ALgorithms for PAngenome Computational Analysis

Livrables

Compilation of a data management plan.

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

Collective scientific advances report 1

Joint report of WP13 on their scientific advances

Publications

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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