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Algorithms and hypothesis selection ...

Varon, Andres.

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Algorithms and hypothesis selection in dynamic homology phylogenetic analysis.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Algorithms and hypothesis selection in dynamic homology phylogenetic analysis./
Author:	Varon, Andres.
Description:	266 p.
Notes:	Source: Dissertation Abstracts International, Volume: 71-04, Section: B, page: 2510.
Contained By:	Dissertation Abstracts International71-04B.
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3397407
ISBN:	9781109692525

Algorithms and hypothesis selection in dynamic homology phylogenetic analysis.
Varon, Andres.

Algorithms and hypothesis selection in dynamic homology phylogenetic analysis. - 266 p.

Source: Dissertation Abstracts International, Volume: 71-04, Section: B, page: 2510.

Thesis (Ph.D.)--City University of New York, 2010.

Phylogeny and alignment estimation are two important, and closely related biological problems. In the typical alignment problem, insertions, deletions, and substitutions need to be inferred, to understand the evolutionary patterns of life. With the technological advances of the last 20 years, phylogenetic analyses will grow to include complete chromosomes and genomes. With these data sets, not only insertions, deletions, and substitutions, but also rearrangements such as duplications, translocations, transpositions, and inversions must be taken into consideration.

ISBN: 9781109692525Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Algorithms and hypothesis selection in dynamic homology phylogenetic analysis.
LDR:02903nam 2200325 4500 001 1399813
005 20110930095836.5
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020 $a 9781109692525
035 $a (UMI)AAI3397407
035 $a AAI3397407
040 $a UMI $c UMI
100 1 $a Varon, Andres. $3 1678825
245 1 0 $a Algorithms and hypothesis selection in dynamic homology phylogenetic analysis.
300 $a 266 p.
500 $a Source: Dissertation Abstracts International, Volume: 71-04, Section: B, page: 2510.
500 $a Advisers: Amotz Bar-Noy; Ward C. Wheeler.
502 $a Thesis (Ph.D.)--City University of New York, 2010.
520 $a Phylogeny and alignment estimation are two important, and closely related biological problems. In the typical alignment problem, insertions, deletions, and substitutions need to be inferred, to understand the evolutionary patterns of life. With the technological advances of the last 20 years, phylogenetic analyses will grow to include complete chromosomes and genomes. With these data sets, not only insertions, deletions, and substitutions, but also rearrangements such as duplications, translocations, transpositions, and inversions must be taken into consideration.
520 $a In this study, phylogenetic analysis is explored at three different levels. At the first level, new heuristic algorithms for the joint estimation of phylogenies and alignments under the Maximum Parsimony optimality criterion are described. Our experimental study showed that the new algorithms perform dramatically better when compared to previous heuristics. These new algorithms will allow biologists to analyze larger data sets in shorter periods of time. At the second level, new and existing algorithms where implemented in the computer program POY version 4. POY has had a significant impact in the biology community, and is used by hundreds of biologists around the world. POY will serve as a platform for long term research both in algorithm engineering, and biology. At the third level, the problem of parameter and model selection in complete chromosome analyses is explored. We propose and describe the use of Kolmogorov Complexity (KC) as optimality criterion, as a unifying criterion for phylogenetic analysis. Our evaluation using simulations showed that KC correctly identifies phylogeny and model with high frequency. These results are evidence that KC is very well suited for the difficulties posed by the phylogenetic analysis of complete genomes.
590 $a School code: 0046.
650 4 $a Biology, Bioinformatics. $3 1018415
650 4 $a Computer Science. $3 626642
690 $a 0715
690 $a 0984
710 2 $a City University of New York. $b Computer Science. $3 1029886
773 0 $t Dissertation Abstracts International $g 71-04B.
790 1 0 $a Bar-Noy, Amotz, $e advisor
790 1 0 $a Wheeler, Ward C., $e advisor
790 1 0 $a St.John, Katherine $e committee member
790 1 0 $a Mishra, Bud $e committee member
790 $a 0046
791 $a Ph.D.
792 $a 2010
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3397407