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We are looking for a talented and motivated PhD student with a special interest in algorithms and data structures and their application in bioinformatics (sequence analysis). The PhD student will be positioned at CWI within the "Algorithms for PAngenome" (ALPACA) network

( funded by the European Commission through the Horizon 2020 Marie Sklodowska-Curie ITN Programme.

The move from sequence- to graph-based pan-genome data structures is unavoidable when seeking to exploit the wealth of genome data, instead of having devices massively congested. Putting the paradigm shift (from sequences to graphs) in effect requires new ways of thinking about genomes, as well as computer programs and mathematical models that reflect this. However, developing, maintaining and computationally exploiting graph-based pan-genomes requires skills that common-day education does not yet provide. The goal of ALPACA is to train a new class of researchers who are able to deal with the masses of genome data in terms of the progressive, graph-based approaches the research of this project deals with.


Objectives: Comparing pan-genomes amounts to comparing two graphs, generalizing the idea to align two genomes. We aim at developing algorithms for 'whole-pan-genome alignment'. Though for aligning two networks approaches already exist, they do not address the peculiarities of pan-genome graphs, in, for example, de Bruijn graph or variation graph based pan-genomic data structures. We will address these particular issues in full detail.


 Supervised by: Solon P. Pissis (


Co-supervised by: Leen Stougie (



Candidates are required to have a Master’s degree in Computer Science, Mathematics or a related discipline, and a specialization in Algorithms, Combinatorics, Combinatorial Optimization or related fields. Preferable qualifications for candidates include proven research talent in a Master’s project, an excellent command of English, and good academic writing and presentation skills.


On the starting date of their employment with CWI, candidates must be in the first four years of their research career and have not (yet) been awarded a doctoral degree. Candidates also must not have resided and/nor have had their main activity (study, work, etc.) in the Netherlands for more than 12 months during the 3 years prior to the starting date of their employment with CWI.


More details and application instructions can be found here:


Application deadline: April 30, 2021

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