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

Københavns Universitet (KU)



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 Postdoc commencing 1 October 2024 or as soon as possible thereafter.

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/

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:

    • 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.
    • 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.
    • 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.
    • 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.
    • CV incl. education, work/research experience, language skills and other skills relevant for the position.
    • 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.
    • List of publications.
    • References and recommendations
    • Link to your GitHub account
    Your job
    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, you will build and apply ChatGPT-like models to figure out which proteins are talking to each other and how.

    Profile
    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.

    The person will be required to relocate to Copenhagen and key responsibilities will include: establishing research ideas together with the principal investigator, leading the research project on a day-to-day basis, presenting research in internal meetings and international conferences, taking an active part in manuscript writing, and translating new knowledge in the subject area into research activity. There will be the opportunity to supervise more junior group members and contribute to teaching and dissemination activities.

    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 starting date is 1st of October 2024 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).

    Currently, the monthly salary starts at 38,575 DKK/approx. 5,170 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 further information please contact principal supervisor, Associate Professor Albert J. Kooistra, e-mail: [email protected], phone: +45 35 32 83 05; www.sund.ku.dk
    Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility).

    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:

      Deadline for applications: 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. 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. 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.

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

      Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.

      Info
      Ansøgningsfrist: 21-07-2024

      Ansættelsesdato: 01-10-2024

      Arbejdstid: Fuldtid

      Afdeling/Sted: Department of Drug Design and Pharmacology

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      Københavns Universitet (KU)

      Nørregade 10, 1165 København K

      Københavns Universitets mål er at drive forskning af højeste kvalitet, at tilbyde forskningsbaseret uddannelse til det højeste akademiske niveau, og at formidle ny og klassisk viden til såvel videnskabelige miljøer som til det omgivende samfund.

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