PhD student in Bioinformatics

Are you interested in working with research with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favorable working conditions? We welcome you to apply for a PhD position at Uppsala University.

The Department of Cell and Molecular Biology is organized into seven research programs which all focus on different areas of cell and molecular biology: Computational Biology and Bioinformatics, Microbiology and Immunology, Molecular Biology, Molecular Biophysics, Molecular Evolution, Molecular Systems Biology and Structural Biology. The scientific basis of what we do lies in biology, but our research overlaps with other areas such as medicine, computer science, mathematics, chemistry, engineering sciences and physics.  In total, we are over 200 staff and ~60 Ph.D. students. Please read more about the department’s work at https://www.uu.se/en/department/cell-and-molecular-biology. 

Read more about our benefits and what it is like to work at Uppsala University.

Duties
In Senior Professor Komorowski’s bioinformatic group the research focus is machine learning for Life Sciences.  Our methods are usually founded in Computer Science and Statistics while problems to be solved are often defined by Life Scientists.  In collaboration between Professor Komorowski’s Bioinformatics group and the group of Professor Michael Gale at University of Washington, Seattle, USA, we are developing combinatorial models of the immune system’s responses to vaccines.  Our primary approach is to use interpretable machine learning techniques, also called transparent, that are not only able to make predictions but most importantly can provide interpretations of the results.  This means that is possible to answer the questions how the predictions are reached in stark contrast to so-called black-box models.  The aim of this PhD position is provision of a deeper understanding of the immune system when it develops protection upon vaccination. This will require further developments of machine learning methods of the transparent type.  The PhD student is expected to be involved both in building machine learning models of the immune system and in the interpretation of the results.  The candidate is expected to assist in teaching a machine learning course.  

Requirements
To meet the entry requirements for doctoral studies, you must

• - hold a Master’s (second-cycle) degree in Bioinformatics, or Computational Biology, or
• - have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• - have acquired substantially equivalent knowledge in some other way.

Significant competence in transparent machine learning methods such as rule based models and decision trees is required, as well as proficiency in general Computer/Data Science methods.  Fluency in English, spoken and written is desirable as all research is in essentially in English. 

Additional qualifications
Experience with the R.ROSETTA learning system, Monte Carlo Feature Selection and basic competence in artificial neural networks are a merit and so is previous experience teaching assistantship. 

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as soon as possible or as otherwise agreed. Placement: Uppsala 

For further information about the position, please contact: Prof Jan Komorowski, jan.komorowski@icm.uu.se.  

Please submit your application by 26 June 2024, UFV-PA 2024/2220.

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