[talks] J Song general exam

Jimin Song jisong at CS.Princeton.EDU
Thu May 10 00:14:31 EDT 2007

The time wasn't mentioned in the last email.
It'll start at 10AM!

On 5/7/07, Melissa M Lawson <mml at cs.princeton.edu> wrote:
> JiMin Song will present her research seminar/general exam on Thursday May 10
> in Room 302 (note room!).  The members of her committee are:  Mona Singh
> (advisor), Olga Troyanskaya, and Tom Funkhouser.  Everyone is invited to attend
> her talk, and those faculty wishing to remain for the oral exam following are
> welcome to do so.  Her abstract and reading list follow below.
> --------------------------------
> Abstract
> Protein interactions play a key role in almost all biological processes.  Recently,
> high-throughput experiments have uncovered large networks of protein-protein interactions
> for several species, including human, fruit fly and yeast.  It has been postulated that
> analysis of these protein interaction maps should provide hints to the cell's higher-level
> organization, and help uncover protein functions, complexes and pathways.
> A protein-protein interaction network is considered as an undirected graph such that nodes
> are proteins and edges are interactions between two proteins. Graph clustering methods
> provide one way for analyzing these networks in order to uncover functional modules and
> protein complexes.   I introduce an evaluation framework for analyzing graph
> clustering methods. I consider six different evaluation measures, taking into account
> biological process, cellular component, and protein complex annotations, to compare four
> diverse graph clustering algorithms. I selected four graph clustering methods, a spectral
> clustering method, a Markov clustering method, a density-periphery based clustering
> method, and a clique-finding clustering method. I find that the clique-finding clustering
> method consistently out performs the others, suggesting that future research along these
> lines should focus on methods with similar properties.
> Reading list
> Textbook:
> Bioinformatics by Mount - Chapters: 3, 4, 5, 7, 10.
> Papers:
> - E Alm and AP Arkin, Biological networks, Curr. Opin. Struct. Biol 2003
> - LH Hartwell et al, From molecular to modular cell biology, Nature 1999
> - Spirin and Mirny, Protein complexes and functional modules in molecular networks, PNAS
> 2003
> - Sharan et al, Network-based prediction of protein function, EMBO 2007
> - Newman, Modularity and community structure in networks, PNAS 2006
> - Enright et al, An efficient algorithm for large-scale detection of protein families, NAR
> 2002
> - Altaf-Ul-Amin, Development and implementation of an algorithm for detection of protein
> complexes in large interaction networks, BMC Bioinformatics 2006
> - Palla et al, Uncovering the overlapping community structure of complex networks in
> nature and society, Nature 2005
> - Brohee and van Helden, Evaluation of clustering algorithms for protein-protein
> interaction networks, BMC Bioinformatics 2006
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