This project focuses on graph theoretical study of molecular evolution. Particular interests include developing graph theoretical methods, models, and algorithms for study multidomain proteins, protein-protein interactions and other biological networks.? The project has the following subtopics:? ? 1.Graph theoretical approaches to character based evolution. Here we consider the so called character overlap graph. The nodes of such graph are characters and there is an edge between two characters if they occur together in some organism. Understanding of properties of this graph provides insights into possible modes of evolution of the corresponding characters.? ? 2.Recovering and representing the dynamics of protein-protein interaction networks. Our approach relies heavily on important results from graph theory; more specifically, the theory of two important graph families: chordal graphs and co-graphs. By using these two graph families in our modeling, we capture the dynamics of signaling pathways and overlapping structure of functional groups. ? ? 3.Predicting domain-domain interactions from protein-protein interaction network. We postulate that protein-protein interactions evolved in a parsimonious way. Consistently with the parsimony postulate, we identify the interacting domain as the smallest (weighted) set of pairs that is necessary to explain the protein interaction network.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Intramural Research (Z01)
Project #
1Z01LM092804-03
Application #
7316285
Study Section
(CBB)
Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2006
Total Cost
Indirect Cost
Name
National Library of Medicine
Department
Type
DUNS #
City
State
Country
United States
Zip Code
Zheng, Jie; Rogozin, Igor B; Koonin, Eugene V et al. (2007) Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation. Mol Biol Evol 24:2583-92
Przytycka, Teresa (2007) Stability of characters and construction of phylogenetic trees. J Comput Biol 14:539-49
Guimaraes, Katia S; Jothi, Raja; Zotenko, Elena et al. (2006) Predicting domain-domain interactions using a parsimony approach. Genome Biol 7:R104
Zotenko, Elena; Guimaraes, Katia S; Jothi, Raja et al. (2006) Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations. Algorithms Mol Biol 1:7
Przytycka, Teresa; Davis, George; Song, Nan et al. (2006) Graph theoretical insights into evolution of multidomain proteins. J Comput Biol 13:351-63
Jothi, Raja; Kann, Maricel G; Przytycka, Teresa M (2005) Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics 21 Suppl 1:i241-50
Przytycka, Teresa M; Yu, Yi-Kuo (2004) Scale-free networks versus evolutionary drift. Comput Biol Chem 28:257-64