ALgorithms for PAngenome Computational Analysis

CORDIS oferuje możliwość skorzystania z odnośników do publicznie dostępnych publikacji i rezultatów projektów realizowanych w ramach programów ramowych HORYZONT.

Odnośniki do rezultatów i publikacji związanych z poszczególnymi projektami 7PR, a także odnośniki do niektórych konkretnych kategorii wyników, takich jak zbiory danych i oprogramowanie, są dynamicznie pobierane z systemu OpenAIRE .

Rezultaty

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

Publikacje

Substring Complexity in Sublinear Space

Autorzy: Giulia Bernardini, Gabriele Fici, Paweł Gawrychowski, and Solon P. Pissis
Opublikowane w: Leibniz International Proceedings in Informatics (LIPIcs), Numer 283, 2023, Strona(/y) 12:1-12:19, ISBN 978-3-95977-289-1
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2023.12

Periodicity of Degenerate Strings

Autorzy: Estéban Gabory and Eric Rivals and Michelle Sweering and Hilde Verbeek and Pengfei Wang
Opublikowane w: Proceedings of the Prague Stringology Conference 2023, 2023, Strona(/y) 42-56, ISBN 978-80-01-07206-6
Wydawca: Prague Stringology Club

Pattern Masking for Dictionary Matching

Autorzy: Panagiotis Charalampopoulos and Huiping Chen and Peter Christen and Grigorios Loukides and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski
Opublikowane w: 32nd International Symposium on Algorithms and Computation (ISAAC 2021), Numer 212, 2021, Strona(/y) 65:1--65:19, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.isaac.2021.65

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Autorzy: Park, Sangsoo; Park, Sung Gwan; Cazaux, Bastien; Park, Kunsoo; Rivals, Eric
Opublikowane w: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numer 191, 2021, Strona(/y) 22:1--22:9, ISBN 978-3-95977-186-3
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.22

On Strings Having the Same Length- k Substrings

Autorzy: Bernardini, Giulia and Conte, Alessio and Gabory, Esteban and Grossi, Roberto and Loukides, Grigorios and Pissis, Solon P. and Punzi, Giulia and Sweering, Michelle
Opublikowane w: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 16:1--16:17, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.16

Approximate Suffix-Prefix Dictionary Queries

Autorzy: Wiktor Zuba and Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan
Opublikowane w: 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024), Numer Vol 306, 2024, Strona(/y) 85:1–85:18
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.mfcs.2024.85

Space-Efficient Indexes for Uncertain Strings

Autorzy: Esteban Gabory, Chang Liu, Grigorios Loukides, Solon P. Pissis, Wiktor Zuba
Opublikowane w: 2024 IEEE 40th International Conference on Data Engineering (ICDE), 2024, Strona(/y) 4828-4842
Wydawca: IEEE
DOI: 10.1109/icde60146.2024.00367

Linear Time Construction of Indexable Elastic Founder Graphs

Autorzy: Nicola Rizzo and Veli Mäkinen
Opublikowane w: International Workshop on Combinatorial Algorithms: Combinatorial Algorithms, Numer 13270, 2022, Strona(/y) 480--493, ISBN 978-3-031-06678-8
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-031-06678-8_35

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

Autorzy: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis, Hilde Verbeek
Opublikowane w: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Strona(/y) 162-177
Wydawca: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_11

Utility-Oriented String Mining

Autorzy: Giulia Bernardini, Huiping Chen, Alessio Conte, Roberto Grossi, Veronica Guerrini, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis
Opublikowane w: Proceedings of the 2024 SIAM International Conference on Data Mining (SDM), 2024, Strona(/y) 190-198
Wydawca: Society for Industrial and Applied Mathematics
DOI: 10.1137/1.9781611978032.22

Faster Algorithms for Longest Common Substring

Autorzy: Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski
Opublikowane w: 29th Annual European Symposium on Algorithms (ESA 2021), Numer 204, 2021, Strona(/y) 30:1--30:17, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast assessment of Eulerian Trails

Autorzy: Conte, Alessio; Grossi, Roberto; Loukides, Grigorios; Pisanti, Nadia; Pissis, Solon P.; Punzi, Giulia; Bampis, Evripidis; Pagourtzis, Aris
Opublikowane w: Fundamentals of Computation Theory, 23rd International Symposium (FCT), Numer 12867, 2021, Strona(/y) 162--175, ISBN 978-3-030-86593-1
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-86593-1_11

Indexable Elastic Founder Graphs of Minimum Height

Autorzy: Nicola Rizzo and Veli Mäkinen
Opublikowane w: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 480--493, ISBN 978-3-031-06678-8
Wydawca: Springer International Publishing
DOI: 10.4230/lipics.cpm.2022.19

Size-Constrained Weighted Ancestors with Applications

Autorzy: Philip Bille and Yakov Nekrich and Solon P. Pissis
Opublikowane w: 19th Scandinavian Symposium and Workshops on Algorithm Theory (SWAT 2024), Numer Vol 294, 2024, Strona(/y) 14:1–14:12
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.swat.2024.14

Longest Palindromic Substring in Sublinear Time

Autorzy: Charalampopoulos, Panagiotis; Pissis, Solon P.; Radoszewski, Jakub; Bannai, Hideo; Holub, Jan
Opublikowane w: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 20:1--20:9, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.20

A new string sampling mechanism

Autorzy: Loukides, Grigorios; Pissis, Solon P.; Mutzel, Petra; Pagh, Rasmus; Herman, Grzegorz
Opublikowane w: 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, Numer 204, 2021, Strona(/y) 64:1--64:21, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Convergence of the Number of Period Sets in Strings

Autorzy: Eric Rivals, Michelle Sweering, and Pengfei Wang
Opublikowane w: Leibniz International Proceedings in Informatics (LIPIcs), Numer 261, 2023, Strona(/y) 100:1--100:14, ISBN 978-3-95977-278-5
Wydawca: Schloss Dagstuhl –- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.icalp.2023.100

Optimal Sequence Alignment to ED-Strings

Autorzy: Njagi Moses Mwaniki and Nadia Pisanti
Opublikowane w: ISBRA 2022: Bioinformatics Research and Applications, Numer 13760, 2023, Strona(/y) 204–216, ISSN 0302-9743
Wydawca: Springer Verlag
DOI: 10.1007/978-3-031-23198-8_19

A BWT-Based Algorithm for Random de Bruijn Sequence Construction

Autorzy: Zsuzsanna Lipták, Luca Parmigiani
Opublikowane w: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Strona(/y) 130-145
Wydawca: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_9

Making de Bruijn Graphs Eulerian

Autorzy: Bernardini, Giulia; Chen, Huiping; Loukides, Grigorios; Pissis, Solon P.; Stougie, Leen; Sweering, Michelle; Bannai, Hideo; Holub, Jan
Opublikowane w: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Numer 223, 2022, Strona(/y) 12:1-12:18, ISBN 978-3-95977-234-1
Wydawca: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2022.12

Suffix-prefix queries on a dictionary

Autorzy: Grigorios Loukides and Solon P. Pissis and Sharma V. Thankachan and Wiktor Zuba
Opublikowane w: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numer Vol 259, 2023, Strona(/y) 21:1--21:20, ISBN 978-3-95977-276-1
Wydawca: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.21

Wheeler Maps

Autorzy: Andrej Baláž, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Opublikowane w: Lecture Notes in Computer Science, LATIN 2024: Theoretical Informatics, 2024, Strona(/y) 178-192
Wydawca: Springer Nature Switzerland
DOI: 10.1007/978-3-031-55598-5_12

Faster Maximal Exact Matches with Lazy LCP Evaluation

Autorzy: Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Opublikowane w: 2024 Data Compression Conference (DCC), 2024, Strona(/y) 123-132
Wydawca: IEEE
DOI: 10.1109/dcc58796.2024.00020

Fast Exact String to D-Texts Alignments

Autorzy: Njagi Mwaniki, Erik Garrison, Nadia Pisanti
Opublikowane w: Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies, 2024, Strona(/y) 70-79
Wydawca: SCITEPRESS - Science and Technology Publications
DOI: 10.5220/0011666900003414

Elastic-Degenerate String Matching with 1 Error

Autorzy: Giulia Bernardini; Esteban Gabory; Solon P. Pissis; Leen Stougie; Michelle Sweering; Wiktor Zuba
Opublikowane w: Latin American Symposium on Theoretical Informatics, Numer 13568, 2022, Strona(/y) 20–37, ISBN 978-3-031-20624-5
Wydawca: Springer International Publishing
DOI: 10.48550/arxiv.2209.01095

On-Line Pattern Matching on D-Texts

Autorzy: Nadia Pisanti
Opublikowane w: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Numer 191, 2021, Strona(/y) 3:1--3:2, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.3

Gapped String Indexing in Subquadratic Space and Sublinear Query Time

Autorzy: Philip Bille and Inge Li Gørtz and Moshe Lewenstein and Solon P. Pissis and Eva Rotenberg and Teresa Anna Steiner
Opublikowane w: 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024), Numer Vol 289, 2024, Strona(/y) 16:1–16:21
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.16

Approximate Circular Pattern Matching

Autorzy: Panagiotis Charalampopoulos and Tomasz Kociumaka and Jakub Radoszewski and Solon P. Pissis and Wojciech Rytter and Tomasz Waleń and Wiktor Zuba
Opublikowane w: 30th Annual European Symposium on Algorithms (ESA 2022), Numer 244, 2022, Strona(/y) 35:1--35:19, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2022.35

Probabilistic Models of k-mer Frequencies (Extended Abstract)

Autorzy: Askar Gafurov, Tomáš Vinař, Broňa Brejová
Opublikowane w: Lecture Notes in Computer Science, Connecting with Computability, 2021, Strona(/y) 227-236
Wydawca: Springer International Publishing
DOI: 10.1007/978-3-030-80049-9_21

Prefix-free graphs and suffix array construction in sublinear space

Autorzy: Baláž, Andrej; Petescia, Alessia
Opublikowane w: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numer 1, 2023, Strona(/y) 232-241
Wydawca: CEUR Workshop Proceedings
DOI: 10.48550/arxiv.2306.14689

Chaining of Maximal Exact Matches in Graphs

Autorzy: Nicola Rizzo, Manuel Cáceres, Veli Mäkinen
Opublikowane w: Lecture Notes in Computer Science, String Processing and Information Retrieval, 2023, Strona(/y) 353-366
Wydawca: Springer Nature Switzerland
DOI: 10.1007/978-3-031-43980-3_29

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

Autorzy: Esteban Gabory and Moses Njagi Mwaniki and Nadia Pisanti and Solon P. Pissis and Jakub Radoszewski and Michelle Sweering and Wiktor Zuba
Opublikowane w: 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), Numer Vol 259, 2023, Strona(/y) 11:1--11:20, ISBN 978-3-95977-276-1
Wydawca: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2023.11

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Autorzy: Konstantinn Bonnet and Tobias Marschall and Daniel Doerr
Opublikowane w: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numer 242, 2022, Strona(/y) 6:1--6:23, ISSN 1868-8969
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.6

Prefix-free parsing for building large tunnelled Wheeler graphs

Autorzy: Adrián Goga and Andrej Baláž
Opublikowane w: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Numer Vol 242, 2022, Strona(/y) 18:1--18:12, ISBN 978-3-95977-243-3
Wydawca: 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

Autorzy: Rocco Ascone and Giulia Bernardini and Alessio Conte and Massimo Equi and Esteban Gabory and Roberto Grossi and Nadia Pisanti
Opublikowane w: 24th International Workshop on Algorithms in Bioinformatics (WABI 2024), Numer Vol 312, 2024, Strona(/y) 14:1–14:21
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2024.14

Identifying Clusters in Graph Representations of Genomes

Autorzy: Eva Herencsárová, Broňa Brejová
Opublikowane w: the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), vol 3498, Numer 1, 2023, Strona(/y) 232-241
Wydawca: CEUR Workshop Proceedings
DOI: 10.1101/2023.07.20.549917v1

Approximate Circular Pattern Matching Under Edit Distance

Autorzy: Panagiotis Charalampopoulos and Solon P. Pissis and Jakub Radoszewski and Wojciech Rytter and Tomasz Waleń and Wiktor Zuba
Opublikowane w: 41st International Symposium on Theoretical Aspects of Computer Science (STACS 2024), Numer Vol 289, 2024, Strona(/y) 24:1–24:22
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.stacs.2024.24

Minimizing the Minimizers via Alphabet Reordering

Autorzy: Verbeek, Hilde and Ayad, Lorraine A.K. and Loukides, Grigorios and Pissis, Solon P.
Opublikowane w: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Numer Vol 296, 2024, Strona(/y) 28:1--28:13
Wydawca: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.28

Finding Maximal Exact Matches in Graphs

Autorzy: Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen
Opublikowane w: Leibniz International Proceedings in Informatics (LIPIcs), Numer 273, 2023, Strona(/y) 10:1--10:17, ISBN 978-3-95977-294-5
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2023.10

Connecting de Bruijn Graphs

Autorzy: 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
Opublikowane w: 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), Numer Vol 296, 2024, Strona(/y) 6:1–6:16
Wydawca: Schloss Dagstuhl – Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2024.6

Text Indexing for Long Patterns: Anchors are All you Need

Autorzy: Lorraine A. K. Ayad, Grigorios Loukides, Solon P. Pissis
Opublikowane w: Proceedings of the VLDB Endowment, Numer 16, 2023, Strona(/y) 2117-2131, ISSN 2150-8097
Wydawca: Proceedings VLDB Endowment
DOI: 10.14778/3598581.3598586

Enhancing Long-Read-Based Strain-Aware Metagenome Assembly

Autorzy: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Opublikowane w: Frontiers in Genetics, Numer 13, 2022, ISSN 1664-8021
Wydawca: Frontiers Media
DOI: 10.3389/fgene.2022.868280

Identification of transposable element families from pangenome polymorphisms

Autorzy: Pío Sierra, Richard Durbin
Opublikowane w: Mobile DNA, Numer 15, 2024, ISSN 1759-8753
Wydawca: 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

Autorzy: Zuzana Holesova, Ondrej Pös, Juraj Gazdarica, Marcel Kucharik, Jaroslav Budis, Michaela Hyblova, Gabriel Minarik, Tomas Szemes
Opublikowane w: BMC Genomics, Numer 25, 2024, ISSN 1471-2164
Wydawca: BioMed Central
DOI: 10.1186/s12864-024-10267-5

Panacus: fast and exact pangenome growth and core size estimation

Autorzy: Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
Opublikowane w: Bioinformatics, Numer 40, 2024, ISSN 1367-4811
Wydawca: Bioinformatics
DOI: 10.1093/bioinformatics/btae720

EPIK: precise and scalable evolutionary placement with informativek-mers

Autorzy: Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals
Opublikowane w: Bioinformatics, Numer 39, 2024, ISSN 1367-4811
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btad692

Palidis: fast discovery of novel insertion sequences

Autorzy: Victoria R. Carr, Solon P. Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L. Moyes
Opublikowane w: Microbial Genomics, Numer 9, 2023, ISSN 2057-5858
Wydawca: Microbial Genomics
DOI: 10.1099/mgen.0.000917

Computing linkage disequilibrium aware genome embeddings using autoencoders

Autorzy: 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
Opublikowane w: Bioinformatics, Numer 40, 2024, ISSN 1367-4811
Wydawca: Bioinformatics
DOI: 10.1093/bioinformatics/btae326

PangeBlocks: customized construction of pangenome graphs via maximal blocks

Autorzy: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti
Opublikowane w: BMC Bioinformatics, Numer 25, 2024, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-024-05958-5

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

Autorzy: Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo
Opublikowane w: Bioinformatics Advances, Numer 2, 2022, ISSN 2635-0041
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Opublikowane w: 2024
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Wydawca: Springer US
DOI: 10.1007/978-1-0716-3838-5_4

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