I studied biology at the University of Leiden, the Netherlands, were I chose to specialise in bioinformatics. One of my one year research topic's was "STAR*PC, Structure Analysis of RNA" and involved co-developing, programming, porting and documenting a bioinformatics software-package that computes (actually: simulates) the secondary structure of RNA based on its primary nucleotide sequence. It 'simulates' because it does not calculate every possible combination of strands and picks the best, but rather 'folds' it piece by piece, starting with those complementary strands that are attracted to each other most. Information about STAR, which is available for PC, Mac and Atari can be requested from
This e-mail address is being protected from spambots. You need JavaScript enabled to view it
.
During my studies, I also worked 1.5 day a week at the Laboratory for Physiology and Physiological Physics as a system administrator for the PC farm. As extra-curricular activities, I was member of the board of the LBC (Leiden Biologists Society) and the Dies LBC. Furthermore, for 4 years I was editor-in-chief of "The Chameleon", the newsletter of the Biology faculty.
At the Centre of Estuarine and Marine Ecology, I analysed a complex estuarine eco-systems model and researched new techniques how to analyse behaviour of complex eco-systems models.
Following that, I transfered to the DLO-Research Institute for Agrobiology and Soil Fertility (AB-DLO, now called Plant Research International). At the department of AgroSystems Research, I worked as bioinformatics support staff for the SARP project (Simulation and System Analysis for Rice Production). The SARP-project was a international co-operation project of AB-DLO, Wageningen University and the International Rice Research Institute (IRRI, Philippines), financed by DGIS (Directorate General International Co-operation, Dutch Government) and aimed at building research capacity in the field of crop simulation and systems analysis in the Asian national research centres.
I developed a user-friendly and open structured simulation environment (FSU 2.0) for crop growth models, and a user-friendly system (MANAGE-N 1.0) that is capable of maximising rice yield by optimising fertiliser applications. The underlying model for MANAGE-N has been developed by dr. H.F.M. ten Berge, together with input from Asian counterparts and me. Tested and applied in China, India and the Philippines for three consecutive years now, recommendations by the MANAGE-N tool result in up to 15% more dry grain yield... and that in countries where the average population growth is 2%. Furthermore, I co-developed crop growth models and new tools and procedures for simulation software. In the course of this project I went to Asia several times and worked at IRRI (Philippines) for 4 months.
In July 1996 I joined the European Bioinformatics Institute as staff scientist in the Industry Support Programme. The Industry Support Programme had (at that time) the overall aim to help to adapt quickly to, and maximise the benefits from, developments in the fast-growing fields of bioinformatics and computational biology. Within this Programme a consortium of twenty-one leading pharmaceutcial companies was formed, for which the key objectives were education/training and technology development. After four years, I moved into the alternative splicing scene, where I was lead developer of the computational pipelines for AltExtron and later the AltSplice databases (as part of the ASD and ATD consortiums). The AltSplice database in it's current form with the various services attached to it is recognised one of the leading databases on alternative splicing in the world. See also my project overview for more information.
