TU Delft – PhD in Computational Microbiology

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.

Requirements
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.

Delft University of Technology
Delft University of Technology (the TU Delft) is a multifaceted institution offering education and carrying out research in the technical sciences at an internationally recognised level. Education, research and design are strongly oriented towards applicability. The TU Delft develops technologies for future generations, focusing on sustainability, safety and economic vitality. At the TU Delft you will work in an environment where technical sciences and society converge. The TU Delft comprises eight faculties, unique laboratories, research institutes and schools.

Electrical Engineering, Mathematics & Computer Science
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. 

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