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Post doctor in machine learning for single-cell data analysis

Institutionen för molekylärbiologi

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before

2022-08-28

  • Type of employment Temporary position longer than 6 months
  • Extent 100%
  • Place Umeå

The Department of Molecular Biology seeks a postdoctoral scientist to work with varational autoencoders to model gene isoforms in single-cell data. The position is funded by the Medical Faculty.  

Department of Molecular Biology

The Department of Molecular Biology has about 200 employees. The department's main tasks involve research, graduate education, and undergraduate education as well as interactions with the community. Affiliated with both the Faculty of Science and Technology and the Faculty of Medicine, the department's research and education activity includes several molecular biological areas within science and medicine: cell biology, microbiology, infection biology, tumour biology and neurobiology in conjunction with the use of genetic model organisms (except plants). The department offers a vital research environment with a broad setup of modern imaging, metabolomics, genomics and screening facilities.


Project description and working tasks

Gene isoforms play key roles in disease etiology and outcome. Despite that gene isoforms are involved in most biological processes, they are commonly ignored because we lack tools to understand them. In this project we will build new large-scale machine learning tools to extract gene isoform information from commonly existing single-cell RNA-seq data.

The approach we consider is based on variational autoencoders and sequence models. The challenges lie in the data being extremely large, sparse, and noisy. The project will open doors into the currently most rapidly expanding field in biology.

You will carry out formulation, implementation and testing of machine learning approaches to model and understand single-cell RNAseq data. You will present your findings, write manuscripts, help supervising students, and actively contribute to a collegial lab culture.

You will be based in the lab of Johan Henriksson (www.henlab.org) in collaboration with the machine learning group of Associate Professor Tommy Löfstedt. The Henriksson lab is based at the Department of Molecular Biology and is part of The Laboratory of Molecular Infection Medicine Sweden (MIMS, www.mims.umu.se), which is the Swedish node within the Nordic EMBL Partnership for Molecular Medicine. The project is run in close collaboration with Tommy Löfstedt, docent and associate professor and head of the machine learning group at the Department of Computing Science.


Eligibility 

A person who has been awarded a doctorate in relevant subject area or a foreign qualification deemed to be the equivalent of a doctorate qualifies for employment as a postdoctoral fellow. This eligibility requirement must be met no later than the time at which the appointment decision is made.

Postdoctoral fellows who are to teach or supervise must have taken relevant courses in teaching and learning in higher education.

You should be highly motivated and able to work productively in a team as well as independently. Excellent communication skills for interacting effectively with senior colleagues and peers are required. Proficiency in written and spoken English also required. Great emphasis will be placed on personal suitability.

A successful candidate should be familiar with Python and at least one framework for deep learning (e.g. PyTorch or TensorFlow/Keras). The candidate should have documented experience in machine learning or mathematical/statistical modelling.


Additional useful qualifications 

Since appointment as a postdoctoral researcher is a career-development position for junior researchers, we are primarily interested in applicants who completed their doctoral degree no more than three years before the application deadline. If there are special reasons, an applicant who has completed their degree earlier than that may be considered. Special reasons include absence due to illness, parental leave, clinical practice, appointments of trust for a trade union organisation or other similar circumstances, and for relevant duties/assignments within the subject area.

Experience in basic biology, and especially sequence analysis, or experience in single-cell analysis is a merit.


More information about the position

The appointment is a full-time, fixed-term position for two years in accordance with the terms of contract for fixed-term employment as a postdoctoral researcher. Access as soon as possible or by agreement.


Application

A full application should include:

  • An introductory letter including a 2-page statement of research interests relative to the above topics and a motivation of why your expertise is appropriate for the position.
  • Curriculum vitae (CV) with publication list,
  • Certified copy of doctoral degree certificate,
  • Certified copies of other diplomas, list of completed academic cources and grades,
  • Copy of doctoral thesis and relevant scientific papers,
  • Contact information for at least two reference persons,
  • Other documents that the applicant wishes to claim.

We will ensure that the formal requirements are met and that we have sufficient information to adequately rank eligible candidates.

The application must be written in English. The application is made through our electronic recruitment system. Documents sent electronically must be in PDF format. Log in to the system and apply via the button at the end of this page. The closing date is 2022-05-26.

Further details are provided by Johan Henriksson, johan.henriksson@umu.se
and Tommy Löfstedt, tommy.lofstedt@umu.se

We look forward to receiving your application!


More about us

The Henriksson lab is part of the Laboratory for Molecular Infection Medicine Sweden (MIMS), the Swedish Node of the Nordic EMBL Partnership for Molecular Medicine, and part of the Umeå Centre for Microbial Research (UCMR), an interdisciplinary research centre devoted to top quality research and novel applications in the field of microbiology. You can find more information about us at http://henlab.org/, www.mims.umu.se and www.ucmr.umu.se. For questions regarding the position, please contact the project supervisors: Johan Henriksson (johan.henriksson@umu.se) or Tommy Löfstedt (tommy.lofstedt@umu.se).

For more information about The Department of Molecular Biology please visit our web page www.umu.se/en/department-of-molecular-biology or for The department of Computing science, https://www.umu.se/en/department-of-computing-science/.

Admission

As soon as possible or by agreement

Contact

Johan Henriksson

johan.henriksson@umu.se

Tommy Löfstedt

tommy.lofstedt@umu.se

Registration number

AN 2.2.1-819-22

Salary

Monthly salary

Union representative

SACO

090-7865296

SEKO

090-7865431

ST

090-7865431

Apply

before

2022-08-28

Umeå University wants to offer an equal environment where open dialogue between people with different backgrounds and perspectives lay the foundation for learning, creativity and development. We welcome people with different backgrounds and experiences to apply for the current employment. We kindly decline offers of recruitment and advertising help.