Descrizione del progetto
Soluzioni computazionali per problemi biologici
La bioinformatica è una disciplina nuova e in rapida evoluzione derivante dai campi della biologia molecolare e della biochimica e dalle discipline algoritmiche dell’informatica e della matematica. Molti problemi del mondo reale di rilevanza biologica possono essere descritti come problemi computazionali ma, a causa di dati incompleti, vengono proposte molte soluzioni, il che rende difficile trovare quella giusta. Il progetto SAFEBIO, finanziato dall’UE, ricaverà i primi algoritmi sicuri per una serie di problemi fondamentali a proposito di grafici, flussi di rete e programmazione dinamica. L’obiettivo sarà quello di creare modi automatizzati ed efficienti per segnalare tutte le soluzioni secondarie sicure per i problemi. Il progetto applicherà questi strumenti pratici interni per l’assemblaggio del genoma, l’assemblaggio dell’RNA e l’analisi del pan-genoma.
Obiettivo
"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."
Campo scientifico
Programma(i)
Argomento(i)
Meccanismo di finanziamento
ERC-STG - Starting GrantIstituzione ospitante
00014 Helsingin Yliopisto
Finlandia