Harvard Medical School, Department of Systems Biology
Alpert Building, Room 513
200 Longwood Ave.
Boston, MA 02115
Lab Size: Between 5 and 10
The experimental effort is focused on aging in C.elegans. The phenomenon of aging raises questions about the limits of biological processes. What type of damage, or "garbage", and how much of it, is generated as a by-product of which molecular processes? Is this damage inescapable? What can be repaired and at what cost? Aging is also a life history trait that has been shaped by evolution. This raises the question about the plasticity of aging. Aging research seems to be lagging other areas of molecular biology in adopting a more quantitative and theoretically founded approach.
The challenge of systems biology is not only experimental in kind. It also is the challenge of reasoning about facts that are rapidly evolving while remaining highly fragmented across research communities. I see a fundamental role for models as reasoning instruments in biology. Models, not databases as we know them today, will become the main vehicles for the computer-assisted storage, communication, and retrieval of biological knowledge. Computer scientists and I have joined forces with several other researchers to design a computational environment that represents biological knowledge, as it pertains to signaling, in an editable and executable fashion. This instrument will lend itself to the collaborative construction and critique of models.
V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine. "Abstracting the ODE semantics of rule-based models: Exact and automatic model reduction" submitted to the 16th International Static Analysis Symposium (SAS) 2009
V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine. "Investigation of a biological repair scheme". Proceedings of the ninth Workshop on Membrane Computing, Lecture Notes in Computer Science, 5391, to appear (2009)
J. Feret, V. Danos, J. Krivine, R. Harmer and W. Fontana. "Internal coarse-graining of molecular systems". Proc. Natl. Acad. Sci. USA, in press (2009)