ogaraK: a population genetics simulator for malaria

被引：4

作者：

Antao, Tiago ^{[1
]}

Hastings, Ian M. ^{[1
]}

机构：

[1] Univ Liverpool, Liverpool Sch Trop Med, Dept Mol & Biochem Parasitol, Liverpool L3 5QA, Merseyside, England

来源：

BIOINFORMATICS | 2011年 / 27卷 / 09期

关键词：

RESISTANCE; SPREAD;

D O I：

10.1093/bioinformatics/btr139

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

Motivation: The evolution of resistance in Plasmodium falciparum malaria against most available treatments is a major global health threat. Population genetics approaches are commonly used to model the spread of drug resistance. Due to uncommon features in malaria biology, existing forward-time population genetics simulators cannot suitably model Plasmodium falciparum malaria. Results: Here we present ogaraK, a population genetics simulator for modelling the spread of drug-resistant malaria. OgaraK is designed to make malaria simulation computationally tractable as it models infections, not individual parasites. OgaraK is also able to model the life cycle of the parasite which includes both haploid and diploid phases and sexual and asexual reproduction. We also allow for the simulation of different inbreeding levels, an important difference between high and low transmission areas and a fundamental factor influencing the outcome of strategies to control or eliminate malaria.

引用

收藏

页码：1335 / 1336

页数：2

相关论文

共 13 条

[1]

Environmental, pharmacological and genetic influences on the spread of drug-resistant malaria [J].

Antao, Tiago ;

Hastings, Ian M. .

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2011, 278 (1712) :1705-1712

[2]

Benefits of using multiple first-line therapies against malaria [J].

Boni, Maciej F. ;

Smith, David L. ;

Laxminarayan, Ramanan .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (37) :14216-14227

[3]

Biopython']python: freely available Python']Python tools for computational molecular biology and bioinformatics [J].

Cock, Peter J. A. ;

Antao, Tiago ;

Chang, Jeffrey T. ;

Chapman, Brad A. ;

Cox, Cymon J. ;

Dalke, Andrew ;

Friedberg, Iddo ;

Hamelryck, Thomas ;

Kauff, Frank ;

Wilczynski, Bartek ;

de Hoon, Michiel J. L. .

BIOINFORMATICS, 2009, 25 (11) :1422-1423

[4]

Artemisinin Resistance in Plasmodium falciparum Malaria. [J].

Dondorp, Arjen M. ;

Nosten, Francois ;

Yi, Poravuth ;

Das, Debashish ;

Phyo, Aung Phae ;

Tarning, Joel ;

Lwin, Khin Maung ;

Ariey, Frederic ;

Hanpithakpong, Warunee ;

Lee, Sue J. ;

Ringwald, Pascal ;

Silamut, Kamolrat ;

Imwong, Mallika ;

Chotivanich, Kesinee ;

Lim, Pharath ;

Herdman, Trent ;

An, Sen Sam ;

Yeung, Shunmay ;

Singhasivanon, Pratap ;

Day, Nicholas P. J. ;

Lindegardh, Niklas ;

Socheat, Duong ;

White, Nicholas J. .

NEW ENGLAND JOURNAL OF MEDICINE, 2009, 361 (05) :455-467

[5]

Complex dynamics and stability of resistance to antimalarial drugs [J].

Hastings, I. M. .

PARASITOLOGY, 2006, 132 :615-624

[6]

A model for the origins and spread of drug-resistant malaria [J].

Hastings, IM .

PARASITOLOGY, 1997, 115 :133-141

[7]

Epidemiological models for the spread of anti-malarial resistance [J].

Koella, JC ;

Antia, R .

MALARIA JOURNAL, 2003, 2 (1)

[8]

Drug resistance hampers our capacity to roll back malaria [J].

Olliaro, P .

CLINICAL INFECTIOUS DISEASES, 2005, 41 :S247-S257

[9]

The Evolutionary Enigma of Sex [J].

Otto, Sarah P. .

AMERICAN NATURALIST, 2009, 174 :S1-S14

[10]

simuPOP: a forward-time population genetics simulation environment [J].

Peng, B ;

Kimmel, M .

BIOINFORMATICS, 2005, 21 (18) :3686-3687