I'm looking to recruit one PhD student (full-time employment, ~3.5 - 4 years) for a Bioinformatics project at the University of Helsinki, involving graph algorithms (focusing on network flows and flow decompositions) for long-read RNA-seq assembly problems and possibly pan-genomics problems.
Ideally, the candidate has a strong algorithmic and/or programming background, but also (strong) knowledge of Bioinformatics and an interest to apply graph algorithms in developing practical Bioinformatics tools. However, there is flexibility in adapting the project to the interests and expertise of the student. The student is expected to take an active role in leading the project, working with the team members and international collaborators, and doing possible research visits abroad.
The person will join my Graph Algorithms team, which is part of the wider Algorithmic Bioinformatics group at the University of Helsinki. The team consists of 3 PhD Students, 2 Postdocs, and we are currently funded also by an ERC Starting Grant.
For some key pointers related to this position, see:
- Dias et al. "Fast, Flexible, and Exact Minimum Flow Decompositions via ILP" https://link.springer.com/chapter/10.1007/978-3-031-04749-7_14 (RECOMB 2022)
- Khan et al. "Safety and Completeness in Flow Decompositions for RNA Assembly" https://arxiv.org/abs/2201.10372 (RECOMB 2022)
- Prjibelski et al. "IsoQuant: a tool for accurate novel isoform discovery with long reads" https://www.researchsquare.com/article/rs-1571850/v1
- Cáceres et al. "Width Helps and Hinders Splitting Flows" https://arxiv.org/abs/2207.02136 (ESA 2022)
The application deadline is August 28, and applications are done via our doctoral school https://hict.fi/admissions/ (mentioning the project "Graph Algorithms for Long-Read Sequencing Data"). After the deadline, the position will remain open until a suitable candidate is found. Applications after the deadline are possible by e-mail to alexandru.tomescu@helsinki.fi . If you are interested in applying shortly after the deadline, please send as soon as possible a notification to my e-mail address including at least your CV.
Required documents:
1. Letter of motivation (max. one page)
2. A curriculum vitae and list of publications
3. A study transcript
4. A copy of the M.Sc. degree certificate
5. Contact details of two possible referees
We are based at the Department of Computer Science, University of Helsinki, Finland, in a city that often ranks among the best places to live in the world. Despite being a capital, Helsinki is a very easy city to live in, with lots of green areas, an efficient public transport system and a housing market rather accessible. Helsinki offers easy access to national parks or islands within the metropolitan area: nature lovers, this is the place to be!
Candidates from a minority background in our field are warmly encouraged to apply!
For any inquiry, please do not hesitate to contact me.
Best regards,
Alexandru Tomescu
Associate Professor and Academy of Finland Research Fellow
alexandru.tomescu@helsinki.fi
https://www.cs.helsinki.fi/u/tomescu/
https://www2.helsinki.fi/en/researchgroups/algorithmic-bioinformatics/teams/graph-algorithms
https://www2.helsinki.fi/en/researchgroups/algorithmic-bioinformatics/teams
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