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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

##
Temporal patterns of *Bordetella pertussis* genome sequence and structural evolution

*Michael R. Weigand, Margaret M. Williams, and Glen Otero*

### in Pertussis: Epidemiology, Immunology, and Evolution

- Published in print:
- 2018
- Published Online:
- February 2019
- ISBN:
- 9780198811879
- eISBN:
- 9780191850011
- Item type:
- chapter

- Publisher:
- Oxford University Press
- DOI:
- 10.1093/oso/9780198811879.003.0009
- Subject:
- Biology, Disease Ecology / Epidemiology, Evolutionary Biology / Genetics

Population genetics of Bordetella pertussis has long wrestled with a conflicting dichotomy of low gene sequence variation and high restriction fragment profile diversity. Recent applications of ... 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

## 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

## 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

## 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

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