Staff Scientist: Bioinformatician in Epidemiology and Biology of Infections

Updated: 12 days ago

Umeå University is one of Sweden’s largest higher education institutions with over 37,000 students and about 4,700 employees. The University offers a diversity of high-quality education and world-leading research in several fields. Notably, the groundbreaking discovery of the CRISPR-Cas9 gene-editing tool, which was awarded the Nobel Prize in Chemistry, was made here. At Umeå University, everything is close. Our cohesive campuses make it easy to meet, work together and exchange knowledge, which promotes a dynamic and open culture.

The ongoing societal transformation and large green investments in northern Sweden create enormous opportunities and complex challenges. For Umeå University, conducting research about – and in the middle of – a society in transition is key. We also take pride in delivering education to enable regions to expand quickly and sustainably. In fact, the future is made here.


Department of Plant Physiology

Closing date: 2024-03-31 

As a national hub for molecular biosciences in Sweden, SciLifeLab develops and maintains unique research infrastructure, services and data resources for life science. The overall aim of SciLifeLab is to facilitate cutting-edge, multi-disciplinary life science research and promote its translation to the benefit of society. About 200 research groups, 1500 researchers and 40 national infrastructure units are associated with SciLifeLab, with two main centers located in Stockholm and Uppsala, but with national SciLifeLab units at all major Swedish universities.

The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) is a 12-year initiative that focuses on data-driven research, within fields essential for improving people’s lives, detecting and treating diseases, protecting biodiversity and creating sustainability. The program will train and recruit the next generation of data-driven life scientists and create strong and globally competitive computational and data science capabilities in Swedish life science. The program aims to strengthen national collaborations between universities, bridge the research communities of life and data sciences, and create partnerships with industry, healthcare and other national and international actors.

The DDLS program is establishing a national Data Science Node in “Epidemiology and Biology of Infections” at Umeå university with a national responsibility to develop data services and to provide advanced data analytics support. As a Staff scientist you will explore molecular, clinical and/or epidemiological data in research projects aiming to increase our understanding of the emergence, prevalence, spread and treatment of infectious disease. You will apply, adapt and develop machine learning approaches to provide data analysis support to data-driven Swedish research projects of scientific excellence, as well as being a driver of advanced data analytics postgraduate training on a national level.

The Data Science Node staff will be well integrated with the local research community, but also connected to the SciLifeLab Data Centre and the SciLifeLab Bioinformatics Platform (National Bioinformatics Infrastructure Sweden, NBIS), a unique national infrastructure with over 120 experts, providing advanced bioinformatics support, infrastructure and training to the Swedish life science research community and participating in international collaborations.


Your future workplace

The Department of Plant Physiology hosts the largest bioinformatic section of Umeå university with over 20 bioinformaticians and the Swedish Metabolomic Facility. You will work in a strong group of bioinformaticians that both help other scientists with analysis and are developing the field themselves. The bioinformatic group works with projects from all fields of life science. 

The department is part of the Umeå Plant Science Centre with a total over 200 scientists in more than 35 research groups and with a strong, multi-disciplinary, collaborative and expanding research. We are also a strong partner in The Chemical-Biological Centre (KBC), a life science hub that hosts several national instrument and technology platforms. For more information about working at Umeå University: www.umu.se/en/work-with-us/. 


Main responsibilities

The main responsibilities are to:

  • Carry out advanced data analyses within nationally prioritized data-driven life science projects, using state-of-the-art bioinformatics and machine learning tools applied to large-scale molecular (omics), imaging, clinical and/or epidemiological data.
  • Develop and implement necessary tools and workflows for such analyses.
  • Educate other life scientists across Sweden in advanced data analytics through collaboration within supported projects, advanced national courses, and consultations.
  • Engage in the continuous development and improvement of the DDLS program, the Data Science Node, and the SciLifeLab Bioinformatics platform.

Qualification requirements

We are looking for a highly motivated candidate with strong skills in applied bioinformatics, data science, and/or machine learning, to provide advanced data analysis support to Swedish life science research projects of scientific excellence. 

(i) Ph.D. in Bioinformatics, Data Science, Biotechnology, Engineering, Physics, or equivalent.
(ii) Extensive (3+ years) experience of applying and/or developing advanced bioinformatics, data science, or machine learning methods.
(iii) Programming knowledge in Python.
(iv) Very good oral and written communication skills in English
(v) Strong skills in cooperation and communication


Additional qualifications

Relevant postdoctoral studies or industry experience are a strong merit but not a requirement. Other strong merits is experience of one or several of the following 

  • Data science tools such as Numpy, Pandas and Matplotlib.
  • Modern deep learning frameworks, such as PyTorch or Tensorflow.
  • Programming knowledge in R and/or other programming languages for statistical computing and data visualization.
  • Advanced integration of multiple layers of molecular (“omics”) data sets
  • Research using real world large scale life science data.
  • Research or development connected to epidemiology and/or biology of infections or other public health questions. 

Experience in machine learning management systems such as Azure ML, machine learning workflow-engines such as MLFlow/Airflow/Metaflow, and/or data storage, databases, and data structures for large data volumes is also a merit.  “Reproducible research” and “FAIR data” are central concepts to us, and expertise in the development of reproducible code by using code sharing platforms, version control, workflow languages and container solutions is a merit.


Terms of employment

The employment is full-time and permanent. Probationary employment may be applied. Starting date according to agreement.


Application

Your application should contain 

  • A personal letter, max 2 pages, including a motivation for why you want to join this effort
  • CV with publication list
  • Doctoral degree certificate

You apply via our recruitment system Varbi. Last application date is 2024-03-31.


Contact

Björn Nystedt, NBIS Support Manager, tel +46 18 471 44 13, [email protected]
Johan Trygg, UmU DDLS Data Science Node, tel +46 730 647 137, [email protected]
Johannes Hanson, Department of Plant Physiology, tel +46 722 243 283, [email protected]



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