Doctoral Position in Genome-Scale Algorithmics

University of Helsinki Department of Computer Science


The University of Helsinki ( is an international scientific community of 40,000 students and researchers. It is one of the leading multidisciplinary research universities in Europe and ranks among the top 100 international universities in the world.

The Department of Computer Science (, which is part of the Faculty of Science, is a leading Computer Science research and teaching unit in Finland. The research themes of the Department cover machine learning and algorithms, computer networks and distributed systems, software systems and bioinformatics.

The Department of Computer Science, Faculty of Science, University of Helsinki invites applications for a

Doctoral Student in Genome-Scale Algorithmics

Position description

The team of Professor Veli Mäkinen is seeking for a PhD candidate in the areas of discrete algorithms, data structures, and computational biology. 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 Mäkinen, with strong links to the broad Algorithmic Bioinformatics community in Helsinki.

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 starting date is in the early autumn 2021, with the exact date negotiable.


The work involves research-related activities, including conducting theoretical and applied research, data analysis, writing research articles, participating in and presenting research at academic conferences, and teaching-related activities. You are also requested to do short stays at our collaborators, both abroad and inside Finland.

The ideal candidate has a strong background in discrete algorithms and data structures, and motivation to develop and apply algorithms in the context of bioinformatics. The following constitute an advantage, but are not required:

• Experience in implementing efficient code.
• Experience with handling high-throughput DNA sequencing data.
• Achievements at international programming contests such as IOI or ACM ICPC.
• Previous research experience and publications.
• Excellent written and oral communication skills in English are needed

Applicants should have an MSc degree in computer science, bioinformatics or a related field.

Applicants should satisfy the requirements of an Early Stage Researcher as defined by the MSC Work Programme: 1) On the starting date of your employment with the University of Helsinki, you are in the first four years of your research career and have not (yet) been awarded a doctoral degree; 2) You have not resided and/or have had your main activity (study, work, etc.) in Finland for more than 12 months during the 3 years prior to the starting date of your anticipated employment with the University of Helsinki.

Applicants are expected to acquire the doctoral student status in the Doctoral Programme in Computer Science at the University of Helsinki during the standard 6-month probationary period.

Salary and benefits

The position is full-time and funded for three years. The salary is competitive and complies with the MSC Work Programme: 3500 euros per month before taxes, consisting of Living and Mobility allowance after compulsory deductions. A conditional Family allowance of 385 euros can be added to the salary.

The University of Helsinki offers comprehensive services to its employees, including occupational health care and health insurance, sports facilities, and opportunities for professional development. The International Staff Services office ( assists employees from abroad with their transition to work and live in Finland.

How to apply

Please submit your application with through the University of Helsinki Recruitment System by clicking the ´Apply for the position` button below.

The application shall include the following attachments as a single pdf file (in English):

• CV with possible publications
• Cover letter describing motivation, research interests, and declaration of satisfying the MSC Work Programme requirements for an Early Stage Researcher
• Contact details of two potential referees who agreed to provide letters of recommendation

Applications will be given full consideration if received by February 15, 2021, 23:59 (CET). Applications received after this date will still be considered, until the position is filled.

Additional information

For more information on the position, please contact Professor Veli Mäkinen (

See also the recent news item on the ITN project:

For more information on the Early Stage Researcher requirements and employment conditions in the MSC Work Programme, please visit

For more information on the Doctoral Programme in Computer Science (DoCS), please visit

And here are some good reasons to move to Finland:

Due date

15.02.2021 23:59 EET


In your application, please refer to


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