PhD fellowship in Evolutionary Modelling for Human Genomics at the Supek Group, BRIC

Faculty of Health and Medical Sciences

University of Copenhagen

We are offering a PhD fellowship in Evolutionary Modelling for Human Genomics commencing 1st February 2024, or soon thereafter (flexible start date).

Our group and research

The Supek group is home to a highly interdisciplinary team, working at the intersection of genomics, molecular biology, and artificial intelligence. In our studies, we are striving for excellence and impact – we aim to do science that pushes the boundaries of human knowledge, and that benefits citizens health. The lab employs cutting-edge technologies in large-scale data analysis (cancer genomics, population genomics), DNA/RNA sequencing (e.g. Nanopore data generation and analysis), gene editing (e.g. Cas12a combinatorial disruption) and artificial intelligence (e.g. DNA and protein language models).

In addition to focus on high-impact research projects (e.g. ERC “HYPER- INSIGHT”, ERC “STRUCTOMATIC”), the Supek group also has a broad network of international collaborators across Europe (see e.g. EU Horizon consortia “DECIDER” and “LUCIA”, where we study ovarian and lung cancer genome evolution, respectively). The lab 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.

Project description

We invite the brightest minds in the world of computational biology to dive into the frontier of evolutionary genomics research using long-read sequencing and machine learning. As a part of our dynamic team, you'll be at the forefront of understanding structural variation (SV) mutations in the human genome, and their impact on disease risk and cancer evolution.

We aim to understand and predict the effects of copy number altering (CNA) SVs, which can change gene dosage. Current methodologies to identify which CNA are pathogenic present a plethora of inaccuracies, because CNAs affect many genes at once and thus the causal gene within a CNA segment is hard to pinpoint. Your studies will innovate by comparing observed CNA SV rates in tumors against a novel machine-learning based SV risk predictions, thereby inferring positive selection (identifying cancer driver genes) or negative selection (identifying new tumor vulnerabilities). Further, you will venture into the less-charted territories of somatic SVs, focusing on those that disrupt gene regulatory regions. By pooling together myriad regulatory regions linked to each gene, you will spearhead the identification of a novel class of non-coding cancer driver mutations that alter gene regulation.

You will work with unique in-house generated datasets, as well as with external large-scale human genomic data, generated using long-read sequencing techniques such as Oxford Nanopore Technologies. Further, you will apply various machine learning techniques to improve SV mutation risk predictions, thereby improving quality of the evolutionary models.

Overall, your PhD work will use cutting-edge technology (long-read sequencing, artificial intelligence, single-cell genomics/transcriptomics), and the results of your studies will be pivotal in pioneering new insights into consequences of genomic rearrangements in human cells, including during somatic/tumor evolution.

For further information 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).

Principal supervisor is Prof. Fran Supek, BRIC, [email protected], +45 35 33 11 06

Start: 1st Feb 2024, or soon thereafter (with flexibility)

Duration: 3 years as a PhD student, with possible extension

Job description Your key tasks as a PhD student at SUND are:

Carrying through an independent research project under supervision.

Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.

Participating in active research environments including a stay at another research team.

Obtaining experience with teaching or other types of dissemination related to your PhD project

Teaching and disseminating your knowledge.

Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants Applicants must have qualifications corresponding to a master's degree related to the subject area of the project, e.g. molecular biology, bioinformatics/genomics, mathematics, physics, computer science. Please note that your master's degree must be equivalent to a Danish master's degree (two years).

Other important criteria are:

The grade point average achieved

Professional qualifications relevant to the PhD project

Previous publications

Relevant work experience

Other professional activities

A curious mind-set with a strong interest in genomics and bioinformatics and evolution

Language skills

Place of employment

The place of employment is at the BRIC, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories and high-performance computing facilities.

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 start date is 1st Feb 2024, or later thereafter, as agreed.

The employment is conditioned upon the applicant's success­ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty's rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 28,993 DKK/Roughly 3,886 EUR (October 2023 level) plus pension.

Questions For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School's website: https: // healthsciences.ku.dk/phd/guidelines/

Application procedure Your application must be submitted electronically by clicking ‘Apply now' below. The application must include the following documents in PDF format:

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master's degree must be equivalent to a Danish master's degree. We encourage you to read more in the assessment database: https: // ufm.dk/en/education/recognition-and-transparency/find- assessments/assessment-database . Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

4. Publication list (if possible), including also preprints, with brief summaries of selected publications, describing the main impact and specifying your contributions to each particular study.

Application deadline: 20 November 2023 , 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.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

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 find information about the recruitment process at: https: // employment.ku.dk/faculty/recruitment-process/

The applicants 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 2023.

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