Projet PANGAIA (Horizon 2020, appel à projets 2019)
Action : Staff Exchanges
Panel : Information Science and Engineering
Statut du projet : SIGNED

Genomes are strings over the letters A,C,G,T, which represent nucleotides, the building blocks of DNA. In view of ultra-large amounts of genome sequence data emerging from ever more and technologically rapidly advancing genome sequencing devices—in the meantime, amounts of sequencing data accrued are reaching into the exabyte scale—the driving, urgent question is: how can we arrange and analyze these data masses in a formally rigorous, computationally efficient and biomedically rewarding manner? Graph based data structures have been pointed out to have disruptive benefits over traditional sequence based structures when representing pan-genomes, sufficiently large, evolutionarily coherent collections of genomes. This idea has its immediate justification in the laws of genetics: evolutionarily closely related genomes vary only in relatively little amounts of letters, while sharing the majority of their sequence content. Graph-based pan-genome representations that allow to remove redundancies without having to discard individual differences, make utmost sense. In this project, we will put this shift of paradigms—from sequence to graph based representations of genomes—into full effect. As a result, we can expect a wealth of practically relevant advantages, among which arrangement, analysis, compression, integration and exploitation of genome data are the most fundamental points. In addition, we will also open up a significant source of inspiration for computer science itself.

Mots clés : algorithmic bionformatics, computational pan genomics, graph algorithms, data structures and indexing, computational comparative genomics, genome data science

Participants :
- University of California System (Etats-Unis) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €
- The University of Tokyo (Japon) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €
- Comenius University Bratislava (Slovaquie) — Partner, beneficiary, Enseignement supérieur ou secondaire, subvention : 128800.0 €
- Geneton (Slovakia) (Slovaquie) — Partner, beneficiary, Organismes privés (hors enseignement), subvention : 322000.0 €
- Institut Pasteur (France) — Partner, beneficiary, Recherche, subvention : 147200.0 €
- Illumina (United Kingdom) (Royaume-Uni) — Partner, beneficiary, Organismes privés (hors enseignement), subvention : 0.0 €
- University of Milano-Bicocca (Italie) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 197800.0 €
- Pennsylvania State University (Etats-Unis) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €
- Cornell University (Etats-Unis) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €
- Dutch Research Council (Pays-Bas) — Partner, beneficiary, Recherche, subvention : 55200.0 €
- Simon Fraser University (Canada) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €
- Bielefeld University (Allemagne) — Partner, beneficiary, Enseignement supérieur ou secondaire, subvention : 289800.0 €
- Hunan University (Chine) — Partner, organization partner, Enseignement supérieur ou secondaire, subvention : 0.0 €