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HICT: Doctoral Candidate in Compressed Indexing for Pangenomics and Genomic Epidemiology

The Helsinki Doctoral Education Network in Information and Communications Technology (HICT) is a collaborative doctoral education network hosted jointly by Aalto University and the University of Helsinki, the two leading universities within this area in Finland. The network serves as a collaboration platform for doctoral education combining all the relevant subfields of computer science and information technology at Aalto University and the University of Helsinki. It involves at present 80 professors and almost 300 doctoral students, and the participating units graduate altogether more than 40 new doctors each year.

We offer the possibility to join world-class research groups in both universities with multiple interesting research projects to choose from. The list of all open Doctoral Candidate positions in this joint call can be found here:

HICT Doctoral Candidate in Compressed Indexing for Pangenomics and Genomic Epidemiology 

Supervisor(s): Simon J. Puglisi (University of Helsinki)

A pangenome is a catalog of all the genetic variation – single base changes, structural variants, regulatory regions and genes – found within a population or species. Pangenomes are revolutionizing biology, providing new insights into evolution and biodiversity. For example, recent breakthroughs in population genomics have demonstrated that mapping and understanding variation within a species (represented by its pangenome) is becoming essential for most high-impact applications, such as biomarker discovery, pathogen surveillance, modeling tumor evolution and prediction of treatment outcomes. However, searching and mining the pangenome of a species is a computational bottleneck in related bioinformatics pipelines. This project will develop the next generation of indexing data structures that allow fast and scalable search and update of pangenomes. The aim is to design memory-efficient compressed data structures that are simultaneously able to store and enable rapid search over the genomic data that makes up the pangenome, and to design accompanying index construction algorithms capable of scaling to terabytes of sequence data. The project draws on the world-leading expertise in compressed data structures of the PI’s group, as well as that of the wider Algorithmic Bioinformatics research cluster at University of Helsinki.

Ready to apply?

If you want to join our community and start your journey towards Doctoral dissertation submit your application via our electronic recruitment system. The application form will close 6th February 2022 at 23:59 Finnish time (UTC +2).

If you are currently working at Aalto University, please submit your application via HR System Workday (Career – Find jobs – Apply).

Please be prepared to add the following attachments:

  • Cover letter
  • CV
  • Transcript of your Master’s studies

You will be asked to provide also the contact details of 2-3 academic referees.

What we offer?

HICT is a network of world-class professors and researchers with huge passion for their field of study. In HICT you will become part of enthusiastic and professional team of bold and innovative thinkers.

During your Doctoral studies you will be a full-time employee in either Aalto University or the University of Helsinki depending on the supervisor and the research area. You will be covered by occupational health care based on the employment contract.

More information:

General information about the joint HICT call and HICT:

General questions about HICT: Christina Sirviö, HICT team

General questions about recruitment process: Sanni Kirmanen, Aalto University HR

[email protected]

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