Description du projet
Des solutions informatiques aux problèmes biologiques
La bio-informatique est une nouvelle discipline en pleine évolution, issue des domaines de la biologie moléculaire et de la biochimie, ainsi que des disciplines algorithmiques de l’informatique et des mathématiques. De nombreux problèmes du monde réel, pertinents sur le plan biologique, peuvent être modélisés sous forme des problèmes calculatoires, mais compte tenu du caractère incomplet des données, un grand nombre de solutions sont proposées, parmi lesquelles il s’avère difficile de trouver la bonne. Le projet SAFEBIO, financé par l’UE, permettra de développer les premiers algorithmes fiables pour un certain nombre de problèmes fondamentaux concernant les parcours de graphes, les flux de réseau et la programmation dynamique. L’objectif consistera à créer des moyens automatisés et efficaces de recenser l’ensemble des sous-solutions fiables pour les problèmes considérés, que le projet appliquera au sein d’outils pratiques d’assemblage du génome, d’assemblage d’ARN et d’analyse pangénomique.
Objectif
"Many real-world problems are modeled as computational problems, but unfortunately with incomplete data or knowledge. As such, they may admit a large number of solutions, and we have no way of finding the correct one. This issue is sometimes addressed by outputting all solutions, which is infeasible for many practical problems. We aim to construct a general methodology for finding the set of all sub-solutions common to all solutions. We can ultimately trust these to be part of the correct solution. We call this set ""safe"". Ultimately, we aim at creating automated and efficient ways of reporting all safe sub-solutions of a problem. The main motivation of this project comes from Bioinformatics, in particular from the analysis of high-throughput sequencing (HTS) of DNA. One of the main applications of HTS data is to assemble it back into the original DNA sequence. This genome assembly problem admits many solutions, and current research has indeed considered outputting only partial solutions that are likely to be present in the correct original DNA sequence. However, this problem has been approached only from an experimental point of view, with no definite answer on what are all the safe sub-solutions to report. In fact, the issue of safe sub-solutions has been mostly overlooked in Bioinformatics and Computer Science in general. This project will derive the first safe algorithms for a number of fundamental problems about walks in graphs, network flows, dynamic programming. We will apply these inside practical tools for genome assembly, RNA assembly and pan-genome analysis. This is very relevant at the moment, because HTS goes from research labs to hospitals, and we need answers that are first of all accurate. Our approach changes the perspective from which we address all real-world problems, and could spur a new line of research in Computer Science/Bioinformatics. The grand aim is a mathematical leap into understanding what can be safely reported from the data."
Champ scientifique
Programme(s)
Thème(s)
Régime de financement
ERC-STG - Starting GrantInstitution d’accueil
00014 Helsingin Yliopisto
Finlande