PhD fellowship in Bioinformatics/Data Science/Machine Learning at Department of Drug Design and Pharmacology

Faculty of Health and Medical Sciences, University of Copenhagen

We are looking for a highly motivated and ambitious bioinformatician / data scientist / Machine Learning specialist for a three-year PhD fellowship commencing 1 October 2024 or as soon as possible thereafter.

Principal supervisor
Associate Professor Albert J. Kooistra, Department of Drug Design and Pharmacology
E-mail (preferred): [email protected], phone: +45 35 32 83 05

Start: 1 October 2024

Duration: 3 years as a PhD student

Our group and research

The “Data Science for Drug Design” (DSDD) research group is dedicated to the development and application of cutting-edge and data-driven technologies to advance network medicine. The DSDD group has a broad expertise encompassing structural bioinformatics, cheminformatics, computer-aided drug discovery & design, research tool/database development and applying machine learning/AI approaches. The research conducted within our research groups revolves around three primary pillars:

1. Data: this pillar involves the systematic curation and annotation of publicly available data encompassing protein structures, protein sequences, protein-protein interactions, cellular compositions, natural variations, drug effects, expression levels, and more. A prime illustration of our work in this realm is the publicly accessible KLIFS resource revolving around the protein kinase family catering to >1600 unique users per month.
2. Protein signaling networks: our second pillar delves into the analysis, simulation, modeling, and prediction of protein signaling networks. This endeavor aims to enhance our comprehension of protein-protein interactions, with a specific emphasis on ultimately understanding the regulation and deregulation of these processes.
3. Drug design: in the third pillar, we harness knowledge-driven and machine learning techniques to design molecules capable of modulating protein-protein signaling within cells. This research is geared towards developing innovative approaches to influence cellular signaling behavior, i.e. network medicine.

Project description

The position is part of a research project generously funded by the Carlsberg Foundation entitled "Look who’s talking: decoding protein-protein dialogue using ChatGPT".

WHAT? Inside every cell of any organism, hundreds to thousands of distinct proteins are constantly interacting with each other. Together, this dialogue between proteins determine virtually every facet of cellular behaviour and function.

WHY? Despite the fundamental importance of these protein-protein interactions, we still do not fully understand this dialogue between proteins. Some of the open questions are: Which proteins are interacting which each other? How do they know who to interact with? How do they precisely interact with each other? And why do they interact with each other?

HOW? The recent breakthroughs in large language models, such as the well-known example of ChatGPT, have astounded the world by its broad applicability and accurate interpretation of human and even programming languages. In this project, we are applying ChatGPT-like models to figure out which proteins are talking to each other and how.

Our department

Department of Drug Design and Pharmacology is committed to research-based teaching and interdisciplinary research that supports the development and understanding of chemical and pharmacological properties of drugs and drug targets. We work as part of a dynamic academic community of research, education and innovation within the Pharmaceutical Sciences bridging Health Sciences and Life Sciences.

Information about the Department can be found at https://drug.ku.dk/

Job description
Your key tasks as a PhD student at the Graduate School of Health and Medical Sciences 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

We are looking for a highly motivated and ambitious bioinformatician, data scientist or machine learning specialist, ideally experienced in large language models and protein-protein interactions.

Essential experience and skills:

• An MSc related to bioinformatics, computational biology, computer science, machine learning, systems biology, pharmaceutical sciences, applied math/statistics/physics, data science, or related fields.
• Excellent programming skills, preferably in Python
• Experience handling (large) datasets, performing data parsing and analysis
• Proficient communication skills and ability to work in teams
• Excellent English skills written and spoken

Desirable experience and skills:

• Experience with Machine learning / Deep learning / Large Language Models
• Experience with software and pipeline design
• Code versioning with Github
• Experience working with protein structures and protein-protein interactions (e.g. structural bioinformatics)
• Knowledge of cell biology, cellular signalling, protein structures, intermolecular interactions, and evolution
• The applicant should be reliable and well organized. The work requires independence and demands flexibility and accuracy. Further, you must have good interpersonal skills and interest in working in an international team.

Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project such as bioinformatics, computational biology, computer science, machine learning, systems biology, pharmaceutical sciences, applied math/statistics/physics, data science, or a related area. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

• A curious mind-set with a strong interest in machine learning and protein science
• Professional qualifications relevant to the PhD project
• Relevant work experience
• Other professional activities
• Previous publications
• The grade point average achieved
• Communication skills

Place of employment

The place of employment is at the of Drug Design and Pharmacology, 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 a computational core facility and modern laboratories. Moreover, we are part of the cluster for Integrated Structural Biology (ISBUC), Center for Health Data Science (HeaDS), and the pharmaceutical informatics research section (link).

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 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 to the Graduate School of Health and Medical Sciences.

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.

The PhD student is expected to be affiliated to the graduate programme in pharmaceutical sciences, Drug Research Academy.

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 30,716 DKK/Roughly 4,100 EUR (April 2024 level) plus pension.

We encourage all - regardless of their personal background and status - to apply.

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). Please mention why you are interested in the position and why this could be the right project for you.
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 applicable)
5. Link to your GitHub account (if applicable)
6. References and recommendations (if possible)

Application deadline: 21 July 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.

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: http://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 in the first half of August

Questions
For further information, applicants may contact the principal supervisor, Associate Professor Albert J. Kooistra, e-mail: [email protected], phone: +45 35 32 83 05 or PhD coordinator Marianne W. Jørgensen, e-mail: [email protected], phone: +45 3533 6449.

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/

For more information on working and living in Denmark visit http://ism.ku.dk (International staff mobility) and https://www.workindenmark.dk

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