PhD fellowship in Structural Bioinformatics

 PhD fellowship in Structural Bioinformatics

PhD Project in Computational modelling to understand and predict protein variant effects

Department of Biology
Faculty of SCIENCE

University of Copenhagen

One or more PhD scholarships are available from Jan 1st, 2023, or as soon as possible thereafter, in the PRISM centre, Department of Biology, Faculty of Science, University of Copenhagen, Denmark. The research within PRISM bridges protein biophysics and genomics using computational and experimental methods.

The PhD projects in this call are focused on computational modelling within structural bioinformatics of protein structure and sequence.

The project

The PhD students will work on one or more of the subprojects within PRISM. Long-term goals include developing predictive and mechanistic models for how genomic variation in protein-coding regions (protein variants) affect the stability, interactions and function of proteins. We are in particular interested in developing predictive models that can be interpreted in terms of specific biological mechanisms. For an introduction to the computational aspects of the research see e.g. our recent review (Stein et al, TiBS, 2019, https://doi.org/10.1016/j.tibs.2019.01.003 ) and recent research papers (e.g. Cagiada et al, https://doi.org/10.1093/molbev/msab095 , Johansson et al, https://doi.org/10.1101/2020.12.03.408732 , Høie et al, https://doi.org/10.1101/2021.06.26.450037 ). Research topics for the PhD projects include:

• Predicting effects of variation on protein stability and protein function across entire proteomes
• Development and application of prediction methods to interpret genomic variation
• Using methods from structural bioinformatics and protein sequence analysis to perform large scale analysis of human genetic variation
• Combining data from multiplexed assays and computational methods to understand protein stability and degradation in a cellular context
• Developing methods to analyse multiplexed assays of protein variant effects

Who are we looking for?

We are seeking motivated applicants with an MSc degree in bioinformatics, biophysics, physics, chemistry or biochemistry or similar fields, ideally with some prior research experience (e.g. through MSc projects) within one or more of these areas:

• Structural bioinformatics
• Computational analyses of the effects of protein sequence variation on protein function and stability
• Large scale analysis of sequencing data focusing on proteins

The ideal candidate has a quantitative mindset and some programming experience, but also a keen interest in and understanding of protein chemistry and biophysics.

About the centre and research environment

The positions are part of an interdisciplinary research centre called PRISM: Protein Interactions and Stability in Medicine and Genomics, funded via a six-year Novo Nordisk Foundation Challenge grant. PRISM is a collaboration between three research groups at the Department of Biology, Copenhagen and researchers at the University of Cambridge, UK, University of Washington, US and the Novo Nordisk Foundation centre for Basic Metabolic Research, DK.

The Ph.D. students will work in the group of Kresten Lindorff-Larsen, located at the Department of Biology in central Copenhagen. The group is also part of an interdisciplinary and collaborative research environment at the Linderstrøm-Lang Centre for Protein Science. The Ph.D. students will work together with scientists from a number of disciplines, and also have the possibility of spending time in one or more of the partner laboratories within PRISM. The group is highly international and a good level of spoken and written English is required.

We offer creative working conditions in dynamic and international research environment. Current members of the research group come from a range of scientific backgrounds, and we value collaborations and interdisciplinary work.

Principal supervisor is Professor Kresten Lindorff-Larsen, Department of Biology, E-mail: lindorff@bio.ku.dk

The PhD programme

The PhD programme consists of a three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. bioinformatics, computational biophysics, physics, chemistry or biochemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database .

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The terms of employment and salary are in accordance to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in both PhD programmes

• Complete and pass the MSc education in accordance with the curriculum of the MSc programme

 (ONLY when you are attending the integrated MSc and PhD programme)

• Carry through an independent research project under supervision

• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

Application and Assessment Procedure

 Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW (SØG STILLINGEN) below. Only applications submitted via this system will be evaluated and you should not submit applications directly via e-mail.

Please include: 

Motivated letter of application (max. one page) explaining your background, key skills and how they are relevant to the research in PRISM

Curriculum vitae (max. 2 pages) including information about your education, experience, language skills and other skills relevant for the position

Publication list (if relevant) including preprints and papers in active preparation. Please do not enclose copies of the papers.

Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another 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.

If you do not yet hold your MSc and would like to apply, please submit a letter from your supervisor regarding your expected graduation date

Name and contact details for 1-2 former supervisors or others who might provide reference. Please do not enclose reference letters.

Application deadline:

The deadline for applications is 30th Oct 2022 23:59 GMT +2.

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 deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/ .

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

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/ .

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.