Doctoral fellow – Department of Mathematics, Computer Science and Statistics

Last application date Sep 15, 2025 00:00

Department WE02 – Department of Mathematics, Computer Science and Statistics

Contract Limited duration

Degree You hold a Master’s degree in Computer Science, Bioinformatics, or a related field

Occupancy rate 100%

Vacancy type Research staff

Job description

You will be responsible for advancing the current state of metaproteomics bioinformatics by developing novel, high-performance algorithms for improved identification and annotation of microbial proteins. Existing tools such as Unipept are limited to exact tryptic peptide matches and lack support for peptide variants such as those containing single nucleotide polymorphisms (SNPs), missed cleavages, or non-tryptic antimicrobial peptides.
To address these limitations, the project will:

• Develop a bi-directional FM-index-based search engine capable of approximate peptide matching
• Extend Unipept with support for metabolic pathway annotation and SNP-tolerant matching
• Integrate results into a unified open-source data analysis pipeline combining tools like Unipept and MetaProteomeAnalyzer

The resulting software will enhance both the taxonomic and functional resolution of MP datasets and increase the sensitivity of microbial effector identification.
This will happen within the Marie Skłodowska-Curie Doctoral network METAMIC 3 – Metaproteome-based leveraged microbiome management in the context of One Health. METAMIC is funded by the European Commission under the Horizon Europe framework programme (Grant Agreement number 101225682).
The METAMIC project will embed Doctoral Candidates (DCs) in a unique training environment to advance microbiome science through metaproteomics. The program addresses One Health challenges by integrating research on microbial mechanisms, microbiome dynamics in various ecosystems, and translational applications in clinical and biotech fields. DCs will benefit from expertise across molecular biology, bioinformatics, clinical research, and environmental science, supported by collaborations among academia, industry, and public sector partners.

Job profile

• You hold a Master’s degree in Computer Science, Bioinformatics, or a related field.
• You are eager to apply your computational expertise to challenges in the life sciences.
• You enjoy working in an interdisciplinary and collaborative research environment.
• You are proficient in scientific English, both written and spoken.
• You are willing to spend several months abroad as part of international research secondments. This position includes the following secondments:
  • o A 3-month secondment at ISAS (Germany) with Prof. Robert Heyer to integrate developed tools into the MetaProteomeAnalyzer software.
  • o A 3-month secondment at the Robert Koch Institute (Germany) with Dr. Thilo Muth to exchange best practices in academic software development and bioinformatics infrastructure

Furthermore, candidates have to fully comply with the following essential eligibility criteria:

• Academic Qualification: The applicant must hold a relevant master’s degree or equivalent and must have obtained the degree or equivalent by the DC start date.
• In order to be recruited to the network as a doctoral candidate, applicants must not already be in possession of a doctoral degree (i.e. a Ph.D. degree).
• Conditions of international mobility of researchers: researchers must not have resided or carried out their main activity (work, studies, etc.) in Belgium for more than 12 months in the 3 years immediately prior to their recruitment.
• 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.
   
  • o The first 36 months are funded by the Marie Skłodowska-Curie Doctoral network.
  • o Ghent University foresees an additional 12-month contract for finalizing the PhD.
• The fellowship amount is 100% of the net salary of an AAP member in equal family circumstances. The individual fellowship amount is determined by Team Personnel Administration 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
• All Ghent University staff members enjoy a number of benefits, such as a wide range of training and education opportunities, 36 days of holiday leave (on an annual basis for a full-time job) supplemented by annual fixed bridge days, bicycle allowance and eco vouchers. Click here for a complete overview of all the staff benefits.
• A clear research topic as well as multi-fold training and support for PhD students in framework of a collaborative training network;
• Working in an outstanding, collaborative, and international network;
• Training and scientific development opportunities in an supportive environment and an excellent working atmosphere in a very dynamic and professional team;
• The opportunity to present your data on international conferences and participate in workshops.

How to apply

Complete applications cover an extended curriculum vitae with full publication list, a cover letter, copies of your diplomas, a 2-page research statement that clearly describes your research profile and interests in the position as well as your expertise and methodological competencies, names and contact information of 2 references, if available. Applications should be submitted to [email protected].
Informal inquiries are welcome and can be submitted to [email protected].