Postdoc/ PhD student Spatial and single cell seed transcriptomics

Job title:

Postdoc/ PhD student Spatial and single cell seed transcriptomics

Company:

Wageningen University

Job description

We invite motivated candidates to apply for a PhD or Postdoctoral position focusing on the analysis of single cell RNA-seq, tomo-seq, and degradome sequencing data in Arabidopsis thaliana seeds. The aim of this project is to unravel the molecular mechanisms underlying seed germination, with a particular emphasis on spatial and temporal gene expression and translational dynamics.Project Overview:
You will collaborate with a postdoc who generates Spatial (tomo-seq), Single-Cell RNA Sequencing and degradome (5Pseq) data of seeds at different stages during seed germination. Using state-of-the-art bioinformatics approaches, you will:

• analyze high-throughput single cell rna-seq datasets to characterize cell-type specific gene expression during seed germination.
• apply tomo-seq techniques to resolve the spatial distribution of transcripts within the seed tissues.
• integrate degradome sequencing data to study translational dynamics during germination.
• develop and implement innovative data analysis pipelines and visualization tools to integrate and interpret these complex datasets.
• collaborate with seed biologists to connect molecular insights with physiological seed behavior and propose follow-up experiments.

Key Responsibilities:

• design and execute bioinformatics analyses for single cell, tomo-seq, and degradome sequencing datasets.
• develop reproducible workflows for data preprocessing, quality control, and statistical analysis.
• interpret and present results in the context of seed germination biology.
• contribute to manuscript writing and presentations at scientific conferences.
• collaborate with a multidisciplinary research team and contribute to the planning and design of complementary experiments.

Requirements

• a PhD or MSc degree in Bioinformatics, Computational Biology or a related field;
• proficiency in programming languages (e.g., R, Python) and experience with bioinformatics pipelines;
• familiarity with high-throughput sequencing data analysis, ideally including single cell RNA-seq, spatial transcriptomics (tomo-seq), and degradome sequencing;
• strong analytical skills, attention to detail, and ability to work both independently and collaboratively;
• excellent written and verbal communication skills in English;
• a good understanding of plant biology or prior experience with plant research is an advantage.

In our international working environment there is an increasing amount of communication in English. For this position it is about C1.If you do not yet have the track-record required in the vacancy, but do have solid work experience, we would also like to invite you to apply.You will work here
The position is shared between the , led by Prof Leónie Bentsink and Bioinformatics chair group under supervision of Dr Harm Nijveen. The WSSC is embedded at the .Conditions of employment Wageningen University & Research offers excellent . A few highlights from our Collective Labour Agreement include:

• partially paid parental leave;
• working hours that can be discussed and arranged so that they allow for the best possible work-life balance;
• there is a strong focus on vitality and you can make use of the sports facilities available on campus for a small fee;
• a fixed year-end bonus of 8.3%;
• excellent pension scheme.

For PhD – In addition to these first-rate employee benefits, you will receive a fully funded PhD position and you will be offered a course program tailored to your needs and the research team.
The gross salary for the first year is € 2.901,- per month rising to € 3.707,- in the fourth year in according to the (scale P). This is based on a full-time working week of 38 hours. We offer a temporary contract for 18 months which will be extended for the duration of the project if you perform well.For Postdoc- Depending on your experience, we offer a competitive gross salary of between € 3.378,- and € 5.331,- for a full-time working week of 38 hours, in accordance with the (scale 10). As for your contract, we initially offer a one-year contract that can be extended for 2 more years on good performance. Of course, we are happy to have a conversation with you if you have any questions about this.Wageningen University & Research offers plenty of opportunities for growth and development, with a strong internal recruitment policy and excellent training programmes.You will work on the greenest and most innovative campus in the Netherlands, in an international and open working environment. For 20 consecutive years, we have been voted the ” ” in the Netherlands! A place to be proud of.Coming from abroad
Wageningen University & Research is the university and research centre for life sciences. The themes we deal with are relevant to everyone around the world and Wageningen, therefore, has a large international community and a lot to offer to international employees.Because we expect you to work and live in the Netherlands our team of advisors on Dutch immigration procedures will help you with the visa application procedures for yourself and, if applicable, for your family.Feeling welcome also has everything to do with being well informed. Wageningen University & Research’s page contains practical information about what we can do to support international employees coming to Wageningen. Furthermore, our can assist you with any additional advice and information about for example housing, opening a bank account, dual career programs or schooling. Finally, certain categories of international staff may be eligible for a tax exemption on a part of their salary during the first five years in the Netherlands.EmployerWageningen University & Research The mission of Wageningen University & Research is “To explore the potential of nature to improve the quality of life”. Under the banner Wageningen University & Research, Wageningen University and the specialised research institutes of the Wageningen Research Foundation have joined forces in contributing to finding solutions to important questions in the domain of healthy food and living environment. With its roughly 30 branches, 7,600 employees (6,700 fte) and 13,100 students and over 150,000 participants to WUR’s Life Long Learning, Wageningen University & Research is one of the leading organisations in its domain. The unique Wageningen approach lies in its integrated approach to issues and the collaboration between different disciplines.Read the why your future colleagues enjoy working at WUR and watch the video below to get an idea of our green campus!We will recruit for the vacancy ourselves, so no employment agencies please. However, sharing in your network is appreciated.Additional information For more information about this position, please contact Prof. Leónie Bentsink, Personal Professor, or Dr. Harm Nijveen, Researcher, .
Questions about the procedure? Get in touch with Noorien Abbas, Corporate Recruiter, via .Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.This vacancy will be listed up to and including 14 April 2025. We hope to schedule the first job interviews in the week of 21 April, 2025.Procedure
As part of our selection process, an assessment may be incorporated within the procedureWelcome, safe, and valued
Wageningen University & Research (WUR) highly values diversity and inclusion because we believe that different insights lead to innovative solutions. We create a work environment where everyone feels welcome, safe, and appreciated, regardless of background, identity, or experience. Together, we are building a culture where everyone’s unique contribution adds to the success of our organization.Application procedure For more information about this position, please contact Prof. Leónie Bentsink, Personal Professor, or Dr. Harm Nijveen, Researcher, .
Questions about the procedure? Get in touch with Noorien Abbas, Corporate Recruiter, via .Do you want to apply?
You can apply directly using the apply button on the vacancy page on our website which will allow us to process your personal information with your approval.This vacancy will be listed up to and including 14 April 2025. We hope to schedule the first job interviews in the week of 21 April, 2025.Procedure
As part of our selection process, an assessment may be incorporated within the procedureWelcome, safe, and valued
Wageningen University & Research (WUR) highly values diversity and inclusion because we believe that different insights lead to innovative solutions. We create a work environment where everyone feels welcome, safe, and appreciated, regardless of background, identity, or experience. Together, we are building a culture where everyone’s unique contribution adds to the success of our organization.

Expected salary

€2901 per month

Location

Wageningen, Gelderland

Job date

Thu, 20 Mar 2025 23:35:18 GMT

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