AAA Data Science Postdoctoral researcher or PhD candidate in Chem- and Bio-informatics

Faculty of Sciences (VU) & Neuro-oncology Research Group (VU Medical Center)

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. VU Medicinal Chemistry and VUmc Cancer Center Amsterdam (CCA) invite applications for a PostDoctoral position or PhD candidate for a collaborative AAA Data Science project on cheminformatics and bioinformatics, entitled: Integration of Phenotypic Drug Efficacy and Molecular Chemogenomics Data.

The section Medicinal Chemistry is part of the Department Chemistry and Pharmaceutical Sciences of VU University Amsterdam and the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), which aims at fundamental breakthroughs in translational molecular medicine, drawing on the integrated study of biological processes that will lead to new diagnostics and treatments The Medicinal Chemistry investigates the molecular features of the binding and the mechanism of action of biologically active molecules by an integrated approach in which bio-computational approaches, synthesis, pharmacological and biochemical studies are combined.

The section of Neuro-oncology is part of the VUmc and located in the Cancer Center Amsterdam (CCA). This multidisciplinary section is interested in integrating preclinical and clinical data to develop tailored drug combination therapies with a special focus on pre-clinical brain tumor research.

Project description

We are looking for a highly motivated scientist with expertise in bioinformatics and cheminformatics to develop new computational tools and workflows that allow the integration and exploitation of chemogenomic and phenotypic data for the prediction of (synergistic) drug efficacy.

The project aims to exploit cell-based anti-cancer drug sensitivity profiles and structural chemogenomics analyses of protein-ligand interaction profiles for the prediction of drug polypharmacology and the identification of efficient anti-cancer drug combinations.

To achieve these goals, the candidate will perform the following tasks:

• cheminformatics analysis of small (potential drug) molecules (structure-activity relationship data mining, ligand-based similarity assessment);
• bioinformatics analysis of biochemical and molecular biological data (RNAi screening data, gene expression profiles, mutations/SNPs);
• chemogenomic analysis and prediction of protein-ligand interactions (protein structure analysis, ligand binding site comparison, molecular docking simulations, molecular interaction fingerprint analysis).

Requirements

• PhD or Master (M.Sc.) in bioinformatics/cheminformatics with proven expertise in the development and application of computational tools and methods for chemical and biological data mining;
• excellent skills in the application of different programming languages (Bash, Python, Java, Perl, R, PHP, Javascript, Scientic Vector Language/SVL, Matlab);
• experience in the construction of bioinformatics and cheminformatics/chemogenomics databases is a strong advantage;
• creative and flexible working attitude and ability to collaborate effectively in an interdisciplinary research environment.

The ideal candidate has significant experience in computer programming using different scripting languages in order to develop automated workflows and new cheminformatics and bioinformatics analysis tools for efficient data mining.

Further information

For information, please contact:

• Dr. Chris de Graaf
  T: +31 (0)20 5987553

• Prof. Iwan de Esch
• Prof. Thomas Wurdinger or
• Dr. Bart Westerman
• Working at VU

Appointment

The appointment will be for a period of three years for a postdoc and four years for a PhD student. The appointment will be either at the VU University, the VUmc, or at both institutes.

For a postdoctoral researcher, 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.

For a PhD candidate, the salary range from a minimum of €2,125 gross per month in the first year up to a maximum of €2,717 based on full-time employment. The Collective Labour Agreement for Dutch Universities is applicable.

Job application

Applications may only be submitted via secrCPS.few@vu.nl. To process your application immediately, please quote vacancy number 15109 and the title of the position you are applying for in the subject-line.

Applications must include a detailed curriculum vitae, 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