[talks] J Farnham general exam

[Melissa Lawson]

Jesse Farnham will present his research seminar/general exam on Thursday May 20 at 2PM 
in Room 402.  The members of his committee are:  Mona Singh (advisor), Andrea LaPaugh, 
and Tom Funkhouser.  Everyone is invited to attend his talk and those faculty wishing to 
remain for the oral exam following are welcome to do so.  His abstract and reading list 
follow below.
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Abstract: "Interface Proteins: Investigating Modular Structure of 
Protein Interaction Networks"

Organisms are able to adapt to and survive in different environments due 
partially to complex networks of interacting proteins within cells. 
These protein-protein interaction (PPI) networks can be represented as 
graphs, in which nodes indicate proteins and edges signify physical 
interactions between proteins. PPI networks are known to be "modular;" 
that is, a given protein is more likely to interact with similar 
proteins than with proteins involved in unrelated biological processes. 
PPI networks contain many "functional modules" of functionally-related, 
interacting proteins. This work investigates the means by which 
information flows between separate biological processes through protein 
interactions.  We identify two protein classes: "Interface proteins", 
which mediate physical interactions between distinct functional modules, 
and "Insulated proteins," which interact primarily with members of their 
own functional module. Thus, interface proteins facilitate crosstalk 
between distinct processes, allowing information to flow through the 
interaction network. Furthermore, we show that functional modules tend 
to reuse the same interface proteins to interact with unrelated modules, 
rather than interacting with each unrelated module through a distinct 
set of interface proteins.

Reading list:

Textbooks:
Mount, David. Bioinformatics: Sequence and Genome Analysis, 2nd Edition.

Cormen, Leiserson, Rivest, and Stein. Introduction to Algorithms, 2nd 
Edition. (Chapters 22-26: Graph Algorithms)

Papers:

Banks et al. Organization of Physical Interactomes as Uncovered by 
Network Schemas. PLoS Computational Biology 4:10 (2008).

Banks et al. NetGrep: Fast network schema searches in interactomes. 
Genome Biology 9:9 (2008).

De Lichtenberg et al. Dynamic complex formation during the yeast cell 
cycle. Science 307 (2005).

Fraser H. Modularity and evolutionary constraint on proteins. Nature 
Genetics 37:4 (2005).

Hartwell et al. From molecular to modular cell biology. Nature 402 (1999).

Komurov K, and White M. Revealing static and dynamic modular 
architecture of the eukaryotic protein interaction network. Molecular 
Systems Biology 3:110 (2007).

Missiuro et al. Information Flow Analysis of Interactome Networks. PLoS 
Computational Biology 5:4 (2009).

Taylor et al. Dynamic modularity in protein interaction networks 
predicts breast cancer outcome. Nature Biotechnology 27:2 (2009).

Zotenko et al. Why do hubs in the yeast protein interaction network tend 
to be essential: Reexamining the connection between the network topology 
and essentiality. PLoS Computational Biology 4:8 (2008).