Postdoctoral Researcher in Bioinformatics & Mass Spectrometry

Job description

Join Our Cutting-Edge Research on Melanoma Biomarkers and Therapeutic Targets!

The University of Groningen is seeking a highly motivated Postdoctoral Researcher to join the Analytical Biochemistry group at the Groningen Research Institute of Pharmacy (GRIP). This two-year position offers an exciting opportunity to work at the intersection of bioinformatics, mass spectrometry, and AI-driven cancer research. You will be part of a dynamic, multidisciplinary team specializing in computational mass spectrometry, proteomics, and glycomics.

Your Role

As a Postdoctoral Researcher, you will play a key role in confirming melanoma subtypes, identifying and validating drug targets, and uncovering companion biomarkers for precision treatment using cutting-edge bioinformatics and proteomics approaches. You will analyze bulk and clonal protein expression data from large melanoma cohorts, integrate molecular, histological, and clinical data through machine learning (ML)/AI-assisted methodologies. Your expertise in ML (Random Forest, SVM, Fully Connected Neural Networks) will be essential for feature selection, model training, and biomarker ranking. Additionally, you will perform proteomics profiling of melanoma clones using AI-driven digital pathology and laser microdissection (LMD), assessing tumor heterogeneity and refining melanoma subtype classifications.

What We Offer

• A high-impact research project at the forefront of melanoma biomarker discovery and precision medicine.
• Access to state-of-the-art mass spectrometry facilities, including 15 high-end mass spectrometers housed at the Interfaculty Mass Spectrometry Center (IMSC) at UMCG.
• Access to 3 high-end computational clusters with 48-96 CPU threads, 512-786 GB RAM and >200TB storage each.
• A collaborative and supportive research environment with leading experts in bioinformatics, proteomics, and oncology.
• Opportunities to publish in top-tier scientific journals and present at (inter)national conferences.

Project & Consortium Involvement

This Postdoctoral project is part of the PerMel-AI consortium, funded by the European Partnership for Personalised Medicine (EP PerMed) under the European Commission. The three-year project brings together leading institutions, including Treat4Life (Sweden), Helmholtz Munich (Germany), HCEM (Hungary), Turbine (Hungary), and Lund University (Sweden). The goal is to leverage AI and large-scale biobanking to validate drug targets and biomarkers for personalized melanoma treatment. As the Postdoctoral Researcher, you will be responsible for performing bioinformatics analyses to confirm melanoma subtypes using bulk and clonal protein expression data.

Supervision & Research Environment

You will be supervised by Dr Guinevere S.M. Lageveen-Kammeijer and Prof. Peter L. Horvatovich, working closely with an interdisciplinary team of researchers. Our well-equipped facilities provide extensive resources for mass spectrometry-based proteomics, phosphoproteomics, lipidomics, and metabolomics, applied to various biological and clinical samples.

Join Us!

If you are passionate about bioinformatics, proteomics, and ML/AI-driven cancer research, we encourage you to apply for this unique opportunity to contribute to cutting-edge melanoma research. Become part of a team making a real impact in precision oncology!

Recent illustrative work

The work will extend on recent research entitled “Unbiased Drug Target Prediction Reveals Sensitivity to Ferroptosis Inducers, HDAC and RTK Inhibitors in Melanoma Subtypes” (Pla I, Szabolcs BL, Péter PN, Ujfaludi Z, Kim Y, Horvatovich P, et al., Int J Dermatol., 2024, PMID: 39722169 (where drug target for melanoma subtypes has been identified with in silico approach. The subtype identification of melanoma using quantitative proteomic profile is described in the article entitled “Histopathology-assisted proteogenomics provides foundations for stratification of melanoma metastases” available in bioRxiv (). More details on the human melanoma abstract can be find in the article “The human melanoma proteome atlas—Defining the molecular pathology” (PMID 34323403).

Organisation

The University of Groningen is an internationally oriented university with a rich academic tradition. Since the establishment in 1614, the university has brought forward striving academics, like the first female student, the first Dutch astronaut and various Nobel prize winners.

Qualifications

We are seeking a candidate with a PhD in Bioinformatics, Machine learning and AI-based statistics, Computational Biology, and expertise in Analytical Chemistry, Biomedical Sciences, or a related field, would be a plus. The main required expertise and skills are

• Bioinformatics analysis of proteomics or multi-omics datasets, preferably in cancer research.
• ML applications for biomarker discovery and validation, and predictive modeling.
• Programming (Python, R, c++ and/or MATLAB) and handling large-scale biological datasets.
• Analysis and statistical evaluation of mass spectrometry-based proteomics data, and AI-assisted digital pathology.
• Integrating molecular and clinical data to advance precision oncology.
• Experience or willingness to learn proteomics sample preparation and LC-MS(/MS) analysis (you will be assisted to learn these wet lab methods).
• Experience in melanoma research, LMD, or high-performance computing is a plus.
• Team player collaborating efficiently with members of our group and members of large international consortium.

We are looking for a motivated, independent researcher with strong analytical and scientific writing skills, eager to contribute to breakthrough discoveries in melanoma therapy.

Organisation

Conditions of employment

We offer you in accordance with the Collective Labour Agreement for Dutch Universities:

• A salary based on qualifications and experience (after obtaining PhD) starting at € 4,060 gross per month (salary scale 10, step 4), based on full-time employment.
• 8% holiday allowance and an 8.3% year-end bonus, participation in a pension scheme for employees, and excellent secondary benefits. We offer 232 holiday hours per calendar year for full-time employment.
• An appointment temporarily for 12 months; subject to a positive evaluation, the contract can be extended with 12 months (or more, depending on available funds).