Genetic Networks Group

Genetic Networks Discussion Group, Summer, 2003.

Joe Chang, 2-0642, joseph.chang@yale.edu

Next meeting: Friday August 8, 2003, 10:30, Statistics Dept. room 107

We decided last time that we would like to understand the paper

Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 1998 Aug;149(4):1633-48.

This will be the focus of discussion this Friday (at least until we get derailed by something else). I hope somebody comes in understanding the paper and willing to explain it!

Previous meetings:

Friday August 1, 2003, 10:30, Statistics Dept. room 107

I didn't manage to get anybody else to lead this session. But I think we want to discuss methods of reconstructing or "reverse-engineering" genetic networks. So I found a couple of papers on the subject that can serve as starting points for discussion:

Genetic Network Inference: From Co-Expression Clustering to Reverse Engineering. D'haeseleer, P., Liang, S. , and Somogyi, R., Bioinformatics 16(8):707-26, 2000.
"Towards reverse engineering of genetic regulatory networks" by Lubovac and Olsson

I also found another paper by people who had the same sort of idea we have, which is to evaluate network reconstruction methods using a simulator. The paper is

V. Anne Smith, Erich D. Jarvis, and Alexander J. Hartemink, Evaluating functional network inference using simulations of complex biological systems
Bioinformatics 2002 18: S216-S224.

And I still think that the goal of doing something like what Ian was talking about last week would likely be aided, at least for me, by understanding what Arkin et al. did in

Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 1998 Aug;149(4):1633-48.

Well, that's 4 papers, which is probably more than enough for now. I haven't really read any of these papers myself as of Wednesday 1:00, so we are in the same boat! (And I warned people that I'd be busy with some other things this week so I hope you will be more prepared than I...)

There are hundreds of relevant papers by now. I hope you will come in with your own favorite suggestions about what you would like to present, or topics you would like to lead discussions on!

July 25, 2003.

Thanks to Ian Laurenzi for a polished and informative presentation on simulation, Gillespie's method, and the faster "son of Gillespie." (The links are to the papers we discussed.)