PhD student on Graph Algorithms with Applications in Bioinformatics

There is an opening for a 4-year PhD position between Centrum Wiskunde & Informatica (CWI) and VU Amsterdam. We are looking for a motivated PhD student with a special interest in algorithms and data structures and their application in bioinformatics. The joint project will be supervised by Yasamin Nazari (VU) and Solon Pissis and Daniel Dadush (CWI).

Genomes are strings containing four characters {A, C, G, T} which encode the DNA and the genetic information of an organism. Computational genomics studies algorithms that can efficiently process such strings. The human genome project effort led to a single genome sequence representing the genome information of human DNA. While the vast majority of genome information is similar for all humans, the small individual differences can still offer important insights. 

Recently, there has been a growing interest in pangenomics, where the goal is to process genome information coming from a huge sample of the population. Pangenomic data is often modeled by a graph that captures interaction between different samples. This has motivated the move from string algorithms to graph algorithms. However handling pangenomic graphs is computationally more expensive than single genomes. Even processing a single genome involves many computational challenges, and a wide range of algorithmic solutions have made such tasks possible. This project aims to develop efficient algorithms for processing pangenomic graphs as well as designing pangenomic graphs that “best fit” a given data set. This also involves graph algorithms in different computational paradigms such as dynamic, distributed or parallel models, as well the use of optimization techniques to design pangenomic graphs.

Candidates are expected to obtain a Master’s degree in Computer Science, Mathematics or a related discipline before starting the position. Expected qualifications include mathematical maturity, and familiarity with algorithms and discrete mathematics. Prior knowledge of bioinformatics is not required. Candidates are expected to have an excellent command of English. 

The PhD student will be affiliated with both CWI and VU, and the official employment contract will be transferred to VU Amsterdam after two years.

The terms of employment are in accordance with the Dutch Collective Labour Agreement for Research Centres ("CAO-onderzoeksinstellingen"). The initial labour agreement will be for a period of 18 months. After a positive evaluation, the agreement will be extended by 30 months. The gross monthly salary, for a PhD student on a full time basis, is € 2,781 during the first year and increases to €3,562 over the four year period. Employees are also entitled to a holiday allowance of 8% of the gross annual salary and a year-end bonus of 8.33%. CWI offers attractive working conditions, including flexible scheduling and help with housing for expat employees.

Please visit our websites for more information about our terms of employment:
https://www.cwi.nl/jobs/terms-of-employment  and
https://www.nwo-i.nl/en/working-at-nwo-i/jobsatnwoi/ ​​​​​

Applications should include a detailed resume, a short motivation letter, copy of masters and bachelor transcripts, contact information of 2 reference providers, and preferably evidence of experience in research, and/or mathematical writing (e.g. thesis chapters, publications, manuscripts or relevant course projects).

Applications submitted by May 15th, 2024 will receive full consideration (applications will be accepted until the position is filled).
Tentative start date: September 1st , 2024 (date negotiable).

For more information about the vacancy, please contact Yasamin Nazari ([email protected] ), or Daniel Dadush, [email protected] .

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

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.

Centrum Wiskunde & Informatica (CWI) is the Dutch national research institute for mathematics and computer science and is part of the Institutes Organisation of the Dutch Research Council (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 27 countries, an informal atmosphere and short lines of communication. We have an activity committee that organizes after-work activities and an informal women’s network.  

CWI is located at Science Park Amsterdam, the home of AMS-IX, that is presently developing into a major location of research in the physical sciences in The Netherlands, housing the sciences of the University of Amsterdam as well as several other national research institutes next to CWI.

To find more information about the Network and Optimization (CWI) and Theoretical Computer Science (VU), please visit the group pages:

https://www.cwi.nl/en/groups/networks-and-optimization/

https://www.cs.vu.nl/~tcs/