[talks] J Farnham general exam
mml at CS.Princeton.EDU
Fri May 14 15:44:38 EDT 2010
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
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.
Mount, David. Bioinformatics: Sequence and Genome Analysis, 2nd Edition.
Cormen, Leiserson, Rivest, and Stein. Introduction to Algorithms, 2nd
Edition. (Chapters 22-26: Graph Algorithms)
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).
More information about the talks