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Bioinformatics Laboratory

Department of Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)

Academic Medical Center (AMC)

  • Visiting address:
    • Meibergdreef 9
    • J1B-207 (J-building, floor 1B)
  • Postal address:
    • PO Box 22700
    • 1100 DE Amsterdam
    • The Netherlands

Introduction

Eelke van der Horst received his MSc degree in Bio-Pharmaceutical Sciences at the University of Leiden in 2003. During his second internship at the group of Medicinal chemistry, he developed an application to calculate and visualize surface area properties of (virtual) molecules. This application helps medicinal chemists predict passive transport over membranes such as the intestinal wall and blood-brain barrier.

After his graduation, Eelke continued to work as a software developer at SemLab, a company that focuses on knowledge discovery and semantic web solutions for the biotechnology domain. Eelke participated in several EU funded research & innovation projects on bioinformatics, collaborating with international universities and companies.

In October 2004, Eelke returned to the division of Medicinal chemistry at Leiden University to work at a spin-off company: Cidrux Pharminformatics B.V. Here, he assisted in development and commercial rollout of the Molecule Evoluator™, an application for interactive design and optimization of lead compounds based on evolutionary principles.

Starting half way 2006, Eelke continued to work at the group as a Ph.D. student, where he participated in the GPCR forum of the Dutch Top Institute Pharma (TI Pharma). As such, he applied computational solutions for the design of new ligands for the Adenosine Receptor.

Current Position

Currently, Eelke works as a scientific programmer/PostDoc as part of the Systems Bioinformatics project in the Netherlands Consortium for Systems Biology (NCSB). As part of this project, he will develop infrastructure components that enable the construction and maintenance of BioExpert knowledge bases.

The overall aim of the BioExpert project is to develop a framework to represent, integrate, and present (curated) knowledge of specific biological systems and to use this information in subsequent modeling applications. The overall framework is based on state-of-the-art approaches for Information Management (e.g. RDF/OWL) and novel approaches for information (re)presentation (i.e. concept map networks).

Eelke’s current work involves the application of semantic web technologies, such as RDF/SKOS, interaction with expert in the corresponding domains, such as (molecular) biologists and clinicians, and further development of the BioExpert application (user interface, navigation/querying, web-services to access data, visualization, etc.) to enhance its use in systems biology.

-- EelkevanderHorst - 2011-11-04
Topic revision: r1 - 04 Nov 2011, EelkevanderHorst
 

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