Doctoral Student in Computational Immune Reprogramming PA2026/1175

The Cell Reprogramming in Hematopoiesis and Immunity research group at the Department of Laboratory Medicine within the Faculty of Medicine studies how hematopoietic cell fate is specified, maintained, and eventually modified or reversed. Inspired from the fields of stem cell biology, immunology, and cancer we use an interdisciplinary approach to mechanistically understand hematopoietic and immune cell identities and translate our findings into novel gene and cell therapies.

Immunotherapy has transformed cancer treatment by enabling durable responses in some patients. However, many patients do not benefit, and several cancer types, including cold solid tumors, remain resistant to current immunotherapies. A major goal in the field is therefore to develop new strategies that increase tumor immunogenicity and improve anti-tumor immune responses. Cell fate reprogramming of cancer cells into immunogenic dendritic cells is a novel and promising approach that is being developed by the Pereira Lab at Lund University [1]. Nevertheless, so far only a limited number of immune cells have been generated using TF-mediated direct reprogramming, which limits the therapeutic potential of immune cells. This project builds on an established combinatorial barcoded transcription factor screening platform with single-cell readout [1] and aims to expand immune cell reprogramming beyond currently accessible cell types.

1. Ascic et al., Science 2024.

You can read more about the research group at https://pereiralab.com/

We offer

Lund University is a public authority which means that employees get particular benefits, generous annual leave and an advantageous occupational pension scheme.

Read more on the University website about being a Lund University employee Work for us.

The Cell Reprogramming in Hematopoiesis and Immunity research group is a diverse group of molecular biologists, MDs, PharmDs, tumor immunologists, stem cell biologists and computational scientists – at all career stages. Our multidisciplinary approach gets inspiration from the fields of immunology, developmental biology, stem cells, cancer biology and bioinformatics, cross-fertilizing ideas and leading to new discoveries. This requires diversity and teamwork both within the lab and with our worldwide academic and industrial collaborators. The position is funded by the SciLifeLab Data-Driven Life Science (DDLS) program and the student will integrate into the DDLS Research School.

Work duties and areas of responsibility

The doctoral student will carry out a project that aims to establish a virtual screening platform for immune cellular reprogramming. To achieve this the student will work with multiplexed single-cell datasets to identify induced immune cell states and the transcription factor combinations that drive them as well as predict new combinations with machine learning approaches. This project will encompass:

• analyse single-cell and multi-omics datasets generated in immune cell reprogramming experiments
• develop and apply computational workflows for cell state annotation, integration, and modelling
• application of statistical and mathematical modelling approaches to understand and predict immune cell fate decisions
• identify transcription factor combinations associated with specific immune cell fates
• contribute to interpretation and presentation of results in collaboration with experimental researchers
• participate in the DDLS Research School and other relevant doctoral training activities
• present research results orally and in writing at group meetings, conferences, and in scientific publications

Qualifications

Applicants must meet the general entry requirements for doctoral studies at Lund University. Requirements for employment are:

• a Master’s degree, or equivalent, in bioinformatics, computational biology, systems biology, biotechnology, biomedicine, computer science, or a related field
• documented experience in analysis of next-generation sequencing data, preferably single-cell RNA-seq and/or other omics data
• documented skills in programming or scripting, for example in Python and/or R
• experience using relevant bioinformatics tools or frameworks, such as Seurat, Scanpy, or similar
• good ability to work independently as well as collaboratively in a multidisciplinary research environment
• good oral and written communication skills in English

Additional qualifications for the position are:

• prior experience in cancer immunology, immunotherapy, or hematopoiesis/immunology-related research
• experience in multi-omics data integration and statistical modelling
• familiarity with machine learning methods for biological data
• experience in data visualization or development of user-friendly tools for sharing biological data

Consideration will also be given to good collaboration skills, drive and independence, as well as how the applicant, through his or her experience and competence, is judged to have the ability needed to complete the doctoral program. Research expertise is the foremost criterion for employment. The evaluation of applicants will take account of their research profile, experience and knowledge.

Eligibility

Students with basic eligibility for third-cycle studies are those who
- have completed a second-cycle degree
- have completed courses of at least 240 credits, of which at least 60 credits are from second-cycle courses, or
- have acquired largely equivalent knowledge in some other way, in Sweden or abroad.

The employment of doctoral students is regulated in the Swedish Code of Statues 1998:80. Only those who are or have been admitted to PhD-studies may be appointed to doctoral studentships. When an appointment to a doctoral studentship is made, the ability of the student to benefit from PhD-studies shall primarily be taken into account. In addition to devoting themselves to their studies, those appointed to doctoral studentships may be required to work with educational tasks, research and administration, in accordance with specific regulations in the ordinance.

Type of employment

Limit of tenure, four years according to HF 5 kap 7§. The intended start date is 1 October 2026, or as agreed.

How to apply

You apply for the position via the University’s recruitment system. The application is to include a personal cover letter describing why you are interested in the position and how you meet the qualification requirements (one page cover letter). The application is also to include a CV with a list of publications, description of previous computational work (one page), a copy of your degrees, two letters of recommendation and any other documents to which you wish to draw attention (copies of degree certificates, grade transcripts, details of referees, etc.).