an integrated computational framework for systems biology ram samudrala university of washington how...
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![Page 1: An Integrated Computational Framework for Systems Biology Ram Samudrala University of Washington How does the genome of an organism specify its behaviour](https://reader035.vdocuments.us/reader035/viewer/2022081519/56649f1c5503460f94c32fc8/html5/thumbnails/1.jpg)
An Integrated Computational Framework for Systems BiologyRam Samudrala
University of Washington
How does the genome of an organism specify its behaviour and characteristics?
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Proteome – all proteins of a particular system
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Modelling proteomes – understand the structure of individual proteins
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Modelling proteomes – understand their individual functions
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Modelling proteomes – understand their expression
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Modelling proteomes – understand their interactions
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Integrated structural and functional annotation of proteomes
structure based methodsmicroenvironment analysis
zinc binding site?
structure comparison
homology function?
sequence based methods
sequence comparisonmotif searches
phylogenetic profilesdomain fusion analyses
+
*
**
*Bioverse
*
*
assign function toentire protein space
experimental datasingle molecule + genomic/proteomic
+EXPRESSION
+INTERACTION
}
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Bioverse – explore relationships among molecules and systems
Jason McDermott/Michal Guerquin/Zach Frazier
http://bioverse.compbio.washington.edu
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Bioverse – explore relationships among molecules and systems
Jason McDermott/Michal Guerquin/Zach Frazier
http://bioverse.compbio.washington.edu
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Bioverse – explore relationships among molecules and systems
Jason McDermott/Michal Guerquin/Zach Frazier
http://bioverse.compbio.washington.edu
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Bioverse – explore relationships among molecules and systems
Jason McDermott/Michal Guerquin/Zach Frazier
http://bioverse.compbio.washington.edu
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Bioverse – prediction of protein interaction networks
Jason McDermott
Interacting protein database
protein α
protein β
experimentallydeterminedinteraction
Target proteome
protein A85%
predictedinteraction
protein B90%
Assign confidence based on similarity and strength of interaction
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Bioverse – E. coli predicted protein interaction network
Jason McDermott
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Bioverse – M. tuberculosis predicted protein interaction network
Jason McDermott
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Bioverse – C. elegans predicted protein interaction network
Jason McDermott
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Bioverse – H. sapiens predicted protein interaction network
Jason McDermott
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Bioverse – network-based annotation for C. elegans
Jason McDermott
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Jason McDermottArticulation point proteins
Bioverse – identifying key proteins on the anthrax predicted network
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Jason McDermott
Bioverse – identification of virulence factors
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Bioverse - Integrator
Aaron Chang
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Take home message
Prediction of protein structure, function, and networks may be used to model whole genomes to
understand organismal function and evolution
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Acknowledgements
Aaron ChangChuck MaderDavid NickleEkachai JenwitheesukGong ChengJason McDermottKai Wang
Ling-Hong HungMike InouyeMichal GuerquinStewart MoughonShing-Chung NganTianyun LiuZach Frazier
National Institutes of HealthNational Science Foundation
Searle Scholars Program (Kinship Foundation)UW Advanced Technology Initiative in Infectious Diseases
http://bioverse.compbio.washington.eduhttp://protinfo.compbio.washington.edu