ALgorithms for PAngenome Computational Analysis

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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

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

Periodicity of Degenerate Strings

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

Pattern Masking for Dictionary Matching

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

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

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

On Strings Having the Same Length- k Substrings

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

Approximate Suffix-Prefix Dictionary Queries

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

Space-Efficient Indexes for Uncertain Strings

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

Linear Time Construction of Indexable Elastic Founder Graphs

Auteurs: Nicola Rizzo and Veli Mäkinen
Publié dans: International Workshop on Combinatorial Algorithms: Combinatorial Algorithms, Numéro 13270, 2022, Page(s) 480--493, ISBN 978-3-031-06678-8
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-031-06678-8_35

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

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

Utility-Oriented String Mining

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

Faster Algorithms for Longest Common Substring

Auteurs: Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski
Publié dans: 29th Annual European Symposium on Algorithms (ESA 2021), Numéro 204, 2021, Page(s) 30:1--30:17, ISSN 1868-8969
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast assessment of Eulerian Trails

Auteurs: Conte, Alessio; Grossi, Roberto; Loukides, Grigorios; Pisanti, Nadia; Pissis, Solon P.; Punzi, Giulia; Bampis, Evripidis; Pagourtzis, Aris
Publié dans: Fundamentals of Computation Theory, 23rd International Symposium (FCT), Numéro 12867, 2021, Page(s) 162--175, ISBN 978-3-030-86593-1
Éditeur: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Indexable Elastic Founder Graphs of Minimum Height

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

Size-Constrained Weighted Ancestors with Applications

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

Longest Palindromic Substring in Sublinear Time

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

A new string sampling mechanism

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

Convergence of the Number of Period Sets in Strings

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

Optimal Sequence Alignment to ED-Strings

Auteurs: Njagi Moses Mwaniki and Nadia Pisanti
Publié dans: ISBRA 2022: Bioinformatics Research and Applications, Numéro 13760, 2023, Page(s) 204–216, ISSN 0302-9743
Éditeur: Springer Verlag
DOI: 10.1007/978-3-031-23198-8_19

A BWT-Based Algorithm for Random de Bruijn Sequence Construction

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

Making de Bruijn Graphs Eulerian

Auteurs: Bernardini, Giulia; Chen, Huiping; Loukides, Grigorios; Pissis, Solon P.; Stougie, Leen; Sweering, Michelle; Bannai, Hideo; Holub, Jan
Publié dans: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numéro 223, 2022, Page(s) 12:1-12:18, ISBN 978-3-95977-234-1
Éditeur: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Suffix-prefix queries on a dictionary

Auteurs: Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan and Wiktor Zuba
Publié dans: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numéro Vol 259, 2023, Page(s) 21:1--21:20, ISBN 978-3-95977-276-1
Éditeur: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Wheeler Maps

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

Faster Maximal Exact Matches with Lazy LCP Evaluation

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

Fast Exact String to D-Texts Alignments

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

Elastic-Degenerate String Matching with 1 Error

Auteurs: Giulia Bernardini; Esteban Gabory; Solon P. Pissis; Leen Stougie; Michelle Sweering; Wiktor Zuba
Publié dans: Latin American Symposium on Theoretical Informatics, Numéro 13568, 2022, Page(s) 20–37, ISBN 978-3-031-20624-5
Éditeur: Springer International Publishing
DOI: 10.48550/arxiv.2209.01095

On-Line Pattern Matching on D-Texts

Auteurs: Nadia Pisanti
Publié dans: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numéro 191, 2021, Page(s) 3:1--3:2, ISSN 1868-8969
Éditeur: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.3

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

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

Approximate Circular Pattern Matching

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

Probabilistic Models of k-mer Frequencies (Extended Abstract)

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

Prefix-free graphs and suffix array construction in sublinear space

Auteurs: Baláž, Andrej; Petescia, Alessia
Publié dans: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numéro 1, 2023, Page(s) 232-241
Éditeur: CEUR Workshop Proceedings
DOI: 10.48550/arxiv.2306.14689

Chaining of Maximal Exact Matches in Graphs

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

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

Auteurs: Esteban Gabory and Moses Njagi Mwaniki and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski and Michelle Sweering and Wiktor Zuba
Publié dans: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numéro Vol 259, 2023, Page(s) 11:1--11:20, ISBN 978-3-95977-276-1
Éditeur: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.11

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

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

Prefix-free parsing for building large tunnelled Wheeler graphs

Auteurs: Adrián Goga and Andrej Baláž
Publié dans: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numéro Vol 242, 2022, Page(s) 18:1--18:12, ISBN 978-3-95977-243-3
Éditeur: 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

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

Identifying Clusters in Graph Representations of Genomes

Auteurs: Eva Herencsárová, Broňa Brejová
Publié dans: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numéro 1, 2023, Page(s) 232-241
Éditeur: CEUR Workshop Proceedings
DOI: 10.1101/2023.07.20.549917v1

Approximate Circular Pattern Matching Under Edit Distance

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

Minimizing the Minimizers via Alphabet Reordering

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

Finding Maximal Exact Matches in Graphs

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

Connecting de Bruijn Graphs

Auteurs: 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
Publié dans: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Numéro Vol 296, 2024, Page(s) 6:1–6:16
Éditeur: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.6

Text Indexing for Long Patterns: Anchors are All you Need

Auteurs: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Publié dans: Proceedings of the VLDB Endowment, Numéro 16, 2023, Page(s) 2117-2131, ISSN 2150-8097
Éditeur: Proceedings VLDB Endowment
DOI: 10.14778/3598581.3598586

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Auteurs: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publié dans: Frontiers in Genetics, Numéro 13, 2022, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Identification of transposable element families from pangenome polymorphisms

Auteurs: Pío Sierra, Richard Durbin
Publié dans: Mobile DNA, Numéro 15, 2024, ISSN 1759-8753
Éditeur: 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

Auteurs: Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Publié dans: BMC Genomics, Numéro 25, 2024, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-024-10267-5

Panacus: fast and exact pangenome growth and core size estimation

Auteurs: Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
Publié dans: Bioinformatics, Numéro 40, 2024, ISSN 1367-4811
Éditeur: Bioinformatics
DOI: 10.1093/bioinformatics/btae720

EPIK: precise and scalable evolutionary placement with informativek-mers

Auteurs: Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals
Publié dans: Bioinformatics, Numéro 39, 2024, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad692

Palidis: fast discovery of novel insertion sequences

Auteurs: Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Publié dans: Microbial Genomics, Numéro 9, 2023, ISSN 2057-5858
Éditeur: Microbial Genomics
DOI: 10.1099/mgen.0.000917

Computing linkage disequilibrium aware genome embeddings using autoencoders

Auteurs: 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
Publié dans: Bioinformatics, Numéro 40, 2024, ISSN 1367-4811
Éditeur: Bioinformatics
DOI: 10.1093/bioinformatics/btae326

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Auteurs: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Publié dans: BMC Bioinformatics, Numéro 25, 2024, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-024-05958-5

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

Auteurs: Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo
Publié dans: Bioinformatics Advances, Numéro 2, 2022, ISSN 2635-0041
Éditeur: Oxford University Press
DOI: 10.1093/bioadv/vbac029

Efficient computation of sequence mappability

Auteurs: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Publié dans: Algorithmica, Numéro 84, 2022, Page(s) 1418–1440, ISSN 1432-0541
Éditeur: Springer Science
DOI: 10.48550/arxiv.1807.11702

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

Auteurs: Grigorios Loukides, Solon P. Pissis, Michelle Sweering
Publié dans: IEEE Transactions on Knowledge and Data Engineering, Numéro 35, 2023, Page(s) 11093-11111, ISSN 1041-4347
Éditeur: Institute of Electrical and Electronics Engineers
DOI: 10.1109/tkde.2022.3231780

Internal shortest absent word queries in constant time and linear space

Auteurs: Golnaz Badkobeh and Panagiotis Charalampopoulos and Dmitry Kosolobov and Solon P. Pissis
Publié dans: Theoretical Computer Science, Numéro 922, 2022, Page(s) 271-282, ISSN 0304-3975
Éditeur: Elsevier BV
DOI: 10.1016/j.tcs.2022.04.029

High-quality metagenome assembly from long accurate reads with metaMDBG

Auteurs: Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
Publié dans: Nature Biotechnology, Numéro 42, 2024, Page(s) 1378-1383, ISSN 1087-0156
Éditeur: 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

Auteurs: Sauer, Lena,; Cánovas, Rodrigo; Roche, Daniel,; Shams-Eldin, Hosam; Ravel, Patrice; Colinge, Jacques; Schwarz, Ralph T.; Mamoun, Choukri Ben; Rivals, Eric; Cornillot, Emmanuel
Publié dans: Malaria Journal, Numéro 22, 2023, Page(s) 27-46, ISSN 1475-2875
Éditeur: BioMed Central
DOI: 10.1186/s12936-022-04430-0

Maximal degenerate palindromes with gaps and mismatches

Auteurs: Mai Alzamel, Christopher Hampson, Costas S. Iliopoulos, Zara Lim, Solon Pissis, Dimitrios Vlachakis, Steven Watts
Publié dans: Theoretical Computer Science, Numéro 978, 2023, Page(s) 114182, ISSN 0304-3975
Éditeur: Elsevier BV
DOI: 10.1016/j.tcs.2023.114182

WarpSTR: determining tandem repeat lengths using raw nanopore signals

Auteurs: Jozef Sitarčík, Tomáš Vinař, Broňa Brejová, Werner Krampl, Jaroslav Budiš, Ján Radvánszky, Mária Lucká
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad388

Efficient mapping of accurate long reads in minimizer space with mapquik

Auteurs: Bariş Ekim, Kristoffer Sahlin, Paul Medvedev, Bonnie Berger, Rayan Chikhi
Publié dans: Genome Research, 2023, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277679.123

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 14, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-38301-2

Revisiting pangenome openness with k-mers

Auteurs: Luca Parmigiani, Roland Wittler, Jens Stoye
Publié dans: Peer Community Journal, Numéro 4, 2024, ISSN 2804-3871
Éditeur: Peer Community Journal
DOI: 10.24072/pcjournal.415

Comparing methods for constructing and representing human pangenome graphs

Auteurs: Francesco Andreace, Pierre Lechat, Yoann Dufresne, Rayan Chikhi
Publié dans: Genome Biology, Numéro 24, 2023, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-023-03098-2

A tutorial on data structures and their applications

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

Pattern Masking for Dictionary Matching: Theory and Practice

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

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

Auteurs: Nico Cillari, Giuseppe Neri, Nadia Pisanti, Paolo Milazzo, Ugo Borello
Publié dans: Database, Numéro 2024, 2025, ISSN 1758-0463
Éditeur: Oxford University Press
DOI: 10.1093/database/baae109

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

Auteurs: Parsoa Khorsand, Luca Denti, null null, Paola Bonizzoni, Rayan Chikhi, Fereydoun Hormozdiari
Publié dans: Bioinformatics Advances, Numéro 1, 2022, ISSN 2635-0041
Éditeur: Oxford University Press
DOI: 10.1093/bioadv/vbab005

Maximum-scoring path sets on pangenome graphs of constant treewidth

Auteurs: Broňa Brejová, Travis Gagie, Eva Herencsárová, Tomáš Vinař
Publié dans: Frontiers in Bioinformatics, Numéro 4, 2024, ISSN 2673-7647
Éditeur: 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

Auteurs: Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btad552

Auteurs: Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi
Publié dans: Microbiome Vol 11, Numéro 1, 2023, Page(s) 243, ISSN 2049-2618
Éditeur: BioMed Central
DOI: 10.1101/2023.01.26.525439

Elastic founder graphs improved and enhanced

Auteurs: Nicola Rizzo, Massimo Equi, Tuukka Norri, Veli Mäkinen
Publié dans: Theoretical Computer Science, Numéro 982, 2023, Page(s) 114269, ISSN 0304-3975
Éditeur: Elsevier BV
DOI: 10.1016/j.tcs.2023.114269

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

Auteurs: Téo Lemane; Rayan Chikhi; Pierre Peterlongo
Publié dans: Bioinformatics, Numéro 38, 2022, Page(s) 5443–5445, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btac689

Critical Assessment of Metagenome Interpretation: the second round of challenges

Auteurs: 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,
Publié dans: Nature Methods, Numéro 19, 2022, Page(s) 429-440, ISSN 1548-7091
Éditeur: 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)

Auteurs: Stefano Porrelli, Michèle Gerbault-Seureau, Roberto Rozzi, Rayan Chikhi, Manon Curaudeau, Anne Ropiquet, Alexandre Hassanin
Publié dans: G3 Genes|Genomes|Genetics, Numéro 12, 2022, ISSN 2160-1836
Éditeur: Genetics Society of America
DOI: 10.1093/g3journal/jkac234

Automated prediction of the clinical impact of structural copy number variations

Auteurs: 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
Publié dans: Scientific Reports, Numéro 12 (1), 2022, Page(s) 555, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Applying rearrangement distances to enable plasmid epidemiology with pling

Auteurs: Daria Frolova, Leandro Lima, Leah Wendy Roberts, Leonard Bohnenkämper, Roland Wittler, Jens Stoye, Zamin Iqbal
Publié dans: Microbial Genomics, Numéro 10, 2024, ISSN 2057-5858
Éditeur: 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

Auteurs: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publié dans: Nature Machine Intelligence, Numéro 5, 2024, Page(s) 114-125, ISSN 2522-5839
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/s42256-022-00604-2

Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation

Auteurs: 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
Publié dans: Nature Communications, Numéro 13 (1), 2022, Page(s) 3298, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-31015-x

HyLight: Strain aware assembly of low coverage metagenomes

Auteurs: Xiongbin Kang, Wenhai Zhang, Yichen Li, Xiao Luo, Alexander Schönhuth
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-52907-0

StrainXpress: strain aware metagenome assembly from short reads

Auteurs: Xiongbin Kang and Xiao Luo and Alexander Schönhuth
Publié dans: Nucleic Acids Research, Numéro 50 (17), 2022, Page(s) e101, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkac543

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

Auteurs: Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi
Publié dans: Bioinformatics, Numéro 38, 2022, Page(s) 4423–4425, ISSN 1367-4803
Éditeur: 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

Auteurs: 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
Publié dans: Scientific Reports, Numéro 13, 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-37352-1

VeChat: correcting errors in long reads using variation graphs

Auteurs: Xiao Luo and Xiongbin Kang and Alexander Schönhuth
Publié dans: Nature Communications, Numéro 13, 2022, Page(s) 6657, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

Finding maximal exact matches in graphs

Auteurs: Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Publié dans: Algorithms for Molecular Biology, Numéro 19, 2024, ISSN 1748-7188
Éditeur: BioMed Central
DOI: 10.1186/s13015-024-00255-5

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

Auteurs: Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
Publié dans: iScience, Numéro 26, 2024, Page(s) 108057, ISSN 2589-0042
Éditeur: Elsevier
DOI: 10.1016/j.isci.2023.108057

Gaps and complex structurally variant loci in phased genome assemblies

Auteurs: 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
Publié dans: Genome Research, Numéro 33, 2023, Page(s) 496-510, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277334.122

Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation

Auteurs: Jorge Avila Cartes; Santosh Anand; Simone Ciccolella; Paola Bonizzoni; Gianluca Della Vedova
Publié dans: GigaScience, Numéro 12, 2022, ISSN 2047-217X
Éditeur: Oxford University Press
DOI: 10.1101/2022.06.13.495912

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

Auteurs: Solon Pissis; Grigorios Loukides
Publié dans: Information Processing Letters, Numéro 178, 2022, Page(s) 106275, ISSN 0020-0190
Éditeur: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

Constructing founder sets under allelic and non-allelic homologous recombination

Auteurs: Konstantinn Bonnet, Tobias Marschall, Daniel Doerr
Publié dans: Algorithms for Molecular Biology, Numéro 18, 2024, ISSN 1748-7188
Éditeur: BioMed Central
DOI: 10.1186/s13015-023-00241-3

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

Auteurs: Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander
Publié dans: Genome Biology, Numéro 23, 2022, Page(s) 1--27, ISSN 1474-760X
Éditeur: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02587-6

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

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

Clustering sequence graphs

Auteurs: Haodi Zhong; Grigorios Loukides; Solon P. Pissis
Publié dans: Data & Knowledge Engineering, Numéro 138, 2022, Page(s) 101981.1-101981.21, ISSN 0169-023X
Éditeur: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

Considerations in the search for epistasis

Auteurs: 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
Publié dans: Genome Biology, Numéro 25, 2025, ISSN 1474-760X
Éditeur: Genome Biology
DOI: 10.1186/s13059-024-03427-z

A draft human pangenome reference

Auteurs: 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
Publié dans: Nature, Numéro 617, 2023, Page(s) 312-324, ISSN 0028-0836
Éditeur: Nature Publishing Group
DOI: 10.1038/s41586-023-05896-x

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

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

RecGraph: recombination-aware alignment of sequences to variation graphs

Auteurs: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti, Xavier Didelot, Davide Cesare Monti, Yuri Pirola
Publié dans: Bioinformatics, Numéro 40, 2024, ISSN 1367-4811
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btae292

Computing Phylo-k-Mers

Auteurs: Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi
Publié dans: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Numéro 20, 2024, Page(s) 2889-2897, ISSN 1545-5963
Éditeur: IEEE Computer Society
DOI: 10.1109/tcbb.2023.3278049

Seedability: optimizing alignment parameters for sensitive sequence comparison

Auteurs: Lorraine A K Ayad, Rayan Chikhi, Solon P Pissis
Publié dans: Bioinformatics Advances, Numéro 3, 2023, ISSN 2635-0041
Éditeur: 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

Auteurs: Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Publié dans: Nature Methods, Numéro 20, 2023, Page(s) 550-558, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/s41592-022-01674-1

Hybrid-hybrid correction of errors in long reads with HERO

Auteurs: Xiongbin Kang, Jialu Xu, Xiao Luo, Alexander Schönhuth
Publié dans: Genome Biology, Numéro 24, 2023, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1186/s13059-023-03112-7

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

Auteurs: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publié dans: Genome Biology, Numéro 22, 2021, Page(s) 1--26, ISSN 1474-760X
Éditeur: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02512-x

dipwmsearch: a Python package for searching di-PWM motifs

Auteurs: Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals
Publié dans: Bioinformatics, Numéro 39, 2023, ISSN 1367-4811
Éditeur: Bioinformatics
DOI: 10.1093/bioinformatics/btad141

Pangenome comparison via ED strings

Auteurs: Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba
Publié dans: Frontiers in Bioinformatics, Numéro 4, 2024, ISSN 2673-7647
Éditeur: 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

Auteurs: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Publié dans: Nature Computational Science, Numéro 4, 2024, Page(s) 104-109, ISSN 2662-8457
Éditeur: Nature Computational Science
DOI: 10.1038/s43588-024-00596-6

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Auteurs: Luc Blassel and Paul Medvedev and Rayan Chikhi
Publié dans: iScience, Numéro 25 (11), 2022, Page(s) 105305, ISSN 2589-0042
Éditeur: Cell Press
DOI: 10.1016/j.isci.2022.105305

Elastic-Degenerate String Matching with 1 Error or Mismatch

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

Elastic-Degenerate String Matching via Fast Matrix Multiplication

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

Constructing phylogenetic networks via cherry picking and machine learning

Auteurs: Giulia Bernardini, Leo van Iersel, Esther Julien, Leen Stougie
Publié dans: Algorithms for Molecular Biology, Numéro 18, 2024, ISSN 1748-7188
Éditeur: BioMed Central
DOI: 10.1186/s13015-023-00233-3

Generating Synthetic Genotypes using Diffusion Models

Auteurs: Philip Kenneweg, Raghuram Dandinasivara, Xiao Luo, Barbara Hammer, Alexander Schönhuth
Publié dans: 2025
Éditeur: Cornell University
DOI: 10.48550/arxiv.2412.03278

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

Auteurs: Wenhai Zhang, Yuansheng Liu, Jialu Xu, Enlian Chen, Alexander Schönhuth, Xiao Luo
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.15.623887

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

Auteurs: Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.15.536996

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

Auteurs: Pisanti, Nadia
Publié dans: Leibniz International Proceedings in Informatics (LIPIcs), vol 191, Numéro 1, 2021, Page(s) 3:1--3:2, ISBN 978-3-95977-186-3
Éditeur: Schloss Dagstuhl – Leibniz-Zentrum für Informatik

MCHelper automatically curates transposable element libraries across eukaryotic species

Auteurs: Simon Orozco-Arias, Pío Sierra, Richard Durbin, Josefa González
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.10.17.562682

Incremental computation of the set of period sets

Auteurs: Eric Rivals
Publié dans: 2024
Éditeur: Cornell University
DOI: 10.48550/arxiv.2410.12077

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

Auteurs: Arthur Frouin, Fabien Laporte, Lukas Hafner, Mylene Maury, Zachary R. McCaw, Hanna Julienne, Léo Henches, Rayan Chikhi, Marc Lecuit, Hugues Aschard
Publié dans: 2023
Éditeur: 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

Auteurs: 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
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.04.01.587621

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

Auteurs: Ali Ghaffaari, Alexander Schönhuth, Tobias Marschall
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.12.637964

Cdbgtricks: Strategies to update a compacted de Bruijn graph

Auteurs: Khodor Hannoush, Camille Marchet, Pierre Peterlongo
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.05.24.595676

Counting overlapping pairs of strings

Auteurs: Eric Rivals, Pengfei Wang
Publié dans: 2024
Éditeur: Cornell University
DOI: 10.48550/arxiv.2405.09393

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

Auteurs: Téo Lemane, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.05.31.543043

Unlocking the microblogging potential for science and medicine

Auteurs: 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
Publié dans: 2022
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.04.22.488804

Petascale Homology Search for Structure Prediction

Auteurs: Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger
Publié dans: 2023
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.10.548308

Methods for Pangenomic Core Detection

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

Recherche de données OpenAIRE...

Livrables

Publications

Partager cette page Partager cette page sur les réseaux sociaux

Télécharger Télécharger le contenu de la page