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Algorithms and Monte Carlo methods i...

Guan, Yongtao.

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Algorithms and Monte Carlo methods in computational biology.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Algorithms and Monte Carlo methods in computational biology./
Author:	Guan, Yongtao.
Description:	106 p.
Notes:	Adviser: Stephen M. Krone.
Contained By:	Dissertation Abstracts International67-05B.
Subject:	Biology, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3217455
ISBN:	9780542696039

Algorithms and Monte Carlo methods in computational biology.
Guan, Yongtao.

Algorithms and Monte Carlo methods in computational biology. - 106 p.

Adviser: Stephen M. Krone.

Thesis (Ph.D.)--University of Idaho, 2006.

We study three different aspects of computational biology: interacting particle systems, phylogenetic distance methods, and Markov Chain Monte Carlo.

ISBN: 9780542696039Subjects--Topical Terms:

1018625
Biology, General.

Algorithms and Monte Carlo methods in computational biology.
LDR:02592nam 2200313 a 45 001 968500
005 20110915
008 110915s2006 eng d
020 $a 9780542696039
035 $a (UMI)AAI3217455
035 $a AAI3217455
040 $a UMI $c UMI
100 1 $a Guan, Yongtao. $3 1292352
245 1 0 $a Algorithms and Monte Carlo methods in computational biology.
300 $a 106 p.
500 $a Adviser: Stephen M. Krone.
500 $a Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2300.
502 $a Thesis (Ph.D.)--University of Idaho, 2006.
520 $a We study three different aspects of computational biology: interacting particle systems, phylogenetic distance methods, and Markov Chain Monte Carlo.
520 $a Our study of interacting particle systems has two components: First, a Windows-based simulator has been developed. It serves as a platform for many spatial biology studies; for example, plasmid transfer in biofilms. Second, a specific ecological model of multi-species cross-feeding has been studied using the simulator, where we have observed spatial self-organization and pattern formation (particularly, spiral waves). A mathematical derivation, which is based on analysis of partial differential equations, explains the phase-transitions observed in simulations.
520 $a Distance methods have been widely used to infer phylogenies (evolution trees among different species) because they are fast and reasonably accurate. In this study, we have proved that a popular distance method named neighbor-joining is in fact a special case of least squares methods. The proof relates neighbor-joining to least squares statistics. Hence it provides an explanation for the robustness and accuracy of neighbor-joining.
520 $a In an empirical study of MCMC, we investigate, through extensive simulations., how a mixture of local and heavy-tailed proposals (a.k.a. "small world proposals") can dramatically increase the convergence rates of Markov chains that admit stationary measures that are multi-modal. In the theoretical part of the study, we have proved, using techniques of state decomposition and isoperimetric inequalities for log-concave distributions, that the ''small world proposals" turn a "slowly mixing" chain into a "rapidly mixing" chain.
590 $a School code: 0089.
650 4 $a Biology, General. $3 1018625
650 4 $a Mathematics. $3 515831
690 $a 0306
690 $a 0405
710 2 0 $a University of Idaho. $3 718915
773 0 $t Dissertation Abstracts International $g 67-05B.
790 $a 0089
790 1 0 $a Krone, Stephen M., $e advisor
791 $a Ph.D.
792 $a 2006
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3217455