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Perspectives

ZIHENG YANG

in Computational Molecular Evolution

Published in print:
2006
Published Online:
April 2010
ISBN:
9780198567028
eISBN:
9780191728280
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198567028.003.0010
Subject:
Biology, Evolutionary Biology / Genetics

This chapter discusses current challenges and future perspectives of the field. Topics covered include theoretical issues in phylogeny reconstruction, computational issues in analysis of large and ... More


Combinatorics of Genome Rearrangements

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Stéphane Vialette

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
book
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.001.0001
Subject:
Mathematics, Mathematical Biology

From one cell to another, from one individual to another, and from one species to another, the content of DNA molecules is often similar. The organization of these molecules, however, differs ... More


Introduction

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0001
Subject:
Mathematics, Mathematical Biology

This introductory chapter first discusses the molecular evolution and the birth of the combinatorics of genome rearrangements. It then describes the genome rearrangement problem; the scope of the ... More


Software

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0015
Subject:
Mathematics, Mathematical Biology

This chapter describes software that implements some of the algorithms mentioned or discussed in this book. It begins in Section 15.1 with tools that analyze rearrangements between two genomes using ... More


Cycles of a Permutation

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0011
Subject:
Mathematics, Mathematical Biology

This chapter begins by providing a model for multichromosomal circular genomes. It then presents a generalization to signed genomes and some results.


Open Problems

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0016
Subject:
Mathematics, Mathematical Biology

The variety of genome rearrangement problems is huge and is increasing every year. While it is possible to design many other variants that have yet to be studied, among the most studied variants, ... More


Rearrangements of Partial Orders

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0005
Subject:
Mathematics, Mathematical Biology

Zheng et al. introduced a new representation of a genome in terms of a partially ordered set (often abbreviated as “poset”). In this model, any linear extension of a poset represents a possible total ... More


Generalities

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0007
Subject:
Mathematics, Mathematical Biology

Duplications are considered one of the most important mechanisms for novel generations in evolution, and almost all data sets on eukaryotes contain duplicated genes. This chapter covers the ... More


Graph-Theoretic and Linear Algebra Formulations

Guillaume Fertin, Anthony Labarre, Irena Rusu, Eric Tannier, and Steéphane Vialette

in Combinatorics of Genome Rearrangements

Published in print:
2009
Published Online:
August 2013
ISBN:
9780262062824
eISBN:
9780262258753
Item type:
chapter
Publisher:
The MIT Press
DOI:
10.7551/mitpress/9780262062824.003.0006
Subject:
Mathematics, Mathematical Biology

This chapter demonstrates the expansion of genome rearrangement problems to a wide mathematical field, including long-standing problems in algebra. It discusses simple permutations and the ... More


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