Theoretical Biology & Bioinformatics

Personalia

Name TJP (John) van Dam Position PhD student Research topics Comparative genomics on signaling pathways Affiliations Department of Physiological Chemistry, UMC Utrecht Bioinformatics group, Utrecht University Promotors Prof. dr. J.L. Bos & dr. B. Snel (supervisor) Address Padualaan 8 3584 CH Utrecht the Netherlands Location Room O509 Phone +31 30 2533004 Fax +31 30 2513655 Email see below

I have moved!!!

I'm currently working as a Post-Doc at the Centre for Molecular and Biomolecular Informatics at UMC St. Radboud, Nijmegen.

Research Project

As part of a collaboration between the Physiological Chemistry Department in the University Medical Center and the Bioinformatics group, my research project is called 'comparative genomics on signal transduction pathways'. The research is funded by the NBIC Biorange programme SP 2.3.1.4. Questions I want to answer in my research are 'How and why did the Ras signaling pathways diverge into multiple tightly interwoven signal pathways?'.

From a cancer research point of view every knowledge obtained which could help unravel these pathways would be very helpful and interesting. From an evolution point of view it could give an interesting view into the evolution of eukaryotes. For some interesting literature on this I recommend Gáspár Jékely (2003).

Scientific motivation and interests

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 were looking mostly at the tiniest parts of some protein or some process. 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 on 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. This only touched the subject of: that BLAST exists... There is a website... And if you put your sequence here, something comes out... I never learned about Psi-BLAST, Pfam/SMART, multiple alignments and how to use then correctly. I now know that these tools are incredibly useful to molecular biologists.

Education

Publications

van Dam TJP, Rehmann H, Bos JL, Snel B (2009) Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi. Cell Signal. 2009 Jun 27. doi:10.1016/j.cellsig.2009.06.004

van Dam TJP, Snel B (2008) Protein Complex Evolution Does Not Involve Extensive Network Rewiring. PLoS Comput Biol 4(7): e1000132. doi:10.1371/journal.pcbi.1000132

Posters

	"Protein complex evolution does not involve extensive network rewiring"* Benelux Bioinformatics Conference, Leuven BE 2007
	"Evolutionary signaling complexity revealed by phylogenetic analysis of the RasGEF domain" BioRange Consortium Meeting on March 5-6, 2008
	"Evolutionary reconstruction of the mTOR pathway"* BioRange Consortium Meeting on March 29, 2010

* Will be made available when published.

Stage projects

• RasGAPs and the evolution of Ras signaling pathways. [DOC]