Centrum Wiskunde & Informatica (CWI) has a vacancy in the Life Sciences and Health (LSH) research group for a talented

PhD student,

on the subject of Computational Pan-genomics: Algorithms & Applications.

Job description

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 (website) 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 genetic 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/statistically exploiting graph-based pan-genomes requires skills that common-day education does not yet provide. The goal of this project is to train a new class of researchers who are able to deal with the (exabyte-scale) 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 and software 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. In addition, we will study phylogenetic relations within and across pan-genomes. In applications, we will compare also 'pan-transcriptomes', e.g. liver cell with colon pan-transcriptome, and microbiomes, integrated into pan-genomes, so as to accurately identify the commonalities and differences between the two entities.

Supervised by: Solon P. Pissis (website) and Leen Stougie (website).

Requirements

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.

Terms and conditions

The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The PhD student will be formally employed by CWI with a full social security coverage, and they will have all the benefits provided for in the Marie Curie ITN fellowships regulations (version 2, 11/11/2019), including a highly competitive remuneration, living allowances and mobility expenses. In principle this results into a starting salary of €2807,- gross monthly salary on a full time basis. The initial labour agreement will be for a period of 18 months. After a positive evaluation, the agreement will be extended by 18 months.

Please visit our website for more information about our terms of employment: https://www.cwi.nl/jobs/terms-of-employment

Information and application

All applications should include a detailed resume, motivation letter, list of your MSc courses and grades, copy of your Master’s thesis and preferably a list of publications.

The deadline for the position is Jan 31, 2021.

For residents outside the EER-area, a Toefl English language test might be required.

For more information about the vacancy, please contact Solon P. Pissis, email solon.pissis@cwi.nl, telephone +31 20 592 4263.

For more information about CWI, please visit www.cwi.nl or watch our video about working at CWI.

Diversity code

CWI encourages a diverse workforce: we endeavour to develop talent and creativity by bringing people from different backgrounds and cultures together. We recruit and select based on capabilities and talent. We strongly encourage everyone with the appropriate qualifications to apply for the vacancy, regardless of age, gender, origin, sexual orientation or physical abilities.

About CWI

Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and is an institute of the Netherlands Organisation for Scientific Research (NWO). The mission of CWI is to conduct pioneering research in mathematics and computer science, generating new knowledge in these fields and conveying it to trade, industry, and society at large. CWI is an internationally oriented institute, with 160 scientists from approximately 30 countries. The facilities are first-rate and include excellent IT support, career planning, training, and courses.  CWI is located at Science Park Amsterdam that is presently developing into a major location of research in the natural sciences in the Netherlands, housing the sciences of the University of Amsterdam as well as several other national research institutes next to CWI.

About Research group

To find more information about the ALPACA network, please visit the ALPACA website. To find more information about the LSH research group, please visit the LSH website.