[BBC] PhD position in Bioinformatics: Investigating protein evolution using machine learning

[BeNeLux bioinformaticians forum]

The Bioinformatics group at Wageningen University is seeking a PhD student - do you want to apply state-of-the-art machine learning methods on gene sequences and protein structures to analyze evolutionary patterns? Then this vacancy may be of interest to you!

Orphan genes are genes that can only be found in one species. Even though more and more sequencing data is available, we cannot find homologs of these genes outside of that single species. The evolution of such genes is particularly intriguing, since they might arise from very fast divergence beyond recognition or entirely novel “from scratch” from a region that did not code for a protein before. Alternatively, some might simply be artefacts of the automatic annotation. Orphan genes have been mainly studied in eukaryotes, where they are associated with organismal novelties and species-specific traits, and are generally thought to be important for adaptation. Much less is known about prokaryotic orphans. However, prokaryotes evolve rapidly and are exposed to changing environments, in which orphan genes might provide novel adaptations.
In this project, we will investigate orphans in human gut microbiome species. We will use state-of-the art machine learning approaches to study the properties of orphans and to learn about their evolutionary origin and potential function. In particular, we plan to use predicted protein structures to detect remote homology and to investigate the properties of proteins with potentially novel functions. This work will contribute to a fundamental understanding of how proteins evolve.

The research is embedded within the Bioinformatics Group at Wageningen University, the Netherlands. Your daily supervisors will be dr. Anne Kupczok and dr. Aalt-Jan van Dijk, with complementary expertise: molecular evolution of microbes (Anne Kupczok) and machine learning and protein structures (Aalt-Jan van Dijk).
Your qualities

The ideal candidate must have the following qualities:

* A successfully completed MSc degree in bioinformatics, biology, data science or a related discipline;
* Proficiency in programming (e.g. in Python);
* Experience in applying machine learning to biological data;
* Strong affinity with molecular evolution and/or prokaryote genomics;
* Good statistical and mathematical skills;
* Perseverance in problem solving;
* Excellent writing and oral communication skills in English.

You can find more information and the application link here: https://www.wur.nl/en/vacancy/phd-researcher-in-bioinformatics-investigating-protein-evolution-using-machine-learning.htm


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Dr. Anne Kupczok
Assistant Professor
Bioinformatics, Department of Plant Sciences, Wageningen University
http://www.wur.nl/en/Expertise-Services/Chair-groups/Plant-Sciences/Bioinformatics.htm


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