Wiki source for GM20090909
Three topics are discussed in the meeting:
1. There are many real applications for a kind of module detection problem. Given a network, there are two kind of edges, say, one is red and the other is blue. The questions is that whether we can detect modules such that the red edges are located in the inner of modules and the blue edges are located between the modules. Since this problme is not formally stated and modeled though there are some heuristic methods. We will propose a optimization model and design algorithm to deal with it. Probably we will propose a more general model to deal with a more general network with different kind of nodes and different kind of edges.
2. About the possible collaborative project with the Dr Qiaofeng Wu. We think it's a typic systems biology problem. Firstly the metabolic network was perturbed, then the response are measured. The remaining task is to identify the key molecules and their interactions (i.e. the active pathways). Also people raised several questions about the data quality and possible bias in it.
3. We discuss the work related to tissue specific protein interaction networks. We figure out the procedure to define the tissue specific proteins and house-keeping genes.
The orignal idea is to use the protein interaction network as a representation of the tissue, then we can explore the relaitonships among tissues by analysis the similarity and difference among the networks.
Tommorrow is the Teacher's day. Best wishes for all the members in our group since most of us become teacher someday. :)
1. There are many real applications for a kind of module detection problem. Given a network, there are two kind of edges, say, one is red and the other is blue. The questions is that whether we can detect modules such that the red edges are located in the inner of modules and the blue edges are located between the modules. Since this problme is not formally stated and modeled though there are some heuristic methods. We will propose a optimization model and design algorithm to deal with it. Probably we will propose a more general model to deal with a more general network with different kind of nodes and different kind of edges.
2. About the possible collaborative project with the Dr Qiaofeng Wu. We think it's a typic systems biology problem. Firstly the metabolic network was perturbed, then the response are measured. The remaining task is to identify the key molecules and their interactions (i.e. the active pathways). Also people raised several questions about the data quality and possible bias in it.
3. We discuss the work related to tissue specific protein interaction networks. We figure out the procedure to define the tissue specific proteins and house-keeping genes.
The orignal idea is to use the protein interaction network as a representation of the tissue, then we can explore the relaitonships among tissues by analysis the similarity and difference among the networks.
Tommorrow is the Teacher's day. Best wishes for all the members in our group since most of us become teacher someday. :)
