Inparablog

Completing my Masters in molecular biology in Leiden, I realized molecular biology was going to have some serious problems in the near future: What to do with all that data & Who’s looking at the bigger picture? Maybe I have been in the wrong parts of the laboratory, but it seemed to me that molecular biologists are looking mostly at the tiniest parts of some protein or some process. Knocking out genes tells you about the function of these genes, in the way that if knocked out, this or that process goes awray. Highly dynamic cellular processes such as the differentiation of cells into specific tissues (organs, limbs) are not easily studied by studying single genes.

I started in a Masters program in Theoretical Biology & Bioinformatics at Utrecht University under Prof. dr. Paulien Hogeweg. Here I discovered the necessity of using computer modeling to research complex processes and to discover which dynamics are responsible for this, and which are not. I also discovered that I have been under-educated in the use of bioinformatic tools as a molecular biologist. I have had only a half hour crash course in the use of BLAST at Leiden. This only touched the subject of: that BLAST exists… This is the website… And if you put your sequence here, something comes out. I never learned about Psi-BLAST, Pfam/SMART or multiple sequence alignments, which I now know to be incredibly useful to molecular biologists.

I am currently working as a post-doc at the Center for Molecular and Biomolecular Informatics, Nijmegen. My current research focusses on reconstructing the evolution of signaling pathways and the eukaryotic cillium.

John van Dam

Publications:

1. Teunis J.P. van Dam, Fried J.T. Zwartkruis, Johannes L Bos, Berend Snel (2011) Evolution of the TOR Pathway. Journal of Molecular Evolution
2. Teunis J.P. van Dam, Johannes L Bos, Berend Snel (2011) Evolution of the Ras-like small GTPases and their regulators . Small GTPases 2(1)
3. Teunis J.P. van Dam, Holger Rehmann, Johannes L. Bos, Berend Snel (2009) Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi. Cellular Signalling, In Press, Accepted Manuscript, Available online 28 June 2009, ISSN 0898-6568, DOI: 10.1016/j.cellsig.2009.06.004
4. Teunis J.P. van Dam, Berend Snel (2008) Protein Complex Evolution Does Not Involve Extensive Network Rewiring. PLoS Comput Biol 4(7): e1000132. DOI:10.1371/journal.pcbi.1000132