BioSB Young Investigator Award 2020

Jasmijn Baaijens

The selection committee of the BioSB Young Investigator Award 2020 unanimously chose for Jasmijn Baaijens as the winner of the BioSB Young Investigator Award 2020! 

Jasmijn will receive the award during the award ceremony on October 2020, 16:00 and she will give
an honorary lecture.

Biography

Jasmijn Baaijens is a mathematician with a strong drive to solve biological problems. She studied mathematics at Utrecht University, during which she also spent a semester at Université Paul Sabatier in Toulouse, France, to follow several courses in biology. In 2014, she completed the master's program on Industrial and Applied Mathematics at Eindhoven University of Technology. Jasmijn then started her PhD in bioinformatics at Centrum Wiskunde & Informatica (CWI) in the group of Prof. Alexander Schönhuth. Her PhD research focused on algorithm development for reconstruction and analysis of microbial genomes, in particular in the context of viral infections. She presented her PhD thesis “De novo approaches to haplotype-aware genome assembly” in September 2019 and obtained her degree at Utrecht University with the distinction cum laude. Besides research, Jasmijn co-organized the 2017 edition of the annual workshop on Data Structures in Bioinformatics (DSB) in Amsterdam and has been on the DSB Steering Committee since. She is currently a postdoctoral fellow with Prof. Michael Baym at Harvard Medical School, working on bacterial genomics in the context of antibiotic resistance.

 

A reference-free solution to the viral quasispecies assembly problem

The viral quasispecies assembly problem deals with assembling fragments stemming from the RNA from the ensemble of virus strains that have populated individual patients, into full-length strain-resolved genomes. The challenge is that RNA viruses are affected by high mutation rates, which implies that very often strain-specific genomes substantially diverge from existing reference genomes. We developed a collection of tools that together provide a reference-free solution to the viral quasispecies assembly problem. First, we show how to assemble strain-specific contigs using overlap graphs; then, we construct variation graphs from these contigs and build full-length strain-specific genomes, along with estimates for their relative abundance. Benchmarking experiments show that our workflow outperforms state-of-the-art approaches on mixed samples from viral genomes in terms of assembly accuracy as well as abundance estimation. Experiments on longer, bacterial sized genomes demonstrate future applications also in bacterial genomics.

This work was performed at Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, the Netherlands.

Current affiliation: Department of Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA 02115, USA 

 

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Call for nominations

During the BioSB 2020 on October 27, we will present the BioSB Young Investigator Award 2020. The winner will receive a voucher of 500 Euros sponsored by the BioSB research school (to be spend on conference or course participation of their choice) and will be invited to present an honorary lecture in the plenary programme.

Criteria

The candidate must have conducted his/her bioinformatics or systems biology research primarily in a Dutch institute. The primary result on which the award will be based will be the PhD thesis written by the candidate. Therefore, the final version of the thesis of the candidate should have been submitted to the PhD committee at the candidate's university on March 21, 2020 at the latest.

Other criteria that might be considered by the award committee are:

• The candidate significantly contributed to the idea of the research;
• The research of the candidate resulted in novel or improved bioinformatics or systems biology methodologies;
• The research of the candidate advanced life sciences research;
• The candidate independently conducted the research;
• The research resulted in a scientific publication, software application or database;
• The work of the candidate has given broad visibility of bioinformatics or systems biology in the life sciences field;
• The candidate has otherwise significantly contributed to bioinformatics/systems biology or the bioinformatics/systems biology community in the Netherlands.

Procedure

Each nomination must be accompanied with:

• Name and affiliation of candidate
• Motivation for nomination by group leader of candidate
• Curriculum Vitae of the candidate
• A URL to the final version of the PhD thesis (preferably to the PDF of the printed version)

Submission deadline: extended: October 1st, 2020

--> Apply here!

Award committee

The 2020 members of the award committee are:

• Andreas Milias-Argeitis, University of Groningen
• Thomas Abeel, TU Delft
• Hanka Venselaar, Radboudumc
• Vera van Noort, KU Leuven/Leiden University

 

Winner of last year's award: Eva Brinkman (SciLifeLab Stockholm)