PhD in Computational Microbiology Delft University of Technology, Department of Electrical Engineering, Mathematics and Computer Science Netherlands

PhD in Computational Microbiology

Department/faculty: Electrical Engineering, Mathematics and Computer Science

Level: Master degree

Working hours: 38 hours per week

Contract: 4 years

Salary: €2222 to €2840 per month gross

Electrical Engineering, Mathematics and Computer Science

The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) is known worldwide for its high academic quality and the social relevance of its research programmes. The faculty’s excellent facilities accentuate its international position in teaching and research. Within this interdisciplinary and international setting the faculty employs more than 1100 employees, including about 400 graduate students and about 2100 students. Together they work on a broad range of technical innovations in the fields of sustainable energy, telecommunications, microelectronics, embedded systems, computer and software engineering, interactive multimedia and applied mathematics.

The Department of Intelligent Systems (INSY) conducts research on processing, interpretation and securing of data. Our aim is to enable man and machine to deal with the increasing volume and complexity of data and communication. We have a strong focus on security, multimedia, and health sciences. The Department pursues its mission by combining fundamental research, engineering and design approaches to model- and knowledge-based methods and algorithms. We actively seek research and technology-transfer collaboration with international scientific peers, companies, and societal organisations.

The Delft Bioinformatics Lab, part of the EEMCS Faculty, performs research and educates students in the field of bioinformatics with broad applications in human, micro- and plant biology. We distinguish ourselves by applying the latest developments in machine learning to design novel, state-of-the-art algorithms that allow the interpretation of biological datasets. We closely collaborate with biochemists, biologists, and geneticists to answer complex biological questions and give direct societal relevance to our tailor-made algorithms.


Job description

Transitioning to a sustainable green economy depends on the creation of efficient ways to convert biomass into useful products such as biofuels or biopolymers. These conversions are often done with micro-organisms engineered to exhibit optimal production characteristics. Understanding the genetic underpinnings of desired phenotypes will open new avenues to create better strains for industrial purposes.


Your goal in this project is to create novel algorithms that resolve haplotypes in microbial genomes. Haplotypes refer to the sequence of all individual chromosome copies typically inherited together from a parent. This within-species genetic heterogeneity is one of the missing pieces in many microbial comparative genomics studies aiming to associate genotypes with phenotypes of interest. For many organisms, we poorly understand the contribution of the diversity within an individual, and one of the key reasons is that we don't have the computational tools to study this diversity.


With the continued improvements in third generation sequencing technology, combined with the vast quantity of data being deposited publicly, this problem is ready for a solution.


You will have three aims:

• Implement reference-guided haplotyping from pangenome reference sequence graphs
• Explore de novo haplotyping from 3rd generation sequencing data
• Investigate copy-number detection at the gene and chromosome scale, and intra-chromosomal DNA variation.



The ideal candidate has an MSc degree in bioinformatics, computer science, or applied mathematics. Affinity with or experience in biology, genomics and/or sequence analysis are desirable. He/she must be able to work effectively in a multidisciplinary team. The candidate shares our view that communication skills are important, as is the ability to interact with peers, students, and technical staff. Programming and scripting experience is required. Experience in microbial genomics is an advantage.


Conditions of employment

The TU Delft offers a customisable compensation package, a discount for health insurance and sport memberships, and a monthly work costs contribution. Flexible work schedules can be arranged. An International Children’s Centre offers childcare and an international primary school. Dual Career Services offers support to accompanying partners. Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities.

As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment; an excellent team of supervisors, academic staff and a mentor; and a Doctoral Education Programme aimed at developing your transferable, discipline-related and research skills. Please visit for more information.


Information and application

For more information about this position, please contact Dr. T. Abeel ( To apply, please e-mail a detailed CV (including grades and English certification if applicable), cover letter and at least two personal letters of reference. Please submit your full application by 15 January 2018 to More information about the section: and the project leader:
When applying for this position, please refer to vacancy number EWI2017-44.

Enquiries from agencies are not appreciated.

If you apply for this position please say you saw it on Computeroxy


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