Postdoc in AI for Cancer Genomics at the Supek Group, BRIC

Faculty of Health and Medical Sciences
University of Copenhagen

We are looking for a highly motivated and dynamic postdoc for a 3-year position, to commence 1 February 2025, or soon thereafter (flexible start date).

The postdoc will be linked to the Danish Cancer Society project “AI-DRIVERS” awarded to Prof. Fran Supek to study cancer driver mutations in non-coding DNA, by developing and applying AI tools for decoding tumor genome evolution.

Our group and research

The Supek group is an interdisciplinary team, working at the intersection of genomics, molecular biology, and artificial intelligence. The lab performs statistical analysis of large-scale datasets (cancer genomics, population genomics) using cutting-edge techniques including artificial intelligence (e.g. DNA and protein language models). We further generate our own genomics data by DNA/RNA sequencing (particularly by Oxford Nanopore), and gene editing to generate models of cancer evolution (e.g. CRISPR/Cas12a system for combinatorial gene disruption).

In our research, we focus in frontier research projects e.g. recently finished ERC project “HYPER-INSIGHT”, and ongoing ERC “STRUCTOMATIC: Mutational processes and impact of structural variants in somatic cells”. Furthermore, we are embedded in a broad network of international collaborators (see e.g. EU Horizon consortia “DECIDER” and “LUCIA”, where we study ovarian cancer and lung cancer genomics, respectively).

The Supek group fosters a dynamic and inclusive atmosphere, where excitement about science is valued. We are highly committed to mentoring and career development of PhD students, postdoctoral fellows, and other team members. We are looking for enthusiastic, driven lab members to join us in our mission in pushing the boundaries of human knowledge, and fighting cancer with genomics.

The lab is at the Biotech Research & Innovation Centre, a flagship Danish biomedical research institute, and a part of the University of Copenhagen, the top-3 ranked university in continental Europe in the latest Shanghai Rankings. More information about the group is given on the lab website https://www.genomedatalab.org/

Your job

We invite brilliant minds in computational biology to join us at the cutting-edge of cancer genomics research, harnessing the power of artificial intelligence and evolutionary modeling. As part of our innovative team, you'll be at the forefront of identifying non-coding driver mutations in cancer genomes, a challenge that has long puzzled traditional analysis methods.

Our AI-DRIVERS project aims to understand of cancer evolution by developing and applying state-of-the-art AI models to predict the functional impact of non-coding mutations. Your work will innovate by combining these AI predictions with novel evolutionary frameworks, allowing us to infer selection on regulatory elements and identify new cancer drivers hidden in the 'dark matter' of the genome.

You'll work with extensive whole-genome sequencing datasets from various cancer types, applying and refining AI models to predict changes in gene regulation. Your research will involve developing new methodologies to account for heterogeneous mutation rates across the genome, a critical step in accurately detecting selection in non-coding regions.

This project offers a unique opportunity to bridge computational genomics, artificial intelligence, and cancer biology. You'll be applying cutting-edge deep learning architectures, including convolutional networks and transformers, to genomic data. Additionally, you'll have the chance to collaborate with experimental biologists to validate your computational predictions using CRISPR-based approaches.

Your postdoc work will employ a powerful combination of AI, evolutionary modeling, and large-scale genomic analysis. The results of your studies will be pivotal in uncovering new diagnostic markers, potential therapeutic targets, and fundamental insights into cancer genome evolution. Join us in this exciting endeavor to unlock the secrets of non-coding cancer drivers and pave the way for new approaches in personalized cancer medicine.

Profile
We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

• You have a PhD in genomics/epigenomics/transcriptomics, evolutionary biology, (bio)statistics or machine learning, or related fields.
• You are experienced in computational biology tools/databases, in statistical data analysis and visualization, and in writing code in at least one programming language.
• You have an active interest in understanding the biology of mutations and their role in genetic disease, and in learning new bioinformatics and artificial intelligence approaches.
• Solid level of written and spoken English
• At least one first-author publication or preprint from your PhD and/or MSc work.

Desirable experience and skills:

• Experience with bioinformatics methods and tools for (a) genetic variant calling; and/or (b) mutational signature analysis; and/or (c) evolutionary modelling (tests for selection); and/or (d) long read sequencing analysis; and/or (e) neural networks.
• Background knowledge in fields related to biomedical genomics or DNA replication/repair or genome evolution or applied AI to omics data.
• Proficiency in R or Python, and genomics and machine learning libraries therein.
• Keen interest in programming, algorithm development, mathematics, complexity, and puzzles.
• Two or more first-author publications and/or preprints from your PhD and/or MSc work.

Place of employment

The place of employment is at the Biotech Research & Innovation Centre (BRIC), University of Copenhagen. We offer creative and stimulating working conditions in dynamic and an international research environment. Our research facilities include modern laboratories and high-performance computing infrastructure.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years. The starting date is 1 February 2025, or as soon as possible thereafter.

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Currently, the monthly salary starts at 38,575 DKK/approx. 5,140 EUR (April 2024 level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % to your pension fund.

Foreign and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the Job Structure for Academic Staff at Universities 2020.

Questions
For informal inquiries about the project and the postdoc position, please contact Prof. Fran Supek; [email protected]

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility office).

Application procedure
Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore, your application must include the following documents/attachments – all in PDF format:

1. Motivated letter of application (max. one page).
2. CV incl. education, work/research experience, language skills and other skills relevant for the position.
3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
4. List of publications and preprints. Please include summaries for up to 3 selected publications, describing the main impact and specifying your contributions to each particular study.

Deadline for applications: 14 November 2024, 23.59pm CET

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held during December 2024.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.