Jobs

About the Lab/PSB

The VIB-UGent Center for Plant Systems Biology (PSB) is a world-leading plant science institute located at the heart of a renowned Plant Biotech campus in Ghent, Belgium. Its mission is to unravel plant biological processes and translate this knowledge into value for society. Please visit us at www.psb.ugent.be for more information. 

Within the framework of an ERC Starting Grant, the lab of Prof. Inge De Clercq (https://www.psb.ugent.be/groups/inter_organelle_stress_signalling) aims to understand how plant cells perceive environmental signals (e.g. from attack by pathogens) and translate this into appropriate defence responses. We focus on studying the central role of intracellular organelles (mitochondria, chloroplasts, and the ER) in stress signal transduction, and uncover the mechanisms of how these organelles communicate with each other through stress-induced contact sites. To this end, we use interdisciplinary approaches by combining high-end cell biology (confocal and super-resolution microscopy), proteomics, proximity labelling, various other omics approaches and bioinformatics.

Job description

An ERC Starting grant-funded postdoc position is available in the group of Prof. Inge De Clercq at the VIB-UGent Center for Plant Systems Biology (PSB) and Ghent University, Belgium.

You will study inter-organelle (between mitochondria, chloroplasts, and the ER) communication during the plant’s interaction with pathogens. Your project is embedded within the ERC-STG grant, entitled “COSI: Understanding organelle communication through COntact SItes in plant stress responses”, which studies the direct association between organelles through stress-induced contact sites by implementing state-of-the-art cell biology and proteomics approaches. With this exciting project, we seek to provide new mechanistic and functional insight into how stress signals are perceived and transduced between intracellular organelles and how they are translated into appropriate defence responses. You will design and implement tools to detect the dynamic (or reversible) association between organelles and use these tools to monitor contact site dynamics during various (biotic and/or abiotic) stress conditions using confocal microscopy and super-resolution microscopy. In addition, you will be involved in the characterization of the dynamic proteome at these stress-induced contact sites. You will also be involved in guiding a Ph.D. project focusing on this topic.

Profile

Essential

  • You have a Ph.D. degree in Biotechnology, Biochemistry, Biology, Bio-engineering, or equivalent.
  • You are an expert in plant molecular biology and cell biology.
  • You can plan and conduct research independently and accurately.
  • You have a keen interest in organelle/cell biology, proteomics, intra-cellular signalling and plant-pathogen interactions.
  • You have excellent English communication skills.

Desirable but not required

  • Experience from Ph.D. and/or postdoc in plant cell biology, confocal microscopy, super-resolution microscopy, proteomics, and/or plant-pathogen assays is a plus as well as a publication record in peer-reviewed journals showing clear expertise in these areas.
  • Experience in supervising Ph.D. students is not required but is also considered a plus.

Key personal characteristics

  • You should work well in a team as you will be integrated into the international research environment of the VIB-UGent Center of Plant Systems Biology and participate in international collaborations.
  • You are proactive in establishing contacts with experts to solve problems and to communicate with other members of different team(s).
  • You have a strong sense of responsibility and maintain a clean working environment.

We offer

  • A 2-year postdoc position with possibilities for prolongation and/or for applying for personal funding.
  • An exciting and innovative project embedded in the ERC-STG 2020 grant ‘COSI’, covering an interesting combination of state-of-the-art techniques including cell biology (confocal microscopy, monitoring dynamic protein-protein interactions and (inter-)organelle dynamics, and high-resolution microscopy), proteomics (proximity labelling based on TurboID, protein pulldown), biochemistry, plant stress assays and various omics approaches.
  • A multidisciplinary and highly stimulating and supporting international research environment.
  • Access to state-of-the-art tools and infrastructure including core facilities for proteomics and super-resolution microscopy.
  • Various training opportunities are organized at VIB to broaden your expertise and skills (training.vib.be).

How to apply?

Interested candidates are asked to apply online.

Additional requirements:

  • A 1–page summary of your motivation for the position, your research experiences and future goals
  • Detailed CV including publication list
  • Contact information of 2-3 referees

in one PDF document.

The first review of applications will start immediately. A shortlist of applicants will be selected and invited for interviews.

The position remains open until a suitable candidate is found.

About the Lab

The VIB-UGent Center for Plant Systems Biology (PSB) is a world-leading plant science institute located at the heart of a renowned plant biotechnology campus in Ghent, Belgium. Its mission is to unravel plant biological processes and translate this knowledge into value for society. The Functional Phosphoproteomics group (https://www.psb.ugent.be/index.php/groups/functional_phosphoproteomics), led by Prof. Ive De Smet at PSB, tackles early temperature signalling in plants, such as the model plant Arabidopsis thaliana and the crop plants wheat and soybean. To unravel this, we focus on dynamic changes in protein phosphorylation status, since temporary and reversible phosphorylation of proteins is essential in regulating various processes. Through a phosphoproteomics approach, the lab has identified potential key regulators of thermomorphogenesis in A. thaliana and wheat, which we started to functionally characterize (see, for example, Zhu et al 2021 Nature Communications 12:4804 and Vu et al 2021 Nature Communications 12:2842).

Job description

The De Smet lab is looking to recruit 1 highly-motivated postdoctoral researcher, who will be involved in elucidating the underlying signalling mechanisms that play a role in regulating plant growth under a changing climate, especially high temperature. The postdoctoral research will leverage Arabidopsis, wheat and soybean data to identify key temperature signaling components. The successful candidate will use a multidisciplinary approach, combining biochemistry (phosphoproteomics), cell biology (confocal microscopy), computational biology (data analyses and modelling), and plant genetics (functional characterization of key regulators). Overall, the project will contribute to our understanding of how an environmental signal (temperature) is perceived by the plant and converted into developmental and physiological responses.

Profile

Essential

  • You have a PhD in (plant) molecular biology with max. 4 years of postdoc experience
  • You are an expert in molecular biology and/or plant biotechnology
  • You are an expert in computational biology
  • You have guided (master/PhD) students and/or technicians
  • You can take initiative, function well in a team, and have a hands-on mentality, perseverance and critical mindset
  • You are proficient in the use of the English language for both oral and written communication
  • You are eligible for Marie Curie and/or EMBO postdoctoral fellowship applications

Desirable but not required 

  • Experience with proteomics, interactomics and/or confocal microscopy
  • Experience with a crop, ideally wheat or soybean, will be to your benefit
  • A publication record in peer-reviewed journals in the field of ‘animal and plant sciences’ is an asset

Key personal characteristics 

  • You are proactive in establishing contacts with experts to solve problems and to communicate with other members of the different team(s).
  • You have a strong sense of responsibility, maintaining a clean working environment.
  • You can accurately compile and document experiments (using an ELN)
  • You have a no-nonsense can-do attitude.
  • You build team interactions quickly. You feel great in a fun team and add to that spirit.
  • You communicate clearly, candidly, and respectfully.

We offer

  • A 1+2-year postdoc position
  • A multidisciplinary, highly stimulating and supporting international research environment at VIB and Ghent University (UGent)
  • Access to state-of-the-art tools and infrastructure, including core facilities for proteomics
  • Various training opportunities are organized at VIB to broaden your expertise and skills (training.vib.be).
  • Tentative start date: 1 August 2024

How to apply? 

Submit your application through the VIB application tool. The call will remain open until a suitable candidate is identified. Make sure that your application includes:

  • A detailed CV
  • A one-page summary of past research activities (e.g. in PhD/PostDoc projects)
  • A one-page letter of intent describing your motivation for this position, how your research experiences and interests are aligned with those of the lab and research topic and future goals
  • The names and contact details of 3 referees

Job description

The Vandepoele research lab (Comparative Network Biology - https://www.vandepoelelab.be/ ) invites applications for a fully-funded PhD project for 1 year and extended with another 3 years (after positive evaluation) to study regulatory genomics in plants using different computational and -omics approaches.

Starting from large-scale experimental datasets (e.g., bulk and single-cell RNA-Seq, ChIP/DAP-Seq protein-DNA interaction data, bulk, and single-cell ATAC-Seq) and the application of diverse supervised machine learning approaches (e.g., feature-based, deep learning, and explainable artificial intelligence), the goal of the project is to unravel the complex regulatory code controlling gene expression in the multicellular model plant Arabidopsis thaliana

Together with your colleagues in the Vandepoele lab, sharing complementary expertise in plant biology, genomics, and informatics, you will focus on characterizing the regulatory sequences driving context-specific gene expression in different organs, cell types, and stress conditions. Experimental validation of your computational results will be performed through collaboration with wet lab colleagues in the VIB-UGent Center for Plant Systems Biology.

Relevant publications

  • Obtaining genetics insights from deep learning via explainable artificial intelligence. Novakovsky G, Dexter N, Libbrecht MW, Wasserman WW, Mostafavi S. Nat Rev Genet. 2023 Feb;24(2):125-137. doi: 10.1038/s41576-022-00532-2
  • Predicting transcriptional responses to heat and drought stress from genomic features using a machine learning approach in rice. Smet D, Opdebeeck H, Vandepoele K. Front Plant Sci. 2023 Jul 17;14:1212073. doi: 10.3389/fpls.2023.1212073
  • MINI-EX: Integrative inference of single-cell gene regulatory networks in plants. Ferrari C, Manosalva Pérez N, Vandepoele K. Mol Plant. 2022 Nov 7;15(11):1807-1824. doi: 10.1016/j.molp.2022.10.016
  • Charting plant gene functions in the multi-omics and single-cell era. Depuydt T, De Rybel B, Vandepoele K. Trends Plant Sci. 2023 Mar;28(3):283-296. doi: 10.1016/j.tplants.2022.09.008

Profile

Essential

  • 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.
  • You have a good understanding of molecular biology and recent RNA and DNA-based -omics profiling methods.
  • You are enthusiastic about computational / systems biology and want to learn more about applying machine learning for (single-cell) 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 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.

Desirable but not required 

  • Experience with machine learning (e.g., Scikit-learn/PyTorch/Tensorflow/Keras) is a plus.
  • Experience with explainable AI (e.g., SHAP) is a plus.
  • Experience with high-performance computing, software containers is a plus.
  • Knowledge about plant biology/genomics is a plus.
  • Experience with software development tools (e.g., GIT/Nextflow) is a plus.

We offer

  • An intellectually stimulating, international and multi-disciplinary research environment
  • Access to state-of-the-art tools and (CPU/GPU) infrastructure
  • High-quality training to develop hard and soft skills (VIB and UGent Doctoral Schools)
  • Opportunities to participate in (inter)national workshops and scientific conferences
  • A competitive salary including benefits

The VIB-UGent Center for Plant Systems Biology is a world-leading science institution on the Techlane Campus in Ghent, Belgium. Ghent University is among the top 100 global universities according to several international rankings.

Tentative starting date: August 2024 (to be discussed).

How to apply?

Interested candidates are invited to submit a detailed CV (clearly mentioning your computational skills), a cover letter outlining their research interests and relevant experience, academic transcripts, and contact information for at least one reference.

Please submit your application via the VIB application tool.

For more information or inquiries about the position, mail to klaas.vandepoele@psb.vib-ugent.be

We look forward to welcoming you to our team at the VIB-UGent Center for Plant Systems Biology!