[talks] E Banks preFPO

Melissa Lawson mml at CS.Princeton.EDU
Tue Sep 16 13:15:29 EDT 2008

Eric Banks will present his preFPO on Monday September 22 at 1:30PM in room 402.  The 
members of his committee are:  Mona Singh, advisor; Olga Troyanskaya and Bernard 
Chazelle, readers; Tom Funkhouser and David Blei, nonreaders.  Everyone is invited to 
attend his talk.  His abstract follows below.

High-throughput experimental and computational approaches are enabling the collection
of large-scale biological networks, consisting of proteins and the interactions
among them, for a growing number of species.  With appropriate computational analysis
and experimental work the potential exists for uncovering the organizational principles
of the cell and, consequently, protein functions and pathways, which are still largely

In this work, we introduce a novel framework for analyzing protein interaction networks
in order to uncover organizational units corresponding to recurring means with which
diverse biological processes are carried out.  We formalize recurring patterns of
interaction among different types of proteins using "network schemas"; network schemas
specify descriptions of proteins and the topology of interactions among them.  We develop
algorithms for systematically uncovering recurring, over-represented schemas in physical
interaction networks and apply these methods to the S. cerevisiae interactome, identifying
hundreds of such organizational units of varying complexity.  We establish the functional
importance of these schemas by showing that they correspond to functionally cohesive sets
of proteins, are enriched in the frequency with which they have instances in the H.
interactome, and are useful for predicting protein function.  Finally, we introduce
a system for searching protein interaction networks for matches to more general network
schemas.  NetGrep provides an advanced graphical interface for specifying schemas and fast
algorithms for extracting their matches.

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