ALgorithms for PAngenome Computational Analysis

Resultado final

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

Publicaciones

Pattern Masking for Dictionary Matching

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

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

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

On Strings Having the Same Length- k Substrings

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

Linear Time Construction of Indexable Elastic Founder Graphs

Autores: Nicola Rizzo and Veli Mäkinen
Publicado en: International Workshop on Combinatorial Algorithms: Combinatorial Algorithms, Edición 13270, 2022, Página(s) 480--493, ISBN 978-3-031-06678-8
Editor: Springer International Publishing
DOI: 10.1007/978-3-031-06678-8_35

Faster Algorithms for Longest Common Substring

Autores: Panagiotis Charalampopoulos and Tomasz Kociumaka and Solon P. Pissis and Jakub Radoszewski
Publicado en: 29th Annual European Symposium on Algorithms (ESA 2021), Edición 204, 2021, Página(s) 30:1--30:17, ISSN 1868-8969
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.30

Beyond the BEST Theorem: Fast assessment of Eulerian Trails

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

Indexable Elastic Founder Graphs of Minimum Height

Autores: Nicola Rizzo and Veli Mäkinen
Publicado en: 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), Edición 223, 2022, Página(s) 480--493, ISBN 978-3-031-06678-8
Editor: Springer International Publishing
DOI: 10.4230/lipics.cpm.2022.19

Longest Palindromic Substring in Sublinear Time

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

A new string sampling mechanism

Autores: Loukides, Grigorios; Pissis, Solon P.; Mutzel, Petra; Pagh, Rasmus; Herman, Grzegorz
Publicado en: 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, Edición 204, 2021, Página(s) 64:1--64:21, ISSN 1868-8969
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.esa.2021.64

Optimal Sequence Alignment to ED-Strings

Autores: Njagi Moses Mwaniki and Nadia Pisanti
Publicado en: ISBRA 2022: Bioinformatics Research and Applications, Edición 13760, 2023, Página(s) 204–216, ISSN 0302-9743
Editor: Springer Verlag
DOI: 10.1007/978-3-031-23198-8_19

Making de Bruijn Graphs Eulerian

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

Elastic-Degenerate String Matching with 1 Error

Autores: Giulia Bernardini; Esteban Gabory; Solon P. Pissis; Leen Stougie; Michelle Sweering; Wiktor Zuba
Publicado en: Latin American Symposium on Theoretical Informatics, Edición 13568, 2022, Página(s) 20–37, ISBN 978-3-031-20624-5
Editor: Springer International Publishing
DOI: 10.48550/arxiv.2209.01095

On-Line Pattern Matching on D-Texts

Autores: Nadia Pisanti
Publicado en: 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021), Edición 191, 2021, Página(s) 3:1--3:2, ISSN 1868-8969
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.cpm.2021.3

Approximate Circular Pattern Matching

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

Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination

Autores: Konstantinn Bonnet and Tobias Marschall and Daniel Doerr
Publicado en: 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022), Edición 242, 2022, Página(s) 6:1--6:23, ISSN 1868-8969
Editor: Schloss Dagstuhl -- Leibniz-Zentrum für Informatik
DOI: 10.4230/lipics.wabi.2022.6

Efficient computation of sequence mappability

Autores: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Publicado en: Algorithmica, Edición 84, 2022, Página(s) 1418–1440, ISSN 1432-0541
Editor: Springer Science
DOI: 10.48550/arxiv.1807.11702

Internal shortest absent word queries in constant time and linear space

Autores: Golnaz Badkobeh and Panagiotis Charalampopoulos and Dmitry Kosolobov and Solon P. Pissis
Publicado en: Theoretical Computer Science, Edición 922, 2022, Página(s) 271-282, ISSN 0304-3975
Editor: 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

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

A tutorial on data structures and their applications

Autores: Baaijens, Jasmijn A.; Bonizzoni, Paola; Boucher, Christina; Della Vedova, Gianluca; Pirola, Yuri; Rizzi, Raffaella; Sirén, Jouni
Publicado en: Natural Computing, Edición 21, 2022, Página(s) 81--108, ISSN 1572-9796
Editor: Springer Nature
DOI: 10.1007/s11047-022-09882-6

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

Autores: Téo Lemane; Rayan Chikhi; Pierre Peterlongo
Publicado en: Bioinformatics, Edición 38, 2022, Página(s) 5443–5445, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btac689

Automated prediction of the clinical impact of structural copy number variations

Autores: 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
Publicado en: Scientific Reports, Edición 12 (1), 2022, Página(s) 555, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation

Autores: 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
Publicado en: Nature Communications, Edición 13 (1), 2022, Página(s) 3298, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31015-x

StrainXpress: strain aware metagenome assembly from short reads

Autores: Xiongbin Kang and Xiao Luo and Alexander Schönhuth
Publicado en: Nucleic Acids Research, Edición 50 (17), 2022, Página(s) e101, ISSN 1362-4962
Editor: Oxford University Press
DOI: 10.1093/nar/gkac543

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

Autores: Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi
Publicado en: Bioinformatics, Edición 38, 2022, Página(s) 4423–4425, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btac528

VeChat: correcting errors in long reads using variation graphs

Autores: Xiao Luo and Xiongbin Kang and Alexander Schönhuth
Publicado en: Nature Communications, Edición 13, 2022, Página(s) 6657, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

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

Autores: Jorge Avila Cartes; Santosh Anand; Simone Ciccolella; Paola Bonizzoni; Gianluca Della Vedova
Publicado en: GigaScience, Edición 12, 2022, ISSN 2047-217X
Editor: Oxford University Press
DOI: 10.1101/2022.06.13.495912

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

Autores: Solon Pissis; Grigorios Loukides
Publicado en: Information Processing Letters, Edición 178, 2022, Página(s) 106275, ISSN 0020-0190
Editor: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

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

Autores: Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander
Publicado en: Genome Biology, Edición 23, 2022, Página(s) 1--27, ISSN 1474-760X
Editor: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02587-6

Clustering sequence graphs

Autores: Haodi Zhong; Grigorios Loukides; Solon P. Pissis
Publicado en: Data & Knowledge Engineering, Edición 138, 2022, Página(s) 101981.1-101981.21, ISSN 0169-023X
Editor: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

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

Autores: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Publicado en: Genome Biology, Edición 22, 2021, Página(s) 1--26, ISSN 1474-760X
Editor: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02512-x

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Autores: Luc Blassel and Paul Medvedev and Rayan Chikhi
Publicado en: iScience, Edición 25 (11), 2022, Página(s) 105305, ISSN 2589-0042
Editor: Cell Press
DOI: 10.1016/j.isci.2022.105305

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autores: Giulia Bernardini and Paweł Gawrychowski and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone
Publicado en: SIAM Journal on Computing, Edición 51 (3), 2022, Página(s) 549--576, ISSN 1095-7111
Editor: Society for Industrial & Applied Mathematics (SIAM)
DOI: 10.1137/20m1368033

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