AAA Data Science Postdoctoral researcher Computer Science with Life Sciences affinity

Informatics Institute (UvA) & Dept. of Computer Science (VU)

VU University Amsterdam is one of the leading institutions for higher education in Europe and aims to be inspiring, innovative, and committed to societal welfare. It compromises twelve faculties and has teaching facilities for 25.000 students.

The Faculty of Sciences performs research in the areas Life & Health, Networked World, Fundamentals of Science, and Energy & Sustainability. More than 1700 students participate in mono- and interdisciplinary bachelor and master courses. The staff is hosted in the departments of Physics, Chemistry & Pharmaceutical Sciences, Mathematics, and Computer Sciences. 

Amsterdam Data Science, an initiative of the University of Amsterdam (UvA), VU University Amsterdam (VU), Amsterdam University of Applied Sciences (HvA), and Centrum Wiskunde & Informatica (CWI) is looking for 14 researchers at the postdoctoral/PhD level. These positions are funded by the Amsterdam Academic Alliance (AAA), a joint initiative of the UvA and VU aimed at intensifying collaboration with each other and knowledge institutions in the region, to cement Amsterdam's position as a hub of academic excellence. These positions are partially co-funded by CWI, Faculty of Social and Behavioural Sciences of the UvA, HvA, ORTEC, Spinoza fund of Prof. Vossen, and VUmc.

Amsterdam Data Science provides a network in which some 300 Amsterdam based scientists exchange Data Science knowledge and forge partnerships within and outside the academic community. This comprises the foundations of data science and data science for the life sciences, social analytics, business analytics, and digital humanities.

This advertisement concerns one of the 14 positions. This postdoctoral researcher position is with Prof. Heringa of the Dept. of Computer Science, VU University, and with Prof. Welling of the Informatics Institute, University of Amsterdam. Data science is a strategic direction for both the Informatics Institute of the UvA and the Department of Computer Science of the VU.

An enormous amount of data has accumulated that can be used to fight complex genetic diseases such as cancer. For example, the Cancer Genome Atlas (TCGA) holds reference data for multiple tumor types from various experimental sources such as DNAseq and RNAseq. Additionally, thousands of molecular pathways are made available via publicly accessible repositories. Together, these data constitute a treasure trove to understand which molecular pathways are affected and may be targeted by (existing) drugs, thus offering an avenue towards personalized medicine.

Project description

Your task will be to gain an improved understanding of the disease biology by integrating pathway knowledge with molecular profiling data. This will be achieved by applying and developing novel machine learning methods that are suitable for this problem. Examples of possible machine learning tools are models such as Bayesian networks, deep neural networks, deep auto-encoders, and probabilistic programs (aka simulators), and inference method such as Markov chain Monte Carlo (MCMC), variational Bayes (VB) and Approximate Bayesian Computation (ABC). These methods will be used to gain a deeper understanding of cancer biology at the systems level.

Requirements

The candidate must have a PhD in computer science, statistics or a closely related field. An ideal candidate has:

• a proven track record in machine learning or a closely related field;
• affinity with or interest in problems in the life sciences;
• a strong background in computer science and programming;
• excellent oral and written communication skills.

Further information

For additional information please contact: 

• Prof. Jaap Heringa 

• Prof. Max Welling
• Working at VU

Appointment

The initial appointment will be for a period of three years. We have excellent employment conditions such as:

• remuneration of 8,3% end-of-year bonus and 8% holiday allowance;
• solid pension scheme (ABP);
• a minimum of 29 holidays In case of full-time employment;
• possibilities to save up holidays for sabbatical leave.

The salary will be in accordance with university regulations for academic personnel, and depending on experience, range from a minimum of €2,476 gross per month up to a maximum of €3,908 gross per month (salary scale 10) based on a full-time employment. The Collective Labour Agreement for Dutch Universities is applicable.

Job application

Applications may only be submitted via informatica.secretariaat.few@vu.nl. To process your application immediately, please quote vacancy number 15108 and the title of the position you are applying for in the subject-line.

Applications must include a detailed curriculum vitae, BSc and MSc academic transcripts, a motivation letter explaining why you are the right candidate, list of projects you have worked on with brief descriptions of your contributions and the names and contact addresses of two academic references from which information about the candidate can be obtained. All these should be grouped in one PDF attachment.

Applications will be accepted until 10 May 2015.

No agencies please