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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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Presentation Transcript
slide1

An Integrated Computational Framework for Systems Biology

Ram Samudrala

University of Washington

How does the genome of an organism

specify its behaviour

and characteristics?

slide7

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

slide8

Bioverse – explore relationships among molecules and systems

http://bioverse.compbio.washington.edu

Jason McDermott/Michal Guerquin/Zach Frazier

slide9

Bioverse – explore relationships among molecules and systems

http://bioverse.compbio.washington.edu

Jason McDermott/Michal Guerquin/Zach Frazier

slide10

Bioverse – explore relationships among molecules and systems

http://bioverse.compbio.washington.edu

Jason McDermott/Michal Guerquin/Zach Frazier

slide11

Bioverse – explore relationships among molecules and systems

http://bioverse.compbio.washington.edu

Jason McDermott/Michal Guerquin/Zach Frazier

slide12

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

slide18

Bioverse – identifying key proteins on the anthrax predicted network

Articulation point proteins

Jason McDermott

slide21

Take home message

Prediction of protein structure, function, and

networks may be used to model whole genomes to

understand organismal function and evolution

slide22

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