PhD student on Graph Algorithms with Applications in Bioinformatics
4 weken geleden
Job description
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.
Requirements
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.
Terms and conditions
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.
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