Aldo Jongejan

Postdoc (AMC) - Whole exome sequence analysis

Room: J1B-205, Phone: +31-(0)20-5664711, Email: a.jongejan@amc.uva.nl

General Info

I studied chemistry at Leiden University with as main focus biochemistry with a keen interest in the fields of organic chemistry and quantum chemistry. The second year of my study I did at the University of Aarhus in Denmark as an exchange student (ERASMUS program). During my intership I looked at the incorporation of the organic cofactor Pyroloquinoline quinone (abbreviated to PQQ) into biosensors. For this, I synthesized various PQQ derivatives (11-step synthesis route) and polypyrrole-ferrocene carrier materials. After graduation I worked half a year in Germany (Geselschaft fuer Biotechnologie in Braunschweig) trying to ready flavoproteins for incorporation into biosensors (D-amino acid oxidase). For this purpose I extracted the original cofactor, FAD, out of the enzyme first, creating an apo-form. After it was reconstituted with a modified FAD-cofactor. Back in the Netherlands, I started to work on molecular modelling of the quinohaemoprotein alchol dehdyrogenase (QH-ADH) from Commamonas testosteroni for a short period, before starting my PhD at the Technical University of Delft. This work involved unraveling the enzyme mechanism of QH-ADH using various approaches. Besides performing wet-lab experiments (growing bacteria, isolating enzymes, measuring enzyme kinetics) I had my first experience in in silico experiments. I constructed various homology models and performed quantum chemical calculations. After finishing my PhD I started working as a post-doc at the Vrije Universteit (VU) in the group of Medicinal Chemistry. Here I worked on the modelling of G-protein coupled receptors (GPCRs) and their interaction with drug molecules. I was also involved in public relation matters for the recruitment of new students. Having worked for 7.5 years at the VU, I became a teacher in Bioinformatics at the Hogeschool Leiden. Here I worked for 3 years, before I was denied a permanent contract, despite good marks and the much appreciated efforts of the students to keep me. During my work at the Hogeschool I collaborated intensively with the TopLab, where I did the de novo assembly of a fungal genome. Since November 2010 I work in the group of Antoine at the KEBB (AMC), mainly on next generation sequencing topics.

I have experience in a couple of programming languages (by no means fluent, I rather hack my way around): python, C, fortran, awk, shellscripting, perl, Java (even did Z-Basic long time ago ...)

And I have been working with many molecular modellng packages (AMBER,GROMACS/GROMOS, Sybyl, Insight, MOE), R, VTK, Taverna, etc..

Next Generation Sequencing


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Topic revision: r3 - 03 Nov 2011, AldoJongejan

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