Archive for the ‘Synthetic Biology’ category

A Top-Down Approach to Network Modelling in Systems Biology

febbraio 22, 2008

Trey Ideker has recently presented an interesting overview of the various strategies his group at the NIH Systems Biology Special Interest Group has been developing in the recent years in order to integrate multiple types of large scale datasets. During his talk he has gone through these points:

  • mapping of transcriptional response pathways
  • functional mapping of protein complexes
  • disease diagnosis and stratification

Trey presented the study recently published in Molecular Systems Biology (Chuang et al, 2007) where the information provided by microarray expression profiling is superposed to a protein-protein physical interaction network to identify ‘subnetwork’ biomarkers that classify metastatic vs non-metastatic breast tumors.

From: the seven stones


An Engineer’s Perspective on Biology

febbraio 20, 2008

Drew Endy gave, some time ago, a quite interesting interview on his view of engineering life. Drew Endy is one of the most appreciated professors at the MIT and one of the most active researchers in the field of synthetic biology. I found his ideas an highly dense but reasonable summary of what bioengineers think about their activity. Here it is an excepert of the interview you can find at;

“Engineers hate complexity. I hate emergent properties. I like simplicity. I don’t want the plane I take tomorrow to have some emergent property while it’s flying.
How do you manage the information going into a DNA synthesizer so that you can construct some useful object that’ll help you do genetics? […] I think George Church and Craig Venter have a lot to contribute to it, which will be terrific. It will be part of synthetic biology, but it will be synthetic biology impacting science, which is the worst case scenario for synthetic biology.
Five years from now, we may have just begun to make some good progress on reliable functional composition of standard biological parts. Nobody knows how expensive solving that problem will be, but because biology works there’s plenty of existence proofs. […] If I had to guess, I’d say we’ll have a collection of tens of thousands of genetic objects that support reliable functional composition between ten and 15 years from now.”