Faculty of Health and Medical Sciences
University of Copenhagen
We are offering a PhD fellowship in Computational analysis of Human Genome Variation commencing on January 1st 2021 or soon as possible hereafter.
Our group and research
The Human Variation group is located at The Novo Nordisk Foundation Center for Protein Research (CPR – www.cpr.ku.dk). The Center has been established at the Faculty of Health and Medical Sciences, University of Copenhagen, to promote basic and applied discovery research on human proteins of medical relevance. The Center comprises a wide range of expertise and resources including proteomics, protein production, bioinformatics and general characterization of disease mechanisms. The Program for Disease Systems Biology (DSB) consists of three research groups covering many systems level aspects of biology and medicine, including large scale analysis of human variation data and integration of molecular-level and healthcare data.
The Human Proteome Variation group (https://www.cpr.ku.dk/research/disease-systems-biology/rasmussen-group/ ) is part of the DSB program and is led by Simon Rasmussen. It focuses on proteome and genome variation, coding variation and deep learning for integration of genomics, proteomics, metagenomics and clinical data.
The PhD candidate will work in a multidisciplinary project team focusing on integrating and analyzing human variation data. Within recent years human genetic variation data has increased rapidly with cohorts comprising hundreds of thousands and even millions. Simultaneously, deep learning has revolutionized several scientific fields, and, in the future, AI based models will be of crucial importance if we are to successfully utilize big health data. Especially deep learning for genomics approaches have the potential to redefine and replace traditional methods for analysis of large genome-wide datasets as well as clinical usable models.
The PhD project will focus on how to interpret large-scale human genome-wide data with a focus on proteogenomic variation as well as deep learning models. The project will be focused on psychiatric diseases and aim to integrate genotype and exome data with existing annotation to model psychiatric and other diseases.
Principal supervisor is Simon Rasmussen, Associate Professor, NNF Center for Protein Research, firstname.lastname@example.org , Direct Phone: +45-35332159.
Start: January 1st 2021 or as soon as possible hereafter
Duration: 3 years as a PhD student
Your key tasks as a PhD student at SUND are:
- Carry through an independent research project under supervision
- Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points
- Participate in active research environments including a stay at another research team
- Obtain experience with teaching or other types of dissemination related to your PhD project
- Teach and disseminate your knowledge
- Write 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. computational biology, bioinformatics or related discipline of biomedical research. You preferably have experience in analysing large scale human genome variation data and have experience in programming in python and/or R. Practical knowledge of Hail is a plus as well.
Additionally, the following criteria represent an advantage:
- Experience in working with Unix environment, especially with cluster architectures based on TORQUE Resource Manager and Moab Workload Manager
- Practical knowledge of a Workflow Management System like Snakemake, Nextflow, or other
- Being able to document your work in a thorough and reproducible manner
- Practical knowledge of Github
- Having an open-minded attitude and an outgoing personality, since you will be employed in a multi-cultural work environment and you will have to disseminate your knowledge, teach, and give talks in front of audiences
Other important criteria are:
- The grade point average achieved
- Professional qualifications relevant to the PhD project
- Previous publications
- Relevant work experience
- Other professional activities
- Curious mind-set with a strong interest in human genome variation and machine learning
- Language skills
Place of employment
The place of employment is at The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include access to High Performance Computing systems such as Computerome 2.
Terms of employment
The employment as PhD fellow is full time and for 3 years.
It 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 (2019) 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 Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins around 27,593 DKK /approx. 3.700 EUR (April 2020-level) plus pension.
For specific information about the PhD fellowship, please contact the principal supervisor.
General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/
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. Master of Science diploma and transcript of records. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor will do
4. Publication list (if possible)
Application deadline: 3 November 2020, 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 can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/
The applicant will be assessed according to the Ministerial Order no. 1443 of 11 December 2020 on the Appointment of Academic Staff at Universities.
Interviews are expected to be held in week 46
The Faculty of Health and Medical Sciences comprises approximately 7500 students, 1500 PhD students and 3200 employees. The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community. The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.
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