Aldo

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

Notes

28/29-01-2012 - Installed PyInstaller-1.5.1 @Bioscope cluster in order to make a Linux executable of a python script. Followed the instruction on how to use PyInstaller, but got errors on not being able to find the Python libraries. There is a python library in /usr/local/lib but it is a static one (ending with .a). Had to re-configure Python to enable shared libraries ($ ./configure --enable-shared) - http://groups.google.com/group/pyinstaller/browse_thread/thread/531db6ac61f1c019 and http://www.hostucan.com/webmaster-tutorials/centos-python-2.6-install Had to rename the present static library to fx. libpython..a to libpython..a.old to get it out of the way.

Then used the PyInstaller again and when it returned errors on not being able to found certain modules I included those in the Python script until the executable was made. I used the "--onefile" option. Hopefully I can now use this executable also on the Grid! (Maybe via installing PyInstaller on the AMC-UI first..)
Topic revision: r5 - 10 Feb 2012, AldoJongejan
 

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