[CPM-SPIRE-L] PhD student position in genome-scale algorithmics

[Mäkinen, Veli A T]

Dear all,

The Department of Computer Science at the University of Helsinki invites applications for a

Doctoral Student in Genome-Scale Algorithmics

The position is funded by the Innovative Training Network (ITN) project “Algorithms for PAngenome Computational Analysis (ALPACA)” of the Horizon 2020 Marie Skłodowska-Curie (MSC) Work Programme. The candidate will join the Genome-Scale Algorithmics team of Professor Veli Mäkinen, with strong links to the broad Algorithmic Bioinformatics community in Helsinki.

*About the project* 

In our recent work we introduced a new concept called founder block graph. This is a graph structure that can model a pangenome (collection of all genomes of a species) in succinct manner. The blocks of this acyclic graph are founder sequences, i.e., predictions of DNA fragments of the ancestors of the species. Founder segments are connected from block to next block if such connections are supported by measurements from current DNA. We gave a linear time algorithm to construct small indexable founder block graphs. This feature allows to efficiently conduct genome analysis tasks on this sophisticated pangenome representation. The topic for the PhD candidate is to apply founder block graphs for human leukocyte antigen (HLA) analysis to support organ donation diagnostics. This research will be conducted together with our collaborators from the ALPACA network.

The application deadline is Feb 15, 2021.

For more information, see:
https://www.helsinki.fi/en/open-positions/doctoral-student-in-genome-scale-algorithmics

Best,

Veli
--
Veli Mäkinen, Professor
Department of Computer Science
University of Helsinki
www.cs.helsinki.fi/u/vmakinen