Alexandru I. Tomescu
Associate Professor and Academy of Finland Research Fellow

Homepage • PublicationsSoftwareTeachingFunding


I lead the Graph Algorithms Team of the Algorithmic Bioinformatics group at the Department of Computer Science, University of Helsinki.

My research is partly funded by the ERC Starting Grant SAFEBIO: Safe and Complete Algorithms for Bioinformatics (see also this short project description).

Research interests

My team and I do research at the intersection of Bioinformatics and Theoretical Computer Science (with a focus on Graph Algorithms):
  • genome assembly × safe and complete algorithms for graph problems, de Bruijn graph construction and k-mer compression
  • RNA transcript assembly × network flows, flow decompositions, (minimum) path covers
  • pangenomics × string matching in graphs, co-linear chaining, complexity lower-bounds (SETH-based)
  • sequence comparison and protein evolution × safe and complete algorithms for dynamic programming problems
  • practical approaches × Integer Linear Programming, parameterized algorithms, approximation algorithms, enumeration

Contact

Postal address: Department of Computer Science, P.O. Box 68, FI-00014 University of Helsinki, Finland
Physical address: Pietari Kalmin katu 5, 00560 Helsinki, Finland
Room: D227, 2nd floor, Exactum building
E-mail: alexandru.tomescu@helsinki.fi

Bio

I obtained my PhD in Computer Science from the University of Udine (Italy) in 2012, under the supervision of Alberto Policriti and Eugenio Omodeo. During my PhD I worked on wonderful graph-teoretic, combinatorial, computational logic problems on well-founded and non-well founded sets (viewed as directed graphs) with Alberto and Eugenio. During this time I was fortunate to collaborate also with Martin Milanič and Romeo Rizzi. I spent 6 months during 2012 in Stephan Kreutzer's group at TU Berlin, working on parity games. From August 2012 I started in Veli Mäkinen's group at the University of Helsinki as a Postdoc in the inspiring world of algorithmic bioinformatics, and then continued during 2014 - 2017 as an Academy of Finland Postdoctoral Fellow (multi-assembly problems via network flows), as Academy of Finland Research Fellow from 2019 (foundations of safe and complete algorithms with applications), and as Associate Professor of Algorithmic Bioinformatics from 2020. In 2019 I obtained the ERC Starting Grant (safe and complete algorithms for bioinformatics) for the period 2020 - 2025. I currently lead the Graph Algorithms Team, of the wider Algorithmic Bioinformatics Group, at the Department of Computer Science, University of Helsinki. I am grateful to collaborators Hajk-Georg Drost, Paul Medvedev, Brendan Mumey, Kristoffer Sahlin, Leena Salmela for the many opportunities to discuss Bioinformatics problems.
Alexandru Tomescu

Selected publications

On Sets and Graphs (Research monograph/textbook)
Perspectives on Logic and Combinatorics
Eugenio G. Omodeo, Alberto Policriti, Alexandru I. Tomescu
Springer, 2017
Genome-Scale Algorithm Design (Bioinformatics textbook)
Biological Sequence Analysis in the Era of High-Throughput Sequencing
Veli Mäkinen, Djamal Belazzougui, Fabio Cunial, Alexandru I. Tomescu
Cambridge University Press, 2015

  • (),

    , ,
    ,
    Supervisors: