Archivio per novembre 2007

System Robustness in Biological Systems (pt.1)

novembre 25, 2007

ystem robustness as well as systems stability are two important properties that control engineers often consider in the analysis of dynamical systems. Although these are concepts that have long been considered only part of the engineering domain, it seems that systems biology is moving toward the investigation of such properties even in biological systems.

Today I would like to bring you some considerations about two papers that I found really interesting in this field. They are:

H. Kitano, Biological Robustness. Nat Genetics. 2004

H. Kitano, Towars a Theory of Biological Robustness. Molecular Systems Biology 3:137. 2007.



The mathematical formula of cancer

novembre 9, 2007

Mathematical biology is finding its way to the wide diffusion. There’s a huge effort, in particular, on the modelling of cancer settlment and progression with mathematical tools (ODEs have been extensively used in this field e.g. in systems biology). Researchers at Harvard and Johns Hopkins Universities have studied a new paradigm for calculating tumor development, showing that it appears to be driven by mutations in many genes.

Niko Beerenwinkel et al. show how tumor progression can be driven by hundreds of genes. As many as 20 different mutated genes might be responsible for driving an individual tumor’s development.
Beerenwinkel et al. used a case of colon cancer to derive their results. Cancer progression proceeds stochastically from a single genetically altered cell to billions of invasive cells through a series of clonal expansions. According to their model, cancer progression is driven by mutations in many genes, each of which confers only a small selective advantage. It was found that the time it takes for a benign tumor to transform into a malignant tumor is dominated by the selective advantage per mutation and by the number of cancer genes, whereas tumor size and mutation rate have smaller impacts.

This new model could help explain the large amount of variation between individual tumors that has long puzzled researchers and clinicians. The increasing amount of high-throughput molecular data that is being generated has resulted in new challenges for understanding complex biosystems such as cancer. New mathematical models like this one can provide unique insights that simplify interpretation and at the same time answer important biomedical questions.

The paper appeared on PLoS Computational Biology this week and this is the link, enjoy!

eBioTools out of the box

novembre 3, 2007

And finally also the eBioTools for the MacOS X came out of the box. It seems to have a quite user friendly interface with a large number of options to carry out the most common analyses in genomics and proteomics.

Here it is the link