Postdoc in Computational Medicine

The Department of Clinical Medicine – The Department of Pathology at Faculty of Health at Aarhus University invites applications for a position as Postdoc in the field of computational medicine as per 1 February 2024 or as soon as possible thereafter. The position is a fixed-term full-time position for 2 years.

Department of Clinical Medicine

As a Postdoc at the Department of Clinical Medicine, you will be part of what is probably the largest health science research department in Denmark. Our clinical research covers all the medical fields and takes place in close collaboration with the university hospital and the regional hospitals in the Central Denmark Region. We have approx. 30,000 square meters of modern research facilities for experimental surgery and medicine, animal facilities and also advanced scanners at our disposal. The department has overall responsibility for the master's degree programs in medicine and in molecular medicine. At the department we are approx. 670 academic employees, 500 PhD students and 160 technical/administrative employees who are cooperating across disciplines. As a Postdoc, you will be working at Aarhus University Hospital or another hospital in the Central Denmark Region. You can read more about the department here and about the faculty here.

About the research project

The research project concerns the development of novel computational methods for the analysis of multimodal data from complex tissues, including histopathological and highly multiplexed immunofluorescence images, transcriptomic and clinical data. The project takes an integrative and translational approach, requiring both biomedical and computational expertise. Furthermore, this position involves multiple international collaborations, requiring excellent English language and communication skills.

Your job responsibilities

As Postdoc you will join the Laboratory for Complex Tissue Analysis led by Prof. Victor Puelles, physically located in The Department of Pathology. Your position is primarily research-based but may also involve teaching assignments. You will be affiliated and contribute to the development of the Department of Clinical Medicine through research of high international quality. In your daily work, you will work closely with colleagues on your project, where you will receive supervision and guidance.

Your main tasks will consist of:

• Independent research of high international quality, including publication.
• Image analysis of highly multiplexed immunofluorescence data.
• Machine learning/deep learning-aided image segmentation.
• Bulk RNA-sequencing analyses.
• Single cell RNA-sequencing analyses.
• Developing novel methods for the analysis of histopathological and immunofluorescence images.
• Developing novel methods for the analysis of transcriptomic data.
• Developing interactive (web) interfaces to present and explore data.
• Participating in reviews on diverse biomedical and computational topics.
• Lab analysis server maintenance and administration.
• Data organization and developing storage concepts.
• Presenting progress at international conferences.
• (Co-)supervision of master and PhD students.
• Work as part of a multidisciplinary, international and multilingual team.

You will report to Professor Victor Puelles.

Your competences

You have academic qualifications at PhD level, for example within the following areas biotechnology or computational medicine. Specific expectations for the position include:

• Degree in a related field, e.g., biotechnology, medicine, biology or similar.
• Advanced biomedical knowledge, particularly in cell physiology, biochemistry and genetics.
• Advanced Python coding skills. Knowledge of other languages used within the field, particularly R, SQL and JavaScript is considered advantageous.
• Experience using best programming practices, e.g., version control, continuous integration, unit tests, documentation, linting, formatting, type checking, and publishing research as open-source software packages.
• Experience with common image analysis tools and software libraries, including ImageJ/FIJI, Napari, scikit-image and OpenCV.
• Experience analyzing highly multiplexed imaging data, particularly from multiplexed immunofluorescence protocols.
• Experience with bulk and single cell RNA-sequencing methods, e.g., (Py)DESeq2, scanpy, integration tools, workflow managers.
• Experience developing deep learning and GPU-accelerated applications in Python, e.g., with PyTorch, Tensorflow, RAPIDS.ai and/or CUDA.
• Experience building complex user-facing interactive applications, e.g., desktop applications with graphical user interface or interactive web applications, e.g., Electron, React, Vue.js.
• Experience setting up and maintaining Linux servers, including Docker container and Jupyter notebook setups.
• Experience with scientific writing and drafting publication quality figures, e.g., with Inkscape or Illustrator.
• Experience (co-)supervising students.
• Experience presenting at international conferences.

As a person, you have good interpersonal skills, are inclusive and team-oriented and able to contribute to a good work environment. We expect you to be fluent in oral and written English. Furthermore, Danish, Spanish and German are also spoken within the laboratory and/or with collaborators and are considered advantageous.
In order to be assessed as qualified for a Postdoc position, you must meet these academic criteria.

Questions about the position

If you have any questions about the position, please contact Professor Victor Puelles via email: vgpuelles@clin.au.dk

Your place of work will be the Department of Clinical Medicine – The Department of Pathology, Palle Juul-Jensens Boulevard 99, DK-8200 Aarhus N, Denmark.

Hybrid and primarily remote work are possible but occasional in person work is required.

Terms of employment

• Appointment as a postdoc requires academic qualifications at PhD level.
• Further information on the appointment procedure can be found in the Ministerial Order on the Appointment of Academic Staff at Universities.
• The appointment is in accordance with the Danish Confederation of Professional Associations (Akademikerne).
• Remuneration is in accordance with the above, and the Salary agreement catalogue for staff at Health.
• The yearly base salary for a fulltime postdoc is between DKK 484.214,84 and DKK 538.720,20 depending on the years of working experience after achieved MSc degree. The base salary includes a position related supplement and pension (17.1 %). Additional supplement(s) for special qualifications can be negotiated. Authorisation supplemement(s) will be granted, if relevant for the position. Your local eligible trade union representative at Aarhus University negotiates your salary on your behalf.
• Researchers recruited from abroad are offered a special researcher tax scheme with a lower tax rate.
• Further information on qualification requirements and job description can be found in the Ministerial Order on Job Structure for Academic Staff

Application

Your application must include the following:

• Motivated application
• Curriculum Vitae
• Diploma
• Template for applicant - postdoc
• A list of publications
• A teaching portfolio. We refer to Guideline on the use of teaching portfolios
• A maximum of five of the publications of greatest relevance to the job may be submitted (optional)
• Research plan can be uploaded (optional)
• Coauthor statement(s) can be uploaded (optional)
• References/recommendations can be uploaded separately in the e-recruitment system (optional)

We refer to the faculty’s Guidelines for applicants.

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants.

Letter of reference
If you want a referee to upload a letter of reference on your behalf, please state the referee’s contact information when you submit your application. We strongly recommend that you make an agreement with the person in question before you enter the referee’s contact information, and that you ensure that the referee has enough time to write the letter of reference before the application deadline.

Unfortunately, it is not possible to ensure that letters of reference received after the application deadline will be taken into consideration.

International applicant?

Aarhus University offers a broad variety of services for international researchers and accompanying families, including assistance with relocation and career counselling to expat partners. Please find more information about the International Staff Office and the range of services here. Aarhus University also has a Junior Researcher Association and offers career development support. You can read more about these resources here.

The application must be submitted via Aarhus University’s recruitment system, which can be accessed under the job advertisement on Aarhus University's website.