Jobs

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!

For the Van de Peer Lab (Bioinformatics and Evolutionary Genomics), in collaboration with the Flemish Research Institute for Agriculture, Fisheries and Food (ILVO) - Plant Sciences Unit, we are looking for a m/f/x doctoral fellow.

About the project

Global climate change will challenge the productivity of major agricultural crops. Therefore, more resilient crops are required to secure sufficient food production worldwide. To create plants with desired productivity and better environmental stress tolerance, strategies such as genome doubling of agriculturally important crops and generating hybrids hold great promise. Yet, just how a plant manages to maintain a double set of chromosomes and how all alleles interact in dynamic genetic networks to create more phenotypic plasticity remains poorly understood.

This fully funded PhD project is part of the Methusalem project granted to Prof. Yves Van de Peer and aims to gain a deeper understanding of polyploidy through genomics, experimental evolution, modeling, and artificial intelligence. Partner institute ILVO explores the benefits of polyploidization in crop breeding by studying genome doubling and interspecific hybrids.

More specifically, this PhD project focuses on species of the nutritious Lolium ryegrass, the drought-tolerant Festuca fescue, the interspecific Lolium hybrids and the intergeneric hybrid Festulolium that combines the parental agronomical traits. Bringing the divergent genomes together widens the range of possible responses to environmental stresses and thus increases the adaptability to new, extreme conditions. However, it also leads to plants with unstable genomes and subsequent elimination of chromosomal fragments over generations, hampering the breeding of superior cultivars. This project aims to unravel the underlying molecular mechanisms driving genome dominance and chromosome elimination in hybrids at different ploidy levels using genomics and transcriptomics together with specialized phenotyping.

About your job

In this project, you will investigate the phenotypic, physiological, and molecular response of interspecific, tetraploid hybrids and their diploid parents in drought experiments and yield trials. Experiments will span the range from single cells to plant populations at the field level, with both fundamental research questions and direct practical applications in plant breeding, through an interdisciplinary approach. You will collect genomic data with high throughput sequencing (HTS) methods, and combine it with phenotypic field observations. Additionally, you will apply molecular markers to study genome constitution and perform single-cell RNA-Seq experiments to study differential gene expression networks. You will apply innovative data analysis workflows to integrate single-cell genotyping with shifts in gene regulatory networks and understand how genome constitution drives phenotypic diversity at the cell, organ, plant, and population levels. You will report the scientific findings through academic publications as well as presentations on (inter)national events.

This project offers the applicant flexibility according to their own interests and a diverse set of learning opportunities within wet lab procedures and bio-informatics. The goal is to obtain a doctoral degree at the end of the research period. The work is performed at ILVO in Melle, a unique and transdisciplinary research institute with an open atmosphere where you will be embedded in a team of fellow PhD students, technicians, and field workers. Finally, the close collaboration with the researchers and plant breeders at ILVO and the interaction with the Van de Peer research group at UGent/VIB offers the applicant the opportunity to develop a broad scientific network.

Profile

• You have a keen interest in applied plant research and in combining wet-lab experiments with bio-informatics.
• Practical experience in a molecular lab and/or HTS data analysis/bio-informatics expertise is strongly recommended.
• You have programming skills in Python or another scripting language, or you are willing to learn it.
• You have good communication and writing skills and have an excellent knowledge of written and spoken English.
• You are highly motivated, enthusiastic and self-critical. You work with attention to detail, and you have an open mindset to learn new skills.
• You combine being a team player with a strong sense of autonomy and responsibility.
• You are willing to apply for additional funding when eligible.
• You are willing to participate in the training and supervision of graduate students.

We offer

• A full-time PhD scholarship of 4 years (starting with 1 year that can be extended with another three years after positive evaluation).
• Your appointment will start by 01/10/2024 at the earliest.
• You will receive a PhD scholarship according to the general conditions at Ghent University. The tax-free scholarship includes full social security coverage. More information on the PhD scholarship can be found on the Ghent University website.
• A multitude of training opportunities organized at Ghent University, VIB and ILVO to broaden your expertise and skill-set.
• You will work in a dynamic research group in a multidisciplinary research institute. All Ghent University staff members enjoy several benefits, such as 36 days of paid leave, bicycle commuting reimbursement, etc.

How to apply? 

Please complete the online application procedure and include a detailed CV, a letter of motivation and the contact details of two referees no later than August 21st, 2024.

For more information about this vacancy please contact Prof. dr. Tom Ruttink or dr. Marlies Peeters (tom.ruttink@ilvo.vlaanderen.be; marlies.peeters@ilvo.vlaanderen.be). Selected candidates will be informed no later than August 28th. Interviews will be held in the second week of September.

The VIB-UGent Center for Plant Systems Biology (PSB, www.psb.vib-ugent.be) is a world-leading plant science institute with the mission to integrate genetics, genomics and computational biology to unravel the biology of plants and to improve the sustainability and climate resilience of crops. The Maere lab at PSB (http://www.maerelab.be) is active in the fields of computational biology, systems biology and evolutionary genomics. Current research topics include testing a novel experimental setup to unravel the molecular wiring of plant phenotypes under field conditions, studying dosage balance-sensitive genes in plants, and modeling the evolution of transcriptional systems in silico. We are currently looking for a talented PhD student to work on experimental evolution of diatoms in the context of a UGent GOA project (4-year position).

Project description

Diatoms are the most productive and species-rich group of microalgae. They have extensively colonized marine, freshwater and terrestrial ecosystems, contributing 20% of all carbon fixation on Earth. Despite the global significance of diatoms, the genetic basis and regulatory mechanisms underlying their evolutionary and ecological success remain largely uncharted territory. Unraveling these mechanisms is crucial to assess how diatoms respond to climate change. In this project, we will experimentally evolve diatoms under selection for resilience against warmer temperatures, and chart the molecular mechanisms underlying diatom adaptation. For the experimental evolution part, we will collaborate closely with the lab of Wim Vyverman at UGent (https://www.ugent.be/we/biology/en/research/protistology).

Profile

• You have an MSc degree in Bioengineering, Biology, Biotechnology, Computational Biology or Bioinformatics.
• You are fascinated by biological evolution.
• Experience with diatom cultivation, experimental evolution and/or evolutionary genomics data analysis is a plus.
• You are fluent in English (spoken and written) and master several programming languages.
• You can work in a team as well as independently.
• You are meticulous, well-organized, responsible and self-critical.
• You take pride in delivering high-quality work.
• You have a passion for science and you can think outside the box.

We offer

• An exciting work environment in a top research institute.
• The opportunity to be part of a dynamic, interdisciplinary and international team.
• A challenging project in a competitive field of science.
• Ample opportunity to learn new skills.
• An attractive salary.

Please complete the online application procedure and include a detailed CV, a letter of motivation and the contact details of two referees. Applications are accepted until the position is filled. For more information, contact Steven Maere (steven.maere@psb.vib-ugent.be).

The VIB-UGent Center for Plant Systems Biology (PSB, www.psb.vib-ugent.be) is a world-leading plant science institute with the mission to unravel the biology of plants and use the insights gained to improve the sustainability of agriculture and the climate change resilience of crops. The Maere lab at PSB (http://www.maerelab.be) is active in the fields of computational biology, evolutionary genomics and plant systems biology. Current research topics include testing a novel experimental setup to unravel the molecular wiring of plant phenotypes under field conditions, studying dosage balance-sensitive genes in plants, and modeling the evolution of transcriptional systems in silico. We are currently looking for a talented postdoc to join our team in the context of the VIB Grand Challenge project ‘Validating the use of endemic rhizobia for sustainable soybean cultivation in Northwestern Europe’.

Project description

Soybean (Glycine max) is one of the most important protein sources in human food and animal feed. Europe is highly dependent on the import of soybean, often from (sub)tropical areas where soybean cultivation is one of the main drivers of deforestation. Establishing European soybean production at scale may not only help curtail deforestation in crucial ecosystems such as the Amazon, Cerrado and Gran Chaco, but would also reduce Europe’s dependence on soybean imports, reduce the associated carbon footprint and facilitate the ongoing transition to more plant protein and less animal protein in the European diets. Moreover, in symbiosis with nitrogen (N)-fixing bacteria (rhizobia) inside root nodules, soybean can manage its own N nutrition, reducing the need for N fertilization. In combination with a reduced import of soybean products (and the associated N) from overseas, local and circular soybean cultivation may help mitigating some of the N pollution issues in Europe. Although soybean is predominantly a (sub)tropical crop, soybean varieties that are better adapted to more temperate climates with cold springs, such as those found in Northwestern (NW) Europe, have already been bred. However, the current commercially available rhizobial inoculants needed to establish N-fixing nodules on soybean roots are based on non-endemic rhizobial strains that are poorly adapted to local environmental conditions, causing soybeans cultivated in NW Europe to have suboptimal and variable yield and protein content. The aim of this project is to assess whether using endemic rhizobia as soybean inoculants instead of exotic strains improves soybean yield, protein content and yield stability.

In the previous VIB Grand Challenge (GC) project ‘Soy in Flanders’ (https://sojain1000tuinen.sites.vib.be/en), we engaged 1000 citizens to grow soybean plants in their garden and trapped several endemic rhizobia that are able to nodulate soybean. In the present GC project, we will test the performance of the most promising of these endemic strains versus commercial strains in field trials and on farmers’ fields across Belgium. In each field, we will profile soil type, nutrient composition, soil and nodule microbiomes, nodule phenotypes, seed yield, seed protein content and biological nitrogen fixation for several combinations of soybean variety and rhizobial strain. Together with Steven Maere, you will be coordinating efforts across 8 participating labs from research institutes across Flanders. Additionally, you will be in charge of data integration and the construction of machine learning models to unravel which environmental factors influence rhizobial strain performance in the field.

Profile

• You have a PhD in Computational Biology, Biotechnology or Bioengineering.
• You have excellent project management and communication skills and you like to take initiative.
• You have solid expertise in machine learning, analysis of genomics data and data integration. Hands-on experience with microbiome data analysis is a plus.
• You are fluent in English (spoken and written) and master several programming languages.
• You found a good balance between working in a team and working independently.
• You are meticulous, well-organized, responsible and self-critical.
• You have a passion for science and you can think outside the box.

We offer

• A 3-year postdoc position with an attractive salary.
• An exciting work environment in a top research institute.
• The opportunity to be part of a dynamic, interdisciplinary and international team.
• A challenging project with high societal value.
• Ample opportunity to learn new skills.

How to apply?

Please complete the online application procedure and include a detailed CV, a letter of motivation and the contact details of two referees. Applications are accepted until the position is filled. For more information, contact Steven Maere (steven.maere@psb.vib-ugent.be).

Postdoctoral researcher and a PhD student to investigate the interplay between the Secretory Carrier Membrane Proteins and the plasma membrane aquaporins in Arabidopsis.

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. 

Research at the Van Damme lab (https://www.vandammelab.be/) is centered around membrane trafficking in plants and we combine cell biological and biochemical/structural approaches to answer our research questions. We are highly passionate about the endocytic pathway that controls the plasma membrane proteome and we investigate its machinery, as well as its downstream cargo.

UCLouvain is the largest university in the French-speaking part of Belgium. It is located in Louvain-la-Neuve, 30 km south of Brussels. The Chaumont laboratory (https://uclouvain.be/en/research-institutes/libst/francois-chaumont.html) belongs to the Institute of Louvain Institute of Biomolecular Science and Technology (LIBST), which brings together more than 180 research staffs working in the field of biochemistry, molecular and cell biology. Chaumont’s team is fascinated by the molecular and cellular mechanisms regulating physiological processes and, especially, by the regulation and function of aquaporins, which are involved in numerous developmental and physiological processes related to water relations but also to the movement of other physiological and signalling molecules.

The Van Damme lab and the Chaumont lab have joined forces via an FWO-weave project. Within this project, there are two 4-year positions available. A postdoctoral researcher position in the Van Damme lab and a PhD position in the Chaumont lab. The PhD student and the postdoc will work in close collaboration on the interplay between the secretory carrier membrane proteins (SCAMPs), which are cargo of the endocytic TPLATE complex (Arora et al., Plant Cell 2020 and Yperman et al. Science Advances 2021), and the plasma membrane aquaporins (PIPs). We aim to identify how the SCAMP proteins are involved in the trafficking and/or activity of the PIPs. The research will involve interactomics, live cell imaging, mutant analysis, structural modelling (e.g. AF2) as well as physiological assays on water permeability in Arabidopsis protoplasts as well as in Xenopus oocytes. The PhD student will be based in UCLouvain and the postdoc will be based in Ghent. As this is a truly joint project, both the student and the postdoc will be able to benefit from the available expertise in both labs.

Profile

Profile 1. PhD student

• Master's degree in biology/bio-engineering, or equivalent, with a strong interest in plant biology and some experience in plant molecular and cellular biology or physiology.

Profile 2. Postdoctoral researcher

• Ph.D. degree in Biotechnology, Biochemistry, Biology, Bio-engineering, or equivalent.
• Required proven expertise in: live cell imaging, cloning (e.g. Golden Gate, Gibson), protein biochemistry, guidance of master and/or PhD students.
• Desired expertise in: interactomics, stomatal dynamics, Alphafold modelling. Experience in supervising Ph.D. students is also considered a plus.

We welcome applications from dynamic individuals with a strong drive for science and motivation. Ideal candidates take initiative, possess a strong sense of responsibility, have critical thinking abilities, have excellent oral and written English communication skills, and have a collaborative mindset. Additionally, they should demonstrate the capacity to independently plan and execute research with precision.

We welcome the willingness of candidates to apply for personal fellowships in order to achieve their own individual funding. For the PhD student, this will imply applying for a FNRS and/or FRIA fellowship. Eligibility for Marie Curie and/or EMBO postdoctoral fellowship applications will be to your benefit.

Join us to undertake a highly innovative project that combines cell biology and plant physiology and that has the potential to discover novel ways how drought tolerance of plants can be increased.

We offer

• State-of-the-art laboratory environment.
• An inclusive group atmosphere and a spot in a dynamic and diverse team of researchers.
• A versatile and challenging academic environment with very diverse contacts.
• Various opportunities to broaden your expertise and to train in many cutting-edge technologies.
• Training courses in academic, technical, and career skills.
• An initial 1-year contract, which can be extended up to 4 years.

Starting Date: as soon as possible.

How to apply?  

Interested candidates can only apply through the VIB online application tool. Candidates should clearly specify whether they apply for the PhD or the postdoc position.

• A complete application file (English, single pdf) should contain the following documents:
• A 1-page summary of your research experiences and future goals
• A one-page letter of intent describing your motivation for this position. The motivation for the position should be focused on the project (what would you like to do when you get it) and not on previous achievements.
• a detailed CV including a publication list
• contact information of 2-3 references

The first review of applications will start from the moment applicants apply. A shortlist of applicants will be selected and invited for interviews. The position remains open until a suitable candidate is found.

For further information and questions, please send an email to both Daniel Van Damme and to Francois Chaumont (dadam@psb.vib-ugent.be and francois.chaumont@uclouvain.be).