Yury Pritykin will present his research seminar/general exam on Wednesday October 20 at 10AM in

Room 402.  The members of his committee are:  Mona Singh, advisor, Tom Funkhouser, and

Moses Charikar.  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
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Biological networks at different organization levels have proved useful for understanding of basic biological principles. Two complementary types of networks can be considered on a cellular level. One is the network of interactions between genes and proteins in a cell. It can be represented as a graph with directed and undirected edges of different types. Various methods have been used to study these kinds of networks in order to improve our understanding of functioning of cells and organisms. Another technique of expression and protein quantitative trait loci (eQTLs and pQTLs) aims to detect associations of locations in the genome with variation in a quantitative trait, in this case gene activity measured as transcript expression or protein abundance. The result of such analysis can be represented as a bipartite graph with linkages between genetic loci and genes or proteins.

This talk will show advantage of mutual analysis of the above two types of networks. As an example, we show that using eQTL linkage information integrated with interaction information can help to infer more pQTLs linkages than the standard approach.


Reading list
============

D. Mount.
Bioinformatics: Sequence and Genome Analysis.
2nd Edition, Cold Spring Harbor Laboratory Press, 2004. Chapters 1-7, 10.


T. Ideker, O. Ozier, B. Schwikowski, A. F. Siegel.
Discovering regulatory and signalling circuits in molecular interaction networks.
Bioinformatics, 18 Suppl 1, 2002, p. S233-40.

V. Spirin, L. Mirny.
Protein complexes and functional modules in molecular networks.
Proceedings of the National Academy of Sciences of the United States of America.
100, 2003, pp. 12123-12128.

M. V. Rockman, L. Kruglyak.
Genetics of global gene expression.
Nature reviews. Genetics, 7 (11), 2006, p. 862-72.

X. Zhu, M. Gerstein, M. Snyder.
Getting connected: analysis and principles of biological networks.
Genes & development, 21 (9), 2007, p. 1010-24.

T. M. Przytycka, M. Singh, D. K. Slonim.
Toward the dynamic interactome: it's about time.
Briefings in bioinformatics, 11 (1), 2010, p. 15-29.


S. Suthram, A. Beyer, R. M. Karp, Y. Eldar, T. Ideker.
eQED: an efficient method for interpreting eQTL associations using protein networks.
Molecular systems biology, 4 (162), 2008, p. 162.

J. Zhu, B. Zhang, E. N. Smith, B. Drees, R. B. Brem, L. Kruglyak, R. E. Bumgarner, E. E. Schadt.
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
Nature genetics, 40 (7), 2008, p. 854-61.

Y. Huang, S. Wuchty, M. T. Ferdig, T. M. Przytycka.
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum.
Bioinformatics (Oxford, England), 25 (12), 2009, p. i15-20.

S. Lee, A. M. Dudley, D. Drubin, P. A. Silver, N. J. Krogan, D. Pe'er, D. Koller.
Learning a prior on regulatory potential from eQTL data.
PLoS genetics, 5 (1), 2009, p. e1000358.