Doctoral Fellow in Biochemistry and Microbiology

Occupancy rate: 100%

Vacancy type: Research staff

ABOUT GHENT UNIVERSITY

DC10: Mining the functional microproteome landscape using thermal proteome profiling

About ORFeus

ORFeus is a Marie Skłodowska-Curie Actions Doctoral Network (MSCA-DN) under Horizon Europe: 15 academic groups, 13 industry and research partners, and a panel of independent academic advisors, training 15 doctoral candidates across Europe. The network investigates the dark proteome, the proteins and peptides made from overlooked or non-canonical open reading frames and what they mean for human disease, combining ribosome profiling and translatomics, proteogenomics, mass spectrometry-based proteomics and immunopeptidomics, large-scale genomics, and machine learning to map novel translation products and test their potential as targets for diagnosis, immunotherapy, and drug development in cancer and beyond.

Each doctoral candidate runs an individual project within this shared program, supported by two academic supervisors, an industry or partner secondment supervisor, and an independent academic advisor. Each project includes a secondment of around three months with a partner organization, as well as network-wide schools, workshops, and conferences.

About Ghent University

Ghent University is a world of its own. Employing more than 15.000 people, it is actively involved in education and research, management and administration, as well as technical and social service provision on a daily basis.

With its 11 faculties and more than 85 departments offering state-of-the-art study programmes grounded in research in a wide range of academic fields, Ghent University is a logical choice for its staff and students.

YOUR TASKS

You will join the group of Prof. Petra Van Damme at the Laboratory of Microbiology, Department of Biochemistry and Microbiology, where you will work in an interdisciplinary research environment combining molecular microbiology, bacterial infection biology, and advanced proteomics, including thermal proteome profiling, to study microproteins and the dark proteome. You will work closely with the group of Dr. Danny Sahtoe at the Hubrecht Institute, who brings complementary expertise in computational protein design and structural biology. You will enroll as a PhD candidate at Ghent University and participate in the doctoral training programme of the Doctoral School of Sciences.

The position

Only a fraction of the genome codes for the proteins in standard reference catalogs. Many small open reading frames (smORFs) scattered across the genome are translated into microproteins that these catalogs miss, and while growing numbers of microproteins are being discovered, their biological functions and the molecular interactions through which they act remain largely unknown. Thermal proteome profiling (TPP), a mass-spectrometry method that measures how the thermal stability of a protein shifts when its binding partners or conditions change, offers a way to assign function to these previously hidden proteins.

This project will systematically characterize the functional landscape of microproteins in the enteropathogen Salmonella enterica serovar Typhimurium, using TPP across smORF deletion strains and multiple conditions to to identify functional associations and candidate interaction partners across the Salmonella microproteome. It sits at the center of ORFeus Work Package 2, which moves from discovery to function: the structural and biophysical data it generates feed an iterative design-test cycle with a computational protein-design project, while the standardized TPP workflows developed here are adapted for host-pathogen proteomics elsewhere in the network. The work also connects to evolutionary analysis of microprotein function and to the wider consortium through the shared ORFeome platform.

Main tasks:

• Develop and standardize thermal proteome profiling protocols to measure changes in protein stability and abundance across a panel of smORF deletion strains and multiple growth conditions in Salmonella.
• Integrate the thermal proteome profiling data with protein structure prediction (for example AlphaFold and RoseTTAFold), working with the computational protein design project of another doctoral candidate (DC) in the network, here DC6, to infer protein-protein interactions involving microproteins.
• Validate high-confidence interactions in vitro using biophysical methods such as biolayer interferometry and SEC-MALS, building a validated interaction map for the Salmonella microproteome.
• Collaborate across the ORFeus network by sharing standardized TPP workflows with related projects, including host-pathogen proteomics in DC4, contributing datasets to the shared ORFeome platform, and contributing to the project's scientific reporting.

Methods and platforms: thermal proteome profiling (TPP) and quantitative mass spectrometry-based proteomics, construction and phenotyping of smORF deletion strains in Salmonella, protein structure prediction (AlphaFold, RoseTTAFold) for interaction modeling, and in vitro biophysical validation (biolayer interferometry, SEC-MALS), with datasets shared through the ORFeome platform.

Secondment: you will spend around three months at Bruker (Bremen, Germany), optimizing the thermal proteome profiling workflows on advanced mass-spectrometry platforms. You will also be guided by an independent academic advisor, with the possibility of a short, primarily virtual research exchange to strengthen the project.

WHAT WE ARE LOOKING FOR

Your profile

MSCA eligibility (do not edit, compliance)
You must meet all of the following on your recruitment date:

• You do not already hold a doctoral degree. If you have defended a doctoral thesis but the degree has not yet been formally awarded, you are not eligible.
• Mobility rule: you must not have lived or carried out your main activity (work, studies, and so on) in Belgium for more than 12 months in the 36 months immediately before your recruitment date. Compulsory national service, short stays such as holidays, and time spent in a procedure to obtain refugee status under the Geneva Convention do not count toward the 12 months.
• You hold, or will hold before the start date, a degree that formally entitles you to enroll in a doctorate, and you can enroll in the doctoral program at Ghent University.

Candidates of any nationality may apply. There is no limit on prior research experience, as long as you do not already hold a doctorate.

• A master's degree (or equivalent) in biochemistry, molecular biology, microbiology, biotechnology, biomedical sciences, analytical chemistry, or a related life-science field.
• Hands-on laboratory experience, ideally including protein biochemistry, mass spectrometry, or proteomics, and comfort working with quantitative data.
• Desirable: experience with mass-spectrometry-based proteomics, bacterial genetics or Salmonella work, biophysical interaction methods (for example biolayer interferometry or SEC-MALS), and an interest in microproteins and the dark proteome.
• Good written and spoken English.
• Motivation for interdisciplinary, collaborative research, and willingness to travel for the secondment and network events.

WHAT WE CAN OFFER YOU

What we offer

• We offer a full-time position as a doctoral fellow, consisting of an initial period of 12 months, which, after a positive evaluation, will be extended to a total maximum of 48 months.
• The fellowship amount is 100% of the net salary of an AAP member in equal family circumstances. The individual fellowship amount is determined by Ghent University HR based on family status and seniority. A grant that meets the conditions and criteria of the regulations for doctoral fellowships is considered free of personal income tax. Click here for more information about our salary scales
• The position is funded within the Marie Skłodowska-Curie Actions Doctoral Network ORFeus. Applicable MSCA-DN mobility and family allowances will be handled in accordance with the MSCA-DN and Ghent University regulations.

Beyond the fellowship, you will receive:

• Supervision by a world-leading, interdisciplinary supervisory team.
• A secondment of around three months with an ORFeus industry partner (Bruker).
• A structured training program: network-wide schools, transferable-skills training, workshops, and international conferences.
• Enrollment in a doctoral program leading to a PhD.
• All Ghent University staff members enjoy a number of benefits, including a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time position), supplemented by annual fixed bridge days, bicycle allowance and eco-vouchers.

Click here for a complete overview of all the staff benefits.

Duration and funding

The doctoral fellowship can run for a total maximum of 48 months, subject to a positive evaluation after the initial 12-month period. The first 36 months are funded through the Marie Skłodowska-Curie Doctoral Network ORFeus. Ghent University provides funding for an additional 12 months to allow the doctoral candidate to finalize the PhD.

INTERESTED?

How to apply

All ORFeus positions use one central hiring platform, linked from the project website; you do not apply to the host institution directly. You submit up to three individual applications and thereby rank up to three of the 15 ORFeus projects in order of preference (this position is DC10). You are considered by every project you rank, not only your first choice. Platform link: orfeus-dn.eu/apply

The application uses structured, criteria-based questions. You will provide:

• Answers to a few eligibility questions, so we can confirm you meet the MSCA rules.
• A checklist of the techniques used in the projects you rank, with a short line of evidence for each technique you have used.
• A short motivation for each project you choose, explaining your interest in it and in ORFeus.
• A curriculum vitae.
• Optionally, a short video introduction. This is not required and you will not be disadvantaged if you do not include one.
• Contact details for two academic referees. We ask your referees for letters directly, and only if you are shortlisted for interview, so you do not need to arrange letters when you apply.

Applications open on 1 October 2026 and close on Thursday 22 October 2026, 23:59 CET. We assess every application against the weighted ORFeus criteria: academic excellence (40%), research potential and motivation (30%), communication (20%), and international experience (10%). Shortlisted candidates have a short introductory call, then a formal interview with both academic supervisors. Every applicant is told the outcome, and shortlisted and interviewed candidates receive feedback. Recruitment is open, transparent, and merit-based, with attention to gender balance. The successful candidate ideally starts on 1 March 2027, and no later than 1 May 2027 if the host institution's start dates require it.

If you need any adjustment to take part in the recruitment process, contact Simon Venneman, ORFeus program manager (s.t.venneman@prinsesmaximacentrum.nl), and we will make reasonable arrangements. For questions about this position, contact Simon Venneman at the same address; please check the ORFeus project website first, as it answers most questions.

Equal opportunities and recruitment

ORFeus and its partners recruit in an open, transparent, and merit-based way, in line with the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers. We welcome applications from all qualified candidates regardless of gender, age, ethnic or national origin, religion or belief, disability, sexual orientation, or any other characteristic, and we are committed to equal opportunity and a balanced research workforce.

Funding acknowledgment

This position is funded by the European Union under the Marie Skłodowska-Curie Actions Doctoral Networks, Horizon Europe (Grant Agreement No. 101309891). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.

Key techniques and methods

Mass spectrometry-based proteomics, Thermal proteome profiling (TPP), Molecular microbiology and bacterial genetics, Protein biochemistry, Quantitative proteomics/data analysis, Protein-protein interaction analysis and/or biophysical characterization