Postdoctoral studies in bioinformatics and computational virus discovery (scholarship)

Do you want to contribute to top quality medical research? 

Do you want to contribute to top-quality medical research and help solve one of the most urgent problems in cancer biology?

We are seeking a highly motivated postdoctoral researcher in bioinformatics to join our multidisciplinary research team at Karolinska Institutet, working in close collaboration with research groups at the University of Turku and the Danish Cancer Institute in Copenhagen.

The successful candidate will work on the project “Causal Role, Mechanistic Impact, and Therapeutic Targeting of Human Cytomegalovirus (HCMV) in Brain Cancer”, which integrates sequencing-based virus discovery, multi-omics analysis, and translational cancer research.

Duties

About the Project

Our research has demonstrated that approximately 99% of glioblastomas are positive for human cytomegalovirus (HCMV), and that high viral activity strongly correlates with poor patient outcome. Importantly, clinical studies show that antiviral therapy combined with standard treatment provides a significant survival benefit, and that radiotherapy induces viral reactivation in a substantial fraction of patients, placing them at high risk for early tumor recurrence.

New data now indicate the presence of a previously unrecognized, HCMV-cancer-associated virus that may explain the strong association between HCMV and glioblastoma, and potentially its link to other tumor types. The central goal of this project is to identify, sequence, and characterize this virus.

We will generate sequencing data using Oxford Nanopore long-read sequencing and Illumina short-read sequencing, and apply advanced bioinformatic analyses to assemble contigs, reconstruct the viral genome, and define its genetic organization. Identified viral sequences will be systematically searched against established public databases to assess novelty, relatedness, and evolutionary origin.

The postdoctoral bioinformatician will play a central role in viral detection, genome assembly, and sequence annotation, as well as in the integration of sequencing, transcriptomic, proteomic, and metabolic datasets. These analyses will be essential to uncover novel virus–host interactions and to understand how this virus contributes to tumor biology and therapeutic vulnerability.

As a Postdoctoral Researcher in bioinformatics, you will play a central role in the discovery and characterization of a novel HCMV-cancer-associated virus linked to glioblastoma and potentially other tumor types.

Your primary mission will be to identify, assemble, and analyze viral genomes from complex sequencing datasets generated from patient material and experimental systems. You will work with Oxford Nanopore long-read sequencing and Illumina short-read sequencing data, developing and applying bioinformatic pipelines to detect viral sequences, build contigs, reconstruct complete or near-complete viral genomes, and assess viral diversity and prevalence.

Beyond genome reconstruction, you will integrate multi-omics datasets, including transcriptomics, proteomics, metabolomics, and clinical data, to uncover novel virus–host interactions, viral integration or persistence mechanisms, and virus-associated metabolic and oncogenic signatures. You will systematically compare identified viral sequences against public and proprietary databases to determine novelty, evolutionary relationships, and potential functional features.

You will work in close collaboration with experimental virologists, cell biologists, and clinician-scientists at Karolinska Institutet, the University of Turku, and the Danish Cancer Institute. Your analyses will directly guide experimental validation, therapeutic targeting strategies, and translational studies in patients.

This scholarship offers a unique opportunity to contribute to high-impact virus discovery research, combining cutting-edge sequencing technologies with integrative bioinformatics to address fundamental questions in cancer biology and viral oncology.

Key Goals of the Project:

• Identify and reconstruct the genome of a novel HCMV-associated cancer virus using long-read (Oxford Nanopore) and short-read (Illumina) sequencing data
• Detect viral sequences, episomal forms, and potential integration events in tumor tissues, blood samples, and control material
• Build high-quality viral contigs and reference genomes through hybrid assembly approaches
• Integrate genomic, transcriptomic, proteomic, and metabolomic datasets to uncover virus–host interactions and virus-associated metabolic reprogramming
• Map viral transcriptional activity and expression patterns across tumor types and treatment conditions
• Determine the prevalence, diversity, and activity of the virus across patient cohorts and publicly available datasets

Key Responsibilities:

• Analyze Oxford Nanopore and Illumina DNA/RNA sequencing data to identify viral reads and reconstruct viral genomes
• Perform de novo assembly, hybrid assembly, and contig refinement for novel virus discovery
• Develop and apply pipelines for viral detection, annotation, and comparative genomics
• Search for viral sequences across in-house and public sequencing datasets (e.g. tumor cohorts, blood samples, controls)
• Integrate sequencing data with transcriptomic, proteomic, and metabolomic datasets to identify virus-associated pathways and host responses
• Analyze viral expression, splice variants, and replication signatures using DNA/RNA-seq data
• Collaborate closely with experimental researchers to guide sequencing strategies and interpret biological relevance of computational findings
• Contribute to publications in high-impact journals and present results at international conferences
• Actively participate in grant writing and the strategic development of bioinformatics approaches within the project

Entry requirements

We are looking for a curious, creative, and highly motivated postdoctoral researcher with a strong interest in virus discovery, genome reconstruction, and integrative bioinformatics at the interface of cancer biology and infection.

Required qualifications

• Ph.D. in bioinformatics, computational biology, genomics, systems biology, or a closely related field
• Demonstrated scientific excellence and strong potential for independent research
• Strong analytical and problem-solving skills, with the ability to work with complex and noisy biological datasets
• Excellent written and oral communication skills in English
• Ability to work collaboratively in a highly interdisciplinary and international research environment
• Documented experience in scientific writing and publishing in peer-reviewed journals

Preferred qualifications

• Strong experience in next-generation sequencing (NGS) data analysis, particularly Oxford Nanopore and/or Illumina sequencing
• Experience in viral sequence detection, de novo assembly, contig construction, and genome reconstruction
• Familiarity with identifying novel or highly divergent viral sequences in host sequencing data
• Experience integrating multi-omics datasets (genomics, transcriptomics, proteomics, metabolomics)
• Hands-on experience with R and/or Python, shell scripting, and Linux-based computational environments
• Experience with proteomics and/or metabolomics LC-MS data analysis is a strong advantage
• International research experience and/or collaboration across laboratories is highly valued
• Additional academic achievements beyond the doctoral degree (e.g. fellowships, awards, independent funding, or high-impact publications) will be considered a merit

Personal qualities

• Strong intellectual curiosity and enthusiasm for discovering new biology from complex sequencing data
• Ability to think mechanistically across disciplines, connecting viral genomics with cellular metabolism, stress responses, and cancer biology
• Scientific rigor, creativity, and motivation to pursue high-risk, high-impact research questions
• Excellent interpersonal skills and ability to work productively in a highly interdisciplinary and international research environment

Postdoctoral scholarships may be established for foreign researchers who pursue their merit in Sweden. A foreign researcher is a person living in another country who comes to Sweden with the intention of only staying in Sweden for all or part of their postdoctoral education at KI. Persons who are resident in Sweden and/or have carried out all or part of their academic education at KI or some other educational institution in Sweden cannot be considered for scholarships. The purpose of scholarships for postdoctoral qualification is to promote internationalization and contribute to research qualification after a doctorate or equivalent.

A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four-year period following the receipt of a doctoral degree or equivalent.

To be eligible for a postdoctoral scholarship, the person must have obtained a doctorate, or a foreign degree deemed to be equivalent to a doctorate. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) start date of the post-doctoral education.

What do we offer?

A creative and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world's leading medical universities. Here, we conduct innovative medical research and provide the largest range of biomedical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Students and employees have free access to our modern gym facilities with trained staff on site.

Location

The position is located within the Department of Medicine, Solna. The department consists of ten divisions and each division consists of several research groups. At SciLifeLab and the Center for Molecular Medicine at Karolinska Institutet, Professors Cecilia Söderberg-Nauclér and Jiri Bartek lead a dynamic, multidisciplinary research team focused on advancing both fundamental and translational cancer research. Our work explores key areas such as virology, cellular metabolism, replication stress, and ribosomal biology in the context of tumor development. With a strong emphasis on brain cancer, our research aims to uncover novel mechanisms driving disease progression and treatment resistance. In addition to laboratory-based studies, we are actively involved in the design and implementation of clinical trials, with the goal of improving prognosis and developing more effective therapies for patients. More information about our team leaders can be found on their Karolinska Institutet profiles: Cecilia Söderberg-Nauclér and Jiri Bartek.

Type of scholarship

The amount is tax free and it is set for twelve months at a time, paid out on a six months basis. In exceptional cases, shorter periods may be acceptable.

Application process

An application must contain the following documents in English or Swedish:

• A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
• A complete list of publications
• A summary of current work (no more than one page)

The application is to be submitted on the Varbi recruitment system.

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