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An Integrated Computational Framework for Systems Biology Ram Samudrala University of Washington. How does the genome of an organism specify its behaviour and characteristics?. Proteome – all proteins of a particular system.
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An Integrated Computational Framework for Systems Biology Ram Samudrala University of Washington How does the genome of an organism specify its behaviour and characteristics?
Modelling proteomes – understand the structure of individual proteins
Integrated structural and functional annotation of proteomes structure based methods microenvironment analysis structure comparison sequence based methods sequence comparison motif searches phylogenetic profiles domain fusion analyses zinc binding site? homology function? + assign function to entire protein space * Bioverse * * } * EXPRESSION + INTERACTION * * + experimental data single molecule + genomic/proteomic
Bioverse – explore relationships among molecules and systems http://bioverse.compbio.washington.edu Jason McDermott/Michal Guerquin/Zach Frazier
Bioverse – explore relationships among molecules and systems http://bioverse.compbio.washington.edu Jason McDermott/Michal Guerquin/Zach Frazier
Bioverse – explore relationships among molecules and systems http://bioverse.compbio.washington.edu Jason McDermott/Michal Guerquin/Zach Frazier
Bioverse – explore relationships among molecules and systems http://bioverse.compbio.washington.edu Jason McDermott/Michal Guerquin/Zach Frazier
Bioverse – prediction of protein interaction networks Target proteome Interacting protein database 85% protein α protein A experimentally determined interaction predicted interaction protein B protein β 90% Assign confidence based on similarity and strength of interaction Jason McDermott
Bioverse – E. coli predicted protein interaction network Jason McDermott
Bioverse – M. tuberculosis predicted protein interaction network Jason McDermott
Bioverse – C. elegans predicted protein interaction network Jason McDermott
Bioverse – H. sapiens predicted protein interaction network Jason McDermott
Bioverse – network-based annotation for C. elegans Jason McDermott
Bioverse – identifying key proteins on the anthrax predicted network Articulation point proteins Jason McDermott
Bioverse – identification of virulence factors Jason McDermott
Bioverse - Integrator Aaron Chang
Take home message Prediction of protein structure, function, and networks may be used to model whole genomes to understand organismal function and evolution
Acknowledgements Aaron Chang Chuck Mader David Nickle Ekachai Jenwitheesuk Gong Cheng Jason McDermott Kai Wang Ling-Hong Hung Mike Inouye Michal Guerquin Stewart Moughon Shing-Chung Ngan Tianyun Liu Zach Frazier National Institutes of Health National Science Foundation Searle Scholars Program (Kinship Foundation) UW Advanced Technology Initiative in Infectious Diseases http://bioverse.compbio.washington.edu http://protinfo.compbio.washington.edu