Postdoctoral researcher Network-based data integration

Faculty of Science – Swammerdam Institute for Life Sciences

Publication date
18 April 2017
Level of education
PhD
Salary indication
€2,552 to €4,028 gross per month
Closing date
16 May 2017
Hours
38 hours per week
Vacancy number
17-188

The Swammerdam Institute for Life Sciences (SILS) is one of the largest institutes of the Faculty of Science. Its approximately 240 scientists and staff members work in 16 research groups that perform excellent research centered on three themes:

  1. Cell & Systems Biology;
  2. Neurosciences, and
  3. Molecular Life Sciences.

The SILS research group of prof. Age Smilde works on Biosystems Data Analysis. This project is part of the Life Science node of the Amsterdam Data Science Center (ADS). It is a collaboration between prof. Smilde’s group, and the group of prof. Bas Teusink (VU University Amsterdam).

The shared postdoctoral researcher will be appointed at the UvA but work in both groups. External collaboration is foreseen with several medical biology groups. For the setup of the ADS Life node, we will explicitly collaborate with the Cancer Centre at the VUmc, where they study a large collections of cancer cell lines. There exist also long-term collaborations with the AMC and with Copenhagen University, in particular the COPSAC group, which owns a world-leading children cohort focussing on asthma. All these collaborations ensure relevant medical research questions and data.

Project description

In a growing number of cases in systems biology, multiple connected data sets are collected. This can be multiple genomics data measured on the same system (e.g. measured on the same subjects/patients) or the same set of biochemical entities on related systems (e.g. gene-expression of cancer cell lines). There is growing awareness that such data should be analysed and modelled simultaneously, in order to arrive at a global understanding of the whole system. A fruitful approach to tackle this problem is to build empirical models of all related data sets simultaneously by using data fusion or data integration methods. In essence, all these methods are based on correlations and are generalizations of component or factor analysis. Hence, they are purely data driven.           

Several extensions of the existing data fusion methods can be envisioned. Increasingly pathway information is available for a system, and then an initial break-down of the data in pathways can be accomplished and the analysis can be focussed on studying the behaviour of a pathway measured under different conditions. In that case, the different conditions have to be encoded and brought in as a priori information in the data fusion method. To take this one step further, it will be of interest to study the relationship between pathways (initially metabolic pathways, but signal transduction pathways will be considered), perhaps also as a function of conditions. In that case, the grouping of the different pathways has to be imposed on the data fusion methods. Finally, it may also be that part of the biological network is known and imposing this known structure (e.g. the topology of this known part) focusses the data analysis and makes the results of the global model more interpretable.

A new set of data fusion methods have to be developed that combine biological information (pathways, network or known biological relationships) and empirical data fusion methods. Vehicles of accomplishing this are penalized methods and Bayesian methods. These methods will be developed, tested and validated in close collaboration with the medical biology partners. 

Requirements

Candidates should have a PhD in the Life Sciences (bioinformatics, systems biology, data analysis or chemometrics). 

Further information

For further information:

Appointment

The appointment will be on a temporary basis for a period of 18 months.

Based on a full-time appointment (38 hours per week) the gross monthly salary will range from €2,552 to maximal €4,028 (scale 10), depending on experience. The Collective Labour Agreement for Dutch Universities is applicable.

Job application

Due to limitations in recruitment budget we will only consider candidates that are currently in Europe. Please do not respond if you are not in this continent.

Applications may only be submitted by electronic mail and should be sent to application-science@uva.nl. To enable us to process your application immediately, please quote  vacancy number 17-188 and the position you are applying for in the subject-line.

Applications must include a curriculum vitae and a letter of motivation. Please combine these documents in one single attachment and also mention the months (not just years) in your CV when referring to your education and work experience.

Applications will be accepted until 16 May 2017. #LI-DNP

No agencies please

Published by  University of Amsterdam