PhD Student

Last application date
Jan 31, 2023 00:00
Department
WE09 - Department of Plant Biotechnology and Bioinformatics
Contract
Limited duration
Degree
You hold a Master’s degree in Sciences: Bioinformatics, Computational Biology, Bio-engineering, Biotechnology or equivalent diploma.
Occupancy rate
100%
Vacancy type
Research staff

Job description

The Laboratory of Comparative Network Biology (UGent-VIB Vandepoele lab) invites applications for a fully-funded PhD project for 1 year and extended with another 3 years (after positive evaluation) to study computational regulatory genomics in diatoms. Tentative starting date: April 2023 (can be discussed).

Our understanding of the molecular processes underlying the genetic/phenotypic diversity of diatoms and other microalgae remains very limited, yet it is of crucial importance to understand and predict their response to global change. The successful applicant will employ large-scale sequence analysis (genome, transcriptome, protein-DNA interactions), workflow development, and machine learning to unravel the transcriptionally regulatory code controlling different facets of the diatom life cycle, such as their peculiar size-dependent clock, their unique sexual reproduction pathway and cell cycle progression. Together with experimental co-workers, your computational predictions will be experimentally validated to further improve, using a systems biology approach, our understanding of genome biology in various diatom species.

The project includes:

  • development and application of computational workflows to
    • process bulk and single-cell RNA-Seq data
    • process DAP-Seq protein-DNA interaction data
    • construct gene regulatory networks (using MINI-EX and related network inference tools)
  • building machine learning models to predicting gene expression and learn the underlying regulatory code
  • compare findings across diatom species with different life cycle strategies using state-of-the-art comparative genomics tools
  • interacting with experimental molecular biologist to share, validate and refine your results
  • publishing your research results in international journals (scientific writing)

We offer an intellectually stimulating, international and multi-disciplinary research environment, access to state-of-the-art tools and infrastructure, high-quality training to develop hard and soft skills, opportunities to participate in (inter)national workshops and scientific conferences, and a competitive salary including a bicycle commuting reimbursement. Ghent University is among the top global universities according to several international rankings. The VIB-UGent Center for Plant Systems Biology is a world-leading science institution on Techlane Campus in Ghent, Belgium.

Job profile

  • You obtained excellent grades in your bachelor and MSc degree (i.e., you belong to the top 25% of your cohort).
  • Good programming (Python) and Linux/Unix/command-line skills are a must; experience with R, Nextflow pipelines and Machine learning is an asset.
  • You are enthusiastic about computational / systems biology and want to learn more about applying computational methods for single-cell and regulatory data analysis.
  • You have good communication and writing skills and have an excellent knowledge of written and spoken English.
  • You are highly motivated, self-critical, you work with rigor and attention for detail, and you work accurately.
  • You combine being a team player with a strong sense of autonomy and responsibility.
  • You are willing to apply for additional funding when eligible.

How to apply

Submit your application to Klaas Vandepoele (Klaas.vandepoele@psb.vib-ugent.be) by sending a detailed CV (clearly mentioning your computational skills), a one-page Motivation letter, and contact info of 2 references (including e-mail addresses and phone numbers).