[talks] J Farnham preFPO

Melissa M. Lawson mml at CS.Princeton.EDU
Wed Apr 3 09:25:41 EDT 2013

Jesse Farnham will present his preFPO on Friday April 12 at 9AM in 
Room 302 (note room!).  The members of his committee are:  Mona 
Singh, advisor; Olga Troyanskaya and Andrea LaPaugh, readers; Vivek 
Pai and Tom Funkhouser, nonreaders.  Everyone is invited to attend 
his talk.  His abstract follows below.

"Organization and function acquisition in cellular networks"

A main goal of biology is to understand the functional organization of 
organisms. In this thesis, we apply computational techniques to large, 
noisy biological datasets such as protein-protein interaction (PPI) 
networks and expression microarrays in order to elucidate principles of 
how genes in PPI networks acquire new functions and contribute to the 
overall functional organization of life. First, we investigate the 
functional organization of PPI networks by presenting a metric, 
functional insularity, that quantifies the degree to which a protein 
interacts with other proteins of similar function. We find high 
variation in insularity values, and we identify several differences 
between high- and low-insularity proteins. Secondly, we investigate 
function acquisition by human genes by identifying changes in 
protein-protein interactions, gene expression, and other markers of 
function as genes age. Our results indicate the presence of a tradeoff 
between modularity and connectivity in PPI network organization; 
furthermore, our results suggest that young genes acquire new functions 
gradually as they age, allowing the functional organization of the cell 
to evolve over time.

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