My talk will be concerned the analysis of networks and the use of networks as a "next-generation annotation" for interpreting personal genomes. I will initially describe current approaches to genome annotation in terms of one-dimension browser tracks. Then I will describe various aspects of networks. In particular, I will touch on
the following topics: (1) I will show how analyzing the structure of the regulatory network indicates that it has a hierarchical layout with the "middle-managers" acting as information-flow bottlenecks and with more "influential" TFs on top. (2) I will show that most human variation occurs at the periphery of the network. (3) I will compare the topology and variation of the regulatory network to the call graph of a computer operating system, showing that they have different patterns of variation. (4) I will talk about web-based tools for the analysis of networks (TopNet and tYNA).
http://networks.gersteinlab.org
http://tyna.gersteinlab.org
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107:9186-91.
Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
Mark Gerstein is the Albert L Williams professor of Biomedical Informatics at Yale University. He is co-director the Yale Computational Biology and Bioinformatics Program, and has appointments in the Department of Molecular Biophysics and Biochemistry and the Department of Computer Science. He received his AB in physics summa cum laude from Harvard College and his PhD in chemistry from Cambridge. He did post-doctoral work at Stanford and took up his post at Yale in early 1997. Since then he has published appreciably in scientific journals. He has >400 publications in total, with a number of them in prominent journals, such as Science, Nature, and Scientific American. (His current publication list is at http://papers.gersteinlab.org .) His research is focused on bioinformatics, and he is particularly interested in large-scale integrative surveys, biological database design, macromolecular geometry, molecular simulation, human genome annotation, gene expression analysis, and data mining.