Computational Biologist / Bio-informatician

Ghent

13 Dec 2019

Ghent

Yvan Saeys Lab, Bert De Rybel Lab

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About the VIB Centers

VIB‐UGent Center for Plant Systems Biology (PSB): The VIB‐UGent Center for Plant Systems Biology wants to gain insight into how plants grow and respond to the environment. Scientists study how leaves and roots are formed, which microorganisms live on and around the plant and which substances the plant makes. They map out the genetic diversity of the plant kingdom. This knowledge can lead to sustainable innovations in agriculture and food.

VIB‐UGent Center for Inflammation Research (IRC): Inflammation is your body’s response to infection or injury. Normally this is a good defense mechanism. But if something goes wrong with the way this mechanism is controlled, it may result in diseases such as asthma, Crohn's disease or rheumatoid arthritis. The VIB‐UGent Center for Inflammation Research investigates the mechanisms that underlie these diseases, they can develop new treatments and improve existing therapies.

About the labs

The De Rybel lab has a key interest in understanding cell division orientation in plants and how this process contributes to vascular proliferation. The lab has a long-standing expertise in using bulk RNA-sequencing to uncover transcriptional networks during plant developmental processes. More recently, a strong investment was made to establish single cell RNA-seq (scRNA-seq) workflows to further increase resolution at spatial and temporal level. In this case, the wet-lab expertise was developed by the De Rybel lab, while the bio-infomatics expertise and all data analysis was optimised in the Saeys lab. 

The Saeys lab is developing state-of-the-art data mining and machine learning methods for biological and medical applications, and is an expert in computational models to analyse high-throughput single-cell data. Recently, the combined action of the De Rybel and Saeys labs have successfully generated and fully validated a high-resolution single cell atlas of the Arabidopsis root meristem and many more datasets are being generated and analysed at the moment.

Your project

  • Embedded in both the Saeys lab and De Rybel lab, you will support the implementation, analysis and ongoing development of single cell transcriptome data-sets in the context of plant biotechnology.
  • As a true go-between these two collaborative groups, you will work at the intersection between the experimental scientists and the computational scientists.
  • You will be involved in the wetlab data generation pipeline with the De Rybel lab and VIB core facilities to further optimize the existing workflows.
  • You will further develop user interface tools to allow visualization and easy access of the single cell data sets, embedded within an already existing research and service platform.

Profile

  • You have a Bachelor, Master or PhD in Computer Sciences, Life Sciences or equivalent through experience.
  • You have good Linux/command line skills and you are experienced with R and/or python programming
  • You have hands-on experience with (single cell) RNA sequencing or other NGS workflows.
  • Attention to detail, accurate reasoning and problem-solving skills are needed. 
  • You must be able to communicate effectively (written and spoken) in English and act as go-between person between the two research groups
  • Ability to work well independently and within a team environment
  • You have strong time management and communication skills to balance multiple experiments between several collaborators
  • Having a multidisciplinary background in laboratory work and bioinformatics is a plus but not required
  • Experience with web technologies (such as PHP, HTML, CSS, Javascript, vue.js or Laravel) is a plus but not required.

We offer

  • Two fantastic teams with a can-do-attitude which have a strong on-going collaboration
  • A modular team where each scientist has a personal project and their own identity 
  • Access to state-of-the-art VIB Core Facilities and platforms (including the Single Cell Platform). 
  • The opportunity to develop as a single-cell transcriptomics expert in the plant field and within a strong network of collaborators.
  • Financial support is available for a minimum of 2 years with a competitive salary.
  • Starting Date: as soon as possible

How to apply?

For more information contact Bert De Rybel and/or Yvan Saeys. Please complete the online application procedure and include a detailed CV incl. list of publications, a motivation letter and the contact information of three referees.