Published in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Page(s) 130-145
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_9

Making de Bruijn Graphs Eulerian

Author(s): Bernardini, Giulia; Chen, Huiping; Loukides, Grigorios; Pissis, Solon P.; Stougie, Leen; Sweering, Michelle; Bannai, Hideo; Holub, Jan
Published in: 33rd Annual Symposium on 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

Suffix-prefix queries on a dictionary

Author(s): Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan and Wiktor Zuba
Published in: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Issue Vol 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

Wheeler Maps

Author(s): Andrej Baláž, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Published in: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Page(s) 178-192
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_12

Faster Maximal Exact Matches with Lazy LCP Evaluation

Author(s): Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Published in: 2024 Data Compression Conference (DCC), 2024, Page(s) 123-132
Publisher: IEEE
DOI: 10.1109/dcc58796.2024.00020

Fast Exact String to D-Texts Alignments

Author(s): Njagi Mwaniki, Erik Garrison, Nadia Pisanti
Published in: Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024, Page(s) 70-79
Publisher: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0011666900003414

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, Issue 13568, 2022, Page(s) 20–37, ISBN 978-3-031-20624-5
Publisher: Springer International Publishing
DOI: 10.48550/arxiv.2209.01095

On-Line Pattern Matching on D-Texts

Author(s): Nadia Pisanti
Published in: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Issue 191, 2021, Page(s) 3:1--3:2, ISSN 1868-8969
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.3

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

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

Approximate Circular Pattern Matching

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

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Author(s): Askar Gafurov, Tomáš Vinař, Broňa Brejová
Published in: Lecture Notes in Computer Science, Connecting with Computability, 2021, Page(s) 227-236
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-80049-9_21

Prefix-free graphs and suffix array construction in sublinear space

Author(s): Baláž, Andrej; Petescia, Alessia
Published in: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Issue 1, 2023, Page(s) 232-241
Publisher: CEUR Workshop Proceedings
DOI: 10.48550/arxiv.2306.14689

Chaining of Maximal Exact Matches in Graphs

Author(s): Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Published in: Lecture Notes in Computer Science, String Processing and Information Retrieval, 2023, Page(s) 353-366
Publisher: Springer Nature Switzerland
DOI: 10.1007/978-3-031-43980-3_29

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

Author(s): Esteban Gabory and Moses Njagi Mwaniki and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski and Michelle Sweering and Wiktor Zuba
Published in: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Issue Vol 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

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Author(s): Konstantinn Bonnet and Tobias Marschall and Daniel Doerr
Published in: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Issue 242, 2022, Page(s) 6:1--6:23, ISSN 1868-8969
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.6

Prefix-free parsing for building large tunnelled Wheeler graphs

Author(s): Adrián Goga and Andrej Baláž
Published in: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Issue Vol 242, 2022, Page(s) 18:1--18:12, ISBN 978-3-95977-243-3
Publisher: 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

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

Identifying Clusters in Graph Representations of Genomes

Author(s): Eva Herencsárová, Broňa Brejová
Published in: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Issue 1, 2023, Page(s) 232-241
Publisher: CEUR Workshop Proceedings
DOI: 10.1101/2023.07.20.549917v1

Approximate Circular Pattern Matching Under Edit Distance

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

Minimizing the Minimizers via Alphabet Reordering

Author(s): Verbeek, Hilde and Ayad, Lorraine A.K. and Loukides, Grigorios and Pissis, Solon P.
Published in: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Issue Vol 296, 2024, Page(s) 28:1--28:13
Publisher: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.28

Finding Maximal Exact Matches in Graphs

Author(s): Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen
Published in: Leibniz International Proceedings in Informatics (LIPIcs), Issue 273, 2023, Page(s) 10:1--10:17, ISBN 978-3-95977-294-5
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2023.10

Connecting de Bruijn Graphs

Author(s): 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
Published in: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Issue Vol 296, 2024, Page(s) 6:1–6:16
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.6

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, 2023, Page(s) 2117-2131, ISSN 2150-8097
Publisher: Proceedings VLDB Endowment
DOI: 10.14778/3598581.3598586

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

Identification of transposable element families from pangenome polymorphisms

Author(s): Pío Sierra, Richard Durbin
Published in: Mobile DNA, Issue 15, 2024, ISSN 1759-8753
Publisher: 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

Author(s): Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Published in: BMC Genomics, Issue 25, 2024, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-024-10267-5

Panacus: fast and exact pangenome growth and core size estimation

Author(s): Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
Published in: Bioinformatics, Issue 40, 2024, ISSN 1367-4811
Publisher: Bioinformatics
DOI: 10.1093/bioinformatics/btae720

EPIK: precise and scalable evolutionary placement with informativek-mers

Author(s): Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals
Published in: Bioinformatics, Issue 39, 2024, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad692

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, 2023, ISSN 2057-5858
Publisher: Microbial Genomics
DOI: 10.1099/mgen.0.000917

Computing linkage disequilibrium aware genome embeddings using autoencoders

Author(s): 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
Published in: Bioinformatics, Issue 40, 2024, ISSN 1367-4811
Publisher: Bioinformatics
DOI: 10.1093/bioinformatics/btae326

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Author(s): Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Published in: BMC Bioinformatics, Issue 25, 2024, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-024-05958-5

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

Author(s): Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo
Published in: Bioinformatics Advances, Issue 2, 2022, ISSN 2635-0041
Publisher: Oxford University Press
DOI: 10.1093/bioadv/vbac029

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 1432-0541
Publisher: Springer Science
DOI: 10.48550/arxiv.1807.11702

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

Author(s): Grigorios Loukides, Solon P. Pissis, Michelle Sweering
Published in: IEEE Transactions on Knowledge and Data Engineering, Issue 35, 2023, Page(s) 11093-11111, 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 and Panagiotis Charalampopoulos and Dmitry Kosolobov and Solon P. Pissis
Published in: Theoretical Computer Science, Issue 922, 2022, Page(s) 271-282, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2022.04.029

High-quality metagenome assembly from long accurate reads with metaMDBG

Author(s): Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
Published in: Nature Biotechnology, Issue 42, 2024, Page(s) 1378-1383, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01983-6

FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species

Author(s): Sauer, Lena,; Cánovas, Rodrigo; Roche, Daniel,; Shams-Eldin, Hosam; Ravel, Patrice; Colinge, Jacques; Schwarz, Ralph T.; Mamoun, Choukri Ben; Rivals, Eric; Cornillot, Emmanuel
Published in: Malaria Journal, Issue 22, 2023, Page(s) 27-46, ISSN 1475-2875
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Maximal degenerate palindromes with gaps and mismatches

Author(s): Mai Alzamel, Christopher Hampson, Costas S. Iliopoulos, Zara Lim, Solon Pissis, Dimitrios Vlachakis, Steven Watts
Published in: Theoretical Computer Science, Issue 978, 2023, Page(s) 114182, ISSN 0304-3975
Publisher: Elsevier BV
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WarpSTR: determining tandem repeat lengths using raw nanopore signals

Author(s): Jozef Sitarčík, Tomáš Vinař, Broňa Brejová, Werner Krampl, Jaroslav Budiš, Ján Radvánszky, Mária Lucká
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press
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Efficient mapping of accurate long reads in minimizer space with mapquik

Author(s): Bariş Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Published in: Genome Research, 2023, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277679.123

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

Author(s): 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
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
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Revisiting pangenome openness with k-mers

Author(s): Luca Parmigiani, Roland Wittler, Jens Stoye
Published in: Peer Community Journal, Issue 4, 2024, ISSN 2804-3871
Publisher: Peer Community Journal
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Comparing methods for constructing and representing human pangenome graphs

Author(s): Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi
Published in: Genome Biology, Issue 24, 2023, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-023-03098-2

A tutorial on data structures and their applications

Author(s): Baaijens, Jasmijn A.; Bonizzoni, Paola; Boucher, Christina; Della Vedova, Gianluca; Pirola, Yuri; Rizzi, Raffaella; Sirén, Jouni
Published in: Natural Computing, Issue 21, 2022, Page(s) 81--108, ISSN 1572-9796
Publisher: Springer Nature
DOI: 10.1007/s11047-022-09882-6

Pattern Masking for Dictionary Matching: Theory and Practice

Author(s): Panagiotis Charalampopoulos, Huiping Chen, Peter Christen, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski
Published in: Algorithmica, Issue 86, 2024, Page(s) 1948-1978, ISSN 0178-4617
Publisher: Springer Verlag
DOI: 10.1007/s00453-024-01213-8

RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape

Author(s): Nico Cillari, Giuseppe Neri, Nadia Pisanti, Paolo Milazzo, Ugo Borello
Published in: Database, Issue 2024, 2025, ISSN 1758-0463
Publisher: Oxford University Press
DOI: 10.1093/database/baae109

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

Author(s): Parsoa Khorsand, Luca Denti, null null, Paola Bonizzoni, Rayan Chikhi, Fereydoun Hormozdiari
Published in: Bioinformatics Advances, Issue 1, 2022, ISSN 2635-0041
Publisher: Oxford University Press
DOI: 10.1093/bioadv/vbab005

Maximum-scoring path sets on pangenome graphs of constant treewidth

Author(s): Broňa Brejová, Travis Gagie, Eva Herencsárová, Tomáš Vinař
Published in: Frontiers in Bioinformatics, Issue 4, 2024, ISSN 2673-7647
Publisher: Frontiers in Bioinformatics
DOI: 10.3389/fbinf.2024.1391086

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, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad552

Author(s): Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi
Published in: Microbiome Vol 11, Issue 1, 2023, Page(s) 243, ISSN 2049-2618
Publisher: BioMed Central
DOI: 10.1101/2023.01.26.525439

Elastic founder graphs improved and enhanced

Author(s): Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
Published in: Theoretical Computer Science, Issue 982, 2023, Page(s) 114269, ISSN 0304-3975
Publisher: Elsevier BV
DOI: 10.1016/j.tcs.2023.114269

kmdiff, large-scale and user-friendly differential k-mer analyses

Author(s): Téo Lemane; Rayan Chikhi; Pierre Peterlongo
Published in: Bioinformatics, Issue 38, 2022, Page(s) 5443–5445, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac689

Critical Assessment of Metagenome Interpretation: the second round of challenges

Author(s): 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,
Published in: Nature Methods, Issue 19, 2022, Page(s) 429-440, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01431-4

Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina)

Author(s): Stefano Porrelli, Michèle Gerbault-Seureau, Roberto Rozzi, Rayan Chikhi, Manon Curaudeau, Anne Ropiquet, Alexandre Hassanin
Published in: G3 Genes|Genomes|Genetics, Issue 12, 2022, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkac234

Automated prediction of the clinical impact of structural copy number variations

Author(s): 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
Published in: Scientific Reports, Issue 12 (1), 2022, Page(s) 555, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Applying rearrangement distances to enable plasmid epidemiology with pling

Author(s): Daria Frolova, Leandro Lima, Leah Wendy Roberts, Leonard Bohnenkämper, Roland Wittler, Jens Stoye, Zamin Iqbal
Published in: Microbial Genomics, Issue 10, 2024, ISSN 2057-5858
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.1099/mgen.0.001300

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

Author(s): Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Published in: Nature Machine Intelligence, Issue 5, 2024, Page(s) 114-125, ISSN 2522-5839
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s42256-022-00604-2

Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation

Author(s): 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
Published in: Nature Communications, Issue 13 (1), 2022, Page(s) 3298, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31015-x

HyLight: Strain aware assembly of low coverage metagenomes

Author(s): Xiongbin Kang, Wenhai Zhang, Yichen Li, Xiao Luo, Alexander Schönhuth
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52907-0

StrainXpress: strain aware metagenome assembly from short reads

Author(s): Xiongbin Kang and Xiao Luo and Alexander Schönhuth
Published in: Nucleic Acids Research, Issue 50 (17), 2022, Page(s) e101, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkac543

The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

Author(s): Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi
Published in: Bioinformatics, Issue 38, 2022, Page(s) 4423–4425, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btac528

Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations

Author(s): 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
Published in: Scientific Reports, Issue 13, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-37352-1

VeChat: correcting errors in long reads using variation graphs

Author(s): Xiao Luo and Xiongbin Kang and Alexander Schönhuth
Published in: Nature Communications, Issue 13, 2022, Page(s) 6657, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

Finding maximal exact matches in graphs

Author(s): Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Published in: Algorithms for Molecular Biology, Issue 19, 2024, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-024-00255-5

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

Author(s): Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
Published in: iScience, Issue 26, 2024, Page(s) 108057, ISSN 2589-0042
Publisher: Elsevier
DOI: 10.1016/j.isci.2023.108057

Gaps and complex structurally variant loci in phased genome assemblies

Author(s): 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
Published in: Genome Research, Issue 33, 2023, Page(s) 496-510, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277334.122

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: 10.1101/2022.06.13.495912

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

Author(s): Solon Pissis; Grigorios Loukides
Published in: Information Processing Letters, Issue 178, 2022, Page(s) 106275, ISSN 0020-0190
Publisher: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

Constructing founder sets under allelic and non-allelic homologous recombination

Author(s): Konstantinn Bonnet, Tobias Marschall, Daniel Doerr
Published in: Algorithms for Molecular Biology, Issue 18, 2024, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-023-00241-3

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

Author(s): Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander
Published in: Genome Biology, Issue 23, 2022, Page(s) 1--27, ISSN 1474-760X
Publisher: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02587-6

Hide and Mine in Strings: Hardness, Algorithms, and Experiments

Author(s): Giulia Bernardini, Alessio Conte, Garance Gourdel, Roberto Grossi, Grigorios Loukides, Nadia Pisanti, Solon Pissis, Giulia Punzi, Leen Stougie, Michelle Sweering
Published in: IEEE Transactions on Knowledge and Data Engineering, 2023, Page(s) 1-1, ISSN 1041-4347
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3158063

Clustering sequence graphs

Author(s): Haodi Zhong; Grigorios Loukides; Solon P. Pissis
Published in: Data & Knowledge Engineering, Issue 138, 2022, Page(s) 101981.1-101981.21, ISSN 0169-023X
Publisher: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

Considerations in the search for epistasis

Author(s): 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
Published in: Genome Biology, Issue 25, 2025, ISSN 1474-760X
Publisher: Genome Biology
DOI: 10.1186/s13059-024-03427-z

A draft human pangenome reference

Author(s): 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
Published in: Nature, Issue 617, 2023, Page(s) 312-324, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-05896-x

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

Author(s): Beatriz Willink, Kalle Tunström, Sofie Nilén, Rayan Chikhi, Téo Lemane, Michihiko Takahashi, Yuma Takahashi, Erik I. Svensson, Christopher West Wheat
Published in: Nature Ecology & Evolution, Issue 8, 2024, Page(s) 83-97, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-023-02243-1

RecGraph: recombination-aware alignment of sequences to variation graphs

Author(s): Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
Published in: Bioinformatics, Issue 40, 2024, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae292

Computing Phylo-k-Mers

Author(s): Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Issue 20, 2024, Page(s) 2889-2897, ISSN 1545-5963
Publisher: IEEE Computer Society
DOI: 10.1109/tcbb.2023.3278049

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
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, 2023, Page(s) 550-558, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01674-1

Hybrid-hybrid correction of errors in long reads with HERO

Author(s): Xiongbin Kang, Jialu Xu, Xiao Luo, Alexander Schönhuth
Published in: Genome Biology, Issue 24, 2023, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1186/s13059-023-03112-7

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

Author(s): Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Published in: Genome Biology, Issue 22, 2021, Page(s) 1--26, ISSN 1474-760X
Publisher: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02512-x

dipwmsearch: a Python package for searching di-PWM motifs

Author(s): Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Bioinformatics
DOI: 10.1093/bioinformatics/btad141

Pangenome comparison via ED strings

Author(s): Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Published in: Frontiers in Bioinformatics, Issue 4, 2024, ISSN 2673-7647
Publisher: Frontiers in Bioinformatics
DOI: 10.3389/fbinf.2024.1397036

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 Computational Science
DOI: 10.1038/s43588-024-00596-6

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Author(s): Luc Blassel and Paul Medvedev and Rayan Chikhi
Published in: iScience, Issue 25 (11), 2022, Page(s) 105305, ISSN 2589-0042
Publisher: Cell Press
DOI: 10.1016/j.isci.2022.105305

Elastic-Degenerate String Matching with 1 Error or Mismatch

Author(s): Giulia Bernardini, Esteban Gabory, Solon P. Pissis, Leen Stougie, Michelle Sweering, Wiktor Zuba
Published in: Theory of Computing Systems, Issue 68, 2024, Page(s) 1442-1467, ISSN 1432-4350
Publisher: Springer Verlag
DOI: 10.1007/s00224-024-10194-8

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Author(s): Giulia Bernardini and Paweł Gawrychowski and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone
Published in: SIAM Journal on Computing, Issue 51 (3), 2022, Page(s) 549--576, ISSN 1095-7111
Publisher: Society for Industrial & Applied Mathematics (SIAM)
DOI: 10.1137/20m1368033

Constructing phylogenetic networks via cherry picking and machine learning

Author(s): Giulia Bernardini, Leo van Iersel, Esther Julien, Leen Stougie
Published in: Algorithms for Molecular Biology, Issue 18, 2024, ISSN 1748-7188
Publisher: BioMed Central
DOI: 10.1186/s13015-023-00233-3

Generating Synthetic Genotypes using Diffusion Models

Author(s): Philip Kenneweg, Raghuram Dandinasivara, Xiao Luo, Barbara Hammer, Alexander Schönhuth
Published in: 2025
Publisher: Cornell University
DOI: 10.48550/arxiv.2412.03278

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

Author(s): Wenhai Zhang, Yuansheng Liu, Jialu Xu, Enlian Chen, Alexander Schönhuth, Xiao Luo
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.15.623887

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Author(s): Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.15.536996

On-Line Pattern Matching on D-Texts (Invited Talk)

Author(s): Pisanti, Nadia
Published in: Leibniz International Proceedings in Informatics (LIPIcs), vol 191, Issue 1, 2021, Page(s) 3:1--3:2, ISBN 978-3-95977-186-3
Publisher: Schloss Dagstuhl – Leibniz-Zentrum für Informatik

MCHelper automatically curates transposable element libraries across eukaryotic species

Author(s): Simon Orozco-Arias, Pío Sierra, Richard Durbin, Josefa González
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.10.17.562682

Incremental computation of the set of period sets

Author(s): Eric Rivals
Published in: 2024
Publisher: Cornell University
DOI: 10.48550/arxiv.2410.12077

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

Author(s): Arthur Frouin, Fabien Laporte, Lukas Hafner, Mylene Maury, Zachary R. McCaw, Hanna Julienne, Léo Henches, Rayan Chikhi, Marc Lecuit, Hugues Aschard
Published in: 2023
Publisher: 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

Author(s): 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
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.01.587621

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

Author(s): Ali Ghaffaari, Alexander Schönhuth, Tobias Marschall
Published in: 2025
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.12.637964

Cdbgtricks: Strategies to update a compacted de Bruijn graph

Author(s): Khodor Hannoush, Camille Marchet, Pierre Peterlongo
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.05.24.595676

Counting overlapping pairs of strings

Author(s): Eric Rivals, Pengfei Wang
Published in: 2024
Publisher: Cornell University
DOI: 10.48550/arxiv.2405.09393

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

Author(s): Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Published in: 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.31.543043

Unlocking the microblogging potential for science and medicine

Author(s): 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
Published in: 2022
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.04.22.488804

Petascale Homology Search for Structure Prediction

Author(s): Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger
Published in: 2023
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.10.548308

Methods for Pangenomic Core Detection

Author(s): Tizian Schulz, Luca Parmigiani, Andreas Rempel, Jens Stoye
Published in: Methods in Molecular Biology, Comparative Genomics, 2024, Page(s) 73-106
Publisher: Springer US
DOI: 10.1007/978-1-0716-3838-5_4

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