PhD position in Translational Tumor Immunology

University of Basel; Schweiz; On-site; CHF 55,000 - 75,000; Full time

Job summary

The Translational Immuno-Oncology research group at University of Basel offers a PhD position in translational tumor immunology. The project investigates how cancer therapy induces endogenous T cell responses and examines epitope spreading in the context of durable tumor control.

The work combines tumor- and blood-based genomics, functional screening, and high-parameter immunoprofiling. You will work with cutting-edge sequencing and immune-assay techniques, collaborating with clinicians to

Qualifications

• Master’s degree in Biological Sciences, Immunology, Molecular Biology, Biomedical Sciences, Medicine or a related field.
• Experience in designing and performing laboratory experiments.
• Excellent communication and writing skills in English.
• Initiative, scientific curiosity and ability to work independently in an interdisciplinary team.
• Interest in quantitative biology and willingness to work with complex biological datasets.

Responsibilities

• Identify patient-specific tumor mutations and candidate tumor antigens from tumor and blood data.
• Develop computational pipelines for HLA typing and neoantigen prediction.
• Perform functional screening to identify tumor-specific T cell epitopes.
• Quantify epitope spreading and endogenous T cell responses over time.
• Conduct single-cell RNA and TCR sequencing to define T cell phenotypes and clonality.
• Collaborate with clinicians and researchers to integrate immunology, molecular data and clinical insights.
• Prepare scientific reports, conference presentations, and journal articles.

Skills

T cell immunology

Quantitative biology

Independent researcher

English writing

R/Python

Education

Master’s degree in Biological Sciences or related field

Tools

Flow cytometry

Single-cell sequencing

R

Python

Job description

Organisation/Company University of Basel Department Department of Biomedicine Research Field Biological sciences » Biology Researcher Profile Established Researcher (R3) Positions PhD Positions Application Deadline 15 Nov 2026 - 12:00 (Europe/Zurich) Country Switzerland Type of Contract Temporary Job Status Full-time Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The Translational Immuno-Oncology research group, co-led by Prof. Dr. Mascha Binder and Dr. Sarah Adamo, offers a PhD position in translational tumor immunology. Our research combines basic and translational immunology with patient-centered cancer research. We investigate mechanisms underlying anti-tumor immunity and immunological memory and develop approaches to improve the precision and durability of cancer immunotherapy.

The successful candidate will investigate how cancer therapy induces endogenous T cell responses against tumor antigens beyond the original therapeutic target, and whether these newly generated responses contribute to long-term tumor control.

Targeted and immune-based cancer therapies can induce profound tumor regression, but long-term disease control remains highly variable. Therapy-induced tumor destruction releases cancer antigens in an inflammatory environment and may promote the generation of new endogenous T cell responses against targets not directly recognized by the therapy, a process known as epitope spreading. Such responses could provide target-independent and potentially long-lasting immunological control of cancer.

The project will combine tumor- and blood-based genomic profiling to identify candidate tumor antigens, functional screening to determine which are recognized by endogenous T cells, and longitudinal antigen-specific T cell profiling to quantify epitope spreading and assess its association with durable clinical benefit.

As a proof of principle, the project will initially focus on patients with B cell lymphoma receiving targeted therapies, including CAR-T cells and bispecific T-cell engagers (BiTEs), providing a well-defined setting in which to study therapy-induced epitope spreading. The long-term aim is to establish a framework that can be extended across different cancer types and therapeutic modalities.

The PhD candidate will work with cutting-edge computational and experimental approaches, including genomic and transcriptomic sequencing, neoantigen prediction and immune-repertoire analysis, followed by functional T cell screening, single-cell RNA and TCR sequencing, peptide–MHC tetramers and high-parameter spectral flow cytometry.

The PhD candidate will be expected to take an active role in shaping the project, supported by Dr. Adamo and close clinical and scientific collaborators, in an environment that encourages academic freedom and scientific independence.

In line with our and Uni Basel values, we are committed to sustaining and promoting an inclusive culture, ensuring equal opportunities and valuing diversity and respect in our working and learning environment.

Your main tasks will be:

• Identification of patient-specific tumor mutations and candidate tumor antigens from tumor- and blood-derived genomic and transcriptomic data.
• Development and application of computational pipelines for HLA typing, neoantigen prediction and prioritization of patient-specific HLA class I- and class II-restricted T cell epitopes.
• Experimental identification and validation of tumor-specific T cell epitopes using functional screening approaches.
• Longitudinal characterization of endogenous anti-tumor T cell responses before, during and after cancer therapy to quantify epitope spreading.
• Single-cell RNA and TCR sequencing of tumor-reactive T cell populations to define their phenotype, clonality and dynamics over time.
• Characterization of antigen-specific T cells using activation-based assays, peptide–MHC tetramers and high-parameter spectral flow cytometry.
• Development and application, in collaboration with internal and external partners, of blood-based molecular approaches to follow tumor evolution alongside endogenous immune responses over time.
• Integration of immunological, molecular and clinical data to identify features associated with durable tumor control.
• Analysis and visualization of high-dimensional genomic, transcriptomic, immune-repertoire and immunological datasets.
• Preparation of scientific reports, conference presentations and journal articles.
• Master’s degree in Biological Sciences, Immunology, Molecular Biology, Biomedical Sciences, Medicine or a related field.
• Experience in designing and performing laboratory experiments.
• Strong interest in T cell immunology, cancer immunotherapy and translational human research.
• Interest in quantitative biology and willingness to work with complex biological datasets.
• Excellent communication and writing skills in English.
• Initiative, scientific curiosity and the ability to work independently as well as within an interdisciplinary team.
• Any of the following will be a plus: experience with primary human samples, flow cytometry, T cell functional assays, molecular biology, cancer genomics, single-cell sequencing, immune-repertoire analysis, R or Python.

Languages ENGLISH Level Excellent

Additional Information

• Access to state-of-the-art infrastructure for flow cytometry, DNA and RNA sequencing, cell culture and high-dimensional data analysis.
• Direct access to longitudinal clinical samples from patients undergoing advanced cancer therapies.
• A highly interdisciplinary environment connecting experimental immunology, translational oncology and clinical research.
• Close collaboration with basic and clinical research groups at the Department of Biomedicine, University Hospital Basel and external partner institutions.
• Cross-disciplinary training opportunities in human immunology, cancer biology, genomics and computational data analysis.
• Support from experienced team members, with substantial scope for scientific independence and project ownership.
• The opportunity to contribute to a broader research program investigating endogenous anti-tumor immunity across cancer types and therapeutic modalities.