ALgorithms for PAngenome Computational Analysis

Rezultaty

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

Publikacje

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

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

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

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

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

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

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

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

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

Efficient computation of sequence mappability

Autorzy: Panagiotis Charalampopoulos; Costas S. Iliopoulos; Tomasz Kociumaka; Solon P. Pissis; Jakub Radoszewski; Juliusz Straszyński
Opublikowane w: Algorithmica, Numer 84, 2022, Strona(/y) 1418–1440, ISSN 1432-0541
Wydawca: Springer Science
DOI: 10.48550/arxiv.1807.11702

Internal shortest absent word queries in constant time and linear space

Autorzy: Golnaz Badkobeh and Panagiotis Charalampopoulos and Dmitry Kosolobov and Solon P. Pissis
Opublikowane w: Theoretical Computer Science, Numer 922, 2022, Strona(/y) 271-282, ISSN 0304-3975
Wydawca: 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

Autorzy: Sauer, Lena,; Cánovas, Rodrigo; Roche, Daniel,; Shams-Eldin, Hosam; Ravel, Patrice; Colinge, Jacques; Schwarz, Ralph T.; Mamoun, Choukri Ben; Rivals, Eric; Cornillot, Emmanuel
Opublikowane w: Malaria Journal, Numer 22, 2023, Strona(/y) 27-46, ISSN 1475-2875
Wydawca: BioMed Central
DOI: 10.1186/s12936-022-04430-0

A tutorial on data structures and their applications

Autorzy: Baaijens, Jasmijn A.; Bonizzoni, Paola; Boucher, Christina; Della Vedova, Gianluca; Pirola, Yuri; Rizzi, Raffaella; Sirén, Jouni
Opublikowane w: Natural Computing, Numer 21, 2022, Strona(/y) 81--108, ISSN 1572-9796
Wydawca: Springer Nature
DOI: 10.1007/s11047-022-09882-6

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

Autorzy: Téo Lemane; Rayan Chikhi; Pierre Peterlongo
Opublikowane w: Bioinformatics, Numer 38, 2022, Strona(/y) 5443–5445, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac689

Automated prediction of the clinical impact of structural copy number variations

Autorzy: 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
Opublikowane w: Scientific Reports, Numer 12 (1), 2022, Strona(/y) 555, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-021-04505-z

Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation

Autorzy: 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
Opublikowane w: Nature Communications, Numer 13 (1), 2022, Strona(/y) 3298, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-31015-x

StrainXpress: strain aware metagenome assembly from short reads

Autorzy: Xiongbin Kang and Xiao Luo and Alexander Schönhuth
Opublikowane w: Nucleic Acids Research, Numer 50 (17), 2022, Strona(/y) e101, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1093/nar/gkac543

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

Autorzy: Yoann Dufresne; Teo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi
Opublikowane w: Bioinformatics, Numer 38, 2022, Strona(/y) 4423–4425, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btac528

VeChat: correcting errors in long reads using variation graphs

Autorzy: Xiao Luo and Xiongbin Kang and Alexander Schönhuth
Opublikowane w: Nature Communications, Numer 13, 2022, Strona(/y) 6657, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-34381-8

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

Autorzy: Jorge Avila Cartes; Santosh Anand; Simone Ciccolella; Paola Bonizzoni; Gianluca Della Vedova
Opublikowane w: GigaScience, Numer 12, 2022, ISSN 2047-217X
Wydawca: Oxford University Press
DOI: 10.1101/2022.06.13.495912

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

Autorzy: Solon Pissis; Grigorios Loukides
Opublikowane w: Information Processing Letters, Numer 178, 2022, Strona(/y) 106275, ISSN 0020-0190
Wydawca: Elsevier BV
DOI: 10.1016/j.ipl.2022.106275

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

Autorzy: Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander
Opublikowane w: Genome Biology, Numer 23, 2022, Strona(/y) 1--27, ISSN 1474-760X
Wydawca: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02587-6

Clustering sequence graphs

Autorzy: Haodi Zhong; Grigorios Loukides; Solon P. Pissis
Opublikowane w: Data & Knowledge Engineering, Numer 138, 2022, Strona(/y) 101981.1-101981.21, ISSN 0169-023X
Wydawca: Elsevier BV
DOI: 10.1016/j.datak.2022.101981

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

Autorzy: Xiao Luo, Xiongbin Kang, Alexander Schönhuth
Opublikowane w: Genome Biology, Numer 22, 2021, Strona(/y) 1--26, ISSN 1474-760X
Wydawca: BioMed Central (BMC)
DOI: 10.1186/s13059-021-02512-x

Mapping-friendly sequence reductions: Going beyond homopolymer compression

Autorzy: Luc Blassel and Paul Medvedev and Rayan Chikhi
Opublikowane w: iScience, Numer 25 (11), 2022, Strona(/y) 105305, ISSN 2589-0042
Wydawca: Cell Press
DOI: 10.1016/j.isci.2022.105305

Elastic-Degenerate String Matching via Fast Matrix Multiplication

Autorzy: Giulia Bernardini and Paweł Gawrychowski and Nadia Pisanti and Solon P. Pissis and Giovanna Rosone
Opublikowane w: SIAM Journal on Computing, Numer 51 (3), 2022, Strona(/y) 549--576, ISSN 1095-7111
Wydawca: Society for Industrial & Applied Mathematics (SIAM)
DOI: 10.1137/20m1368033

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