Projektbeschreibung
Computergestützte Lösungen für biologische Probleme
Bioinformatik ist eine neue, sich schnell entwickelnde Disziplin, die aus den Bereichen Molekularbiologie und Biochemie und von den algorithmischen Disziplinen der Informatik und Mathematik abstammt. Viele reale Probleme mit biologischer Relevanz können als Rechenprobleme modelliert werden, aber aufgrund von unvollständigen Daten wird eine große Zahl an Lösungen vorgeschlagen, was es schwierig macht, die richtige zu finden. Das EU-finanzierte Projekt SAFEBIO wird die ersten sicheren Algorithmen für eine Reihe grundlegender Probleme bei Pfaden in Graphen, Netzwerkflussdiagrammen und dynamischer Programmierung ableiten. Ziel wird sein, automatisierte und effiziente Wege zu finden, um alle sicheren Teillösungen für Probleme zu melden. Im Rahmen des Projekts werden diese in praktische Instrumente zur Genomassemblierung, RNA-Assemblierung und Pangenomanalyse integriert.
Ziel
"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."
Wissenschaftliches Gebiet
Programm/Programme
Thema/Themen
Finanzierungsplan
ERC-STG - Starting GrantGastgebende Einrichtung
00014 Helsingin Yliopisto
Finnland