Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Saturday, December 03, 2005

Leroy Hood, Institute for Systems Biology
"An Analysis of Gene Regulatory and Protein Networks in Halobacteria"

Halobacter is involved in bio-energy and bio-remediation. Discussed how the study of halobacteria drives the development of new computational tools at ISB.

The acidic nature of Halobacter makes it easier to do ab initio protein folding (using rosetta). Does anyone know why that is?

Used this for gene annotation:

Also because of the success of rosetta protein folding they started to do protein folding @home in a collaboration with IBM

They have a pipeline set up were they find co-regulated groups through biclustering using 'cMonkey' (to appear) as well as 'inferelator' (to appear) to identify the responsible TF for the regulation

Looks at disease progression in prostate/ovarian cancer by molecular fingerprints (biomarkers) in the blood. Using MPSS for sequencing.
In the future he says that in each organ there is blood that is a status reporter for the health of they system. Estimates that you need between 1000-2000 markers to get a good diagnostic. How do you read out this many markers? Hes convinced that microfluidics/nanotechnology platforms hold the key.


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