VIB Postdoc in Plant Single Cell Biology

Ghent VIB-UGent Center for Plant Systems Biology

17 Jun 2020

Ghent

VIB-UGent Center for Plant Systems Biology

Yvan Saeys Lab, Bert De Rybel Lab

Post-doctoral

1

A postdoctoral research position in the De Rybel lab (VIB) in the area of single cell transcriptomics in crop plants is available. This position is a close collaboration between the De Rybel and Saeys labs at VIB in collaboration with BASF as industrial partner in the framework of an approved VLAIO project. The successful candidate will adapt existing wet lab single cell transcriptomics methodologies to crop plant species and initiate statistical analysis of this data. As such, this position entails the integration of both wet lab and dry lab into one collaborative project.

About the Partners

The De Rybel lab at the VIB‐UGent Center for Plant Systems Biology (PSB) 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 at the VIB-UGent Center for Inflammation Research (IRC) studies the design and application of data mining and machine learning techniques for biomedical applications.  The lab is renowned for its research on single-cell technologies, including flow and mass cytometry, single-cell RNA sequencing, and is currently pioneering novel single-cell technologies including spatial transcriptomics and single-cell multi-omics (e.g. CITE-seq).

The BASF Innovation Center in Gent aims to deliver innovative solutions for BASFs seed business by developing valuable traits for various crops through biotechnology solutions and modern breeding techniques. The activities of the Innovation Center cover all aspects involved with the R&D process, from the initial stages of research to life cycle management, or as we call it, from the lab to the field. The Innovation Center employs a workforce of approximately 400 from 20 different countries at state-of-the-art laboratories space for plant biotechnology research in Zwijnaarde and greenhouse and breeding installations in Astene, Zwijnaarde, and Bottelare.

Your project

  • Embedded in the De Rybel lab at VIB and in close collaboration with the Saeys lab at VIB and BASF as industrial partner, 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 collaborative groups, you will work at the intersection between the experimental scientists and the computational scientists.
  • You will be involved in the wet lab data generation pipeline with the De Rybel lab, BASF and VIB core facilities to further optimize the existing workflows.
  • You will be involved in the dry lab data analysis pipeline with the Saeys lab and BASF to establish and optimise the bio-informatic workflows.

Profile

  • You have a PhD in Plant biotechnology with a strong interest or experience in bioinformatics/computational biology; OR you have a PhD in bioinformatics/computational biology with a clear experience in plant biotechnology.
  • 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 research groups and the company
  • 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 requested. Experience with web technologies (such as PHP, HTML, CSS, Javascript, vue.js or Laravel) is a plus but not required.

We offer

  • A full time post-doc position in the De Rybel lab for 3 years within the framework of a successful VLAIO grant application between the De Rybel lab, the Saeys lab and BASF (Starting Date: September 2020)
  • Working at the interface between Academic (VIB) and Industrial (BASF) teams with a can-do-attitude and a strong on-going collaboration
  • Entrance into our Plant Single Cell Platform with access to state-of-the-art VIB Core Facilities. 
  • The opportunity to develop as a single-cell transcriptomics expert in the plant field and within a strong network of both scientific and industrial collaborators.

How to apply?

For more information contact Bert De Rybel. 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.