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Search Results: 1 - 10 of 6095 matches for " Maliepaard Chris "
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The simulation of meiosis in diploid and tetraploid organisms using various genetic models
Voorrips Roeland E,Maliepaard Chris A
BMC Bioinformatics , 2012, DOI: 10.1186/1471-2105-13-248
Abstract: Background While the genetics of diploid inheritance are well studied and software for linkage mapping, haplotyping and QTL analysis are available, for tetraploids the available tools are limited. In order to develop such tools it would be helpful if simulated populations based on a variety of models of the tetraploid meiosis would be available. Results Here we present PedigreeSim, a software package that simulates meiosis in both diploid and tetraploid species and uses this to simulate pedigrees and cross populations. For tetraploids a variety of models can be used, including both bivalent and quadrivalent formation, varying degrees of preferential pairing of hom(oe)ologous chromosomes, different quadrivalent configurations and more. Simulation of quadrivalent meiosis results as expected in double reduction and recombination between more than two hom(oe)ologous chromosomes. The results are shown to match theoretical predictions. Conclusions This is the first simulation software that implements all features of meiosis in tetraploids. It allows to generate data for tetraploid and diploid populations, and to investigate different models of tetraploid meiosis. The software and manual are available from http://www.plantbreeding.nl/UK/software_pedigreeSim.html and as Additional files 1, 2, 3 and 4 with this publication. Additional file 1 Archive containing the compiled version of PedigreeSim and instructions on how to run it. Click here for file Additional file 2 Archive containing the full source code of PedigreeSim. Click here for file Additional file 3 The PedigreeSim Manual. Click here for file Additional file 4: Archive containing the example input files for PedigreeSim. Click here for file
Comparison of analyses of the QTLMAS XIII common dataset. I: genomic selection
Bastiaansen John,Bink Marco,Coster Albart,Maliepaard Chris
BMC Proceedings , 2010,
Abstract: Background Genomic selection, the use of markers across the whole genome, receives increasing amounts of attention and is having more and more impact on breeding programs. Development of statistical and computational methods to estimate breeding values based on markers is a very active area of research. A simulated dataset was analyzed by participants of the QTLMAS XIII workshop, allowing a comparison of the ability of different methods to estimate genomic breeding values. Methods A best case scenario was analyzed by the organizers where QTL genotypes were known. Participants submitted estimated breeding values for 1000 unphenotyped individuals together with a description of the applied method(s). The submitted breeding values were evaluated for correlation with the simulated values (accuracy), rank correlation of the best 10% of individuals and error in predictions. Bias was tested by regression of simulated on estimated breeding values. Results The accuracy obtained from the best case scenario was 0.94. Six research groups submitted 19 sets of estimated breeding values. Methods that assumed the same variance for markers showed accuracies, measured as correlations between estimated and simulated values, ranging from 0.75 to 0.89 and rank correlations between 0.58 and 0.70. Methods that allowed different marker variances showed accuracies ranging from 0.86 to 0.94 and rank correlations between 0.69 and 0.82. Methods assuming equal marker variances were generally more biased and showed larger prediction errors. Conclusions The best performing methods achieved very high accuracies, close to accuracies achieved in a best case scenario where QTL genotypes were known without error. Methods that allowed different marker variances generally outperformed methods that assumed equal marker variances. Genomic selection methods performed well compared to traditional, pedigree only, methods; all methods showed higher accuracies than those obtained for breeding values estimated solely on pedigree relationships.
Comparative Methods for Association Studies: A Case Study on Metabolite Variation in a Brassica rapa Core Collection
Dunia Pino Del Carpio,Ram Kumar Basnet,Ric C. H. De Vos,Chris Maliepaard,Maria Jo?o Paulo,Guusje Bonnema
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0019624
Abstract: Association mapping is a statistical approach combining phenotypic traits and genetic diversity in natural populations with the goal of correlating the variation present at phenotypic and allelic levels. It is essential to separate the true effect of genetic variation from other confounding factors, such as adaptation to different uses and geographical locations. The rapid availability of large datasets makes it necessary to explore statistical methods that can be computationally less intensive and more flexible for data exploration.
Composition of Human Skin Microbiota Affects Attractiveness to Malaria Mosquitoes
Niels O. Verhulst, Yu Tong Qiu, Hans Beijleveld, Chris Maliepaard, Dan Knights, Stefan Schulz, Donna Berg-Lyons, Christian L. Lauber, Willem Verduijn, Geert W. Haasnoot, Roland Mumm, Harro J. Bouwmeester, Frans H. J. Claas, Marcel Dicke, Joop J. A. van Loon, Willem Takken, Rob Knight, Renate C. Smallegange
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028991
Abstract: The African malaria mosquito Anopheles gambiae sensu stricto continues to play an important role in malaria transmission, which is aggravated by its high degree of anthropophily, making it among the foremost vectors of this disease. In the current study we set out to unravel the strong association between this mosquito species and human beings, as it is determined by odorant cues derived from the human skin. Microbial communities on the skin play key roles in the production of human body odour. We demonstrate that the composition of the skin microbiota affects the degree of attractiveness of human beings to this mosquito species. Bacterial plate counts and 16S rRNA sequencing revealed that individuals that are highly attractive to An. gambiae s.s. have a significantly higher abundance, but lower diversity of bacteria on their skin than individuals that are poorly attractive. Bacterial genera that are correlated with the relative degree of attractiveness to mosquitoes were identified. The discovery of the connection between skin microbial populations and attractiveness to mosquitoes may lead to the development of new mosquito attractants and personalized methods for protection against vectors of malaria and other infectious diseases.
The Stationary Distributions of a Class of Markov Chains  [PDF]
Chris Cannings
Applied Mathematics (AM) , 2013, DOI: 10.4236/am.2013.45105
Abstract:

The objective of this paper is to find the stationary distribution of a certain class of Markov chains arising in a biological population involved in a specific type of evolutionary conflict, known as Parkers model. In a population of such players, the result of repeated, infrequent, attempted invasions using strategies from{0,1,2,,m-1}, is a Markov chain. The stationary distributions of this class of chains, for m ε {3,4,,} are derived in terms of previously known integer sequences. The asymptotic distribution (for m →∞) is derived.

The Prevalence of Sexual Partner Concurrency Is Not Correlated with Markers of Poverty or Gender Inequality: An Ecological Analysis  [PDF]
Chris Kenyon
World Journal of AIDS (WJA) , 2015, DOI: 10.4236/wja.2015.54035
Abstract: High rates of overlapping sexual relationships (concurrency) are believed to be important in the generation of generalized HIV epidemics in sub-Saharan Africa. Different authors favor socioeconomic, gender-equity or cultural explanations for the high concurrency rates in this region. We performed linear regression to analyze the association between the point-prevalence of concurrency in 15 - 49 years old males and various indicators of socioeconomic status and gender-equity using data from 11 countries surveyed in 1989/1990. We found no meaningful association between concurrency and the various markers of socioeconomic status and gender-equity. This analysis supports the findings of other studies that high concurrency rates in sub-Saharan Africa could be reduced without having to address socioeconomic and gender-equity factors.
Some Models of Reproducing Graphs: II Age Capped Vertices  [PDF]
Richard Southwell, Chris Cannings
Applied Mathematics (AM) , 2010, DOI: 10.4236/am.2010.14031
Abstract: In the prequel to this paper we introduced eight reproducing graph models. The simple idea behind these models is that graphs grow because the vertices within reproduce. In this paper we make our models more realistic by adding the idea that vertices have a finite life span. The resulting models capture aspects of systems like social networks and biological networks where reproducing entities die after some amount of time. In the 1940’s Leslie introduced a population model where the reproduction and survival rates of individuals depends upon their ages. Our models may be viewed as extensions of Leslie’s model-adding the idea of network joining the reproducing individuals. By exploiting connections with Leslie’s model we are to describe how many aspects of graphs evolve under our systems. Many features such as degree distributions, number of edges and distance structure are described by the golden ratio or its higher order generalisations.
Some Models of Reproducing Graphs: I Pure Reproduction  [PDF]
Richard Southwell, Chris Cannings
Applied Mathematics (AM) , 2010, DOI: 10.4236/am.2010.13018
Abstract: Many real world networks change over time. This may arise due to individuals joining or leaving the network or due to links forming or being broken. These events may arise because of interactions between the vertices which occasion payoffs which subsequently determine the fate of the nodes, due to ageing or crowding, or perhaps due to isolation. Such phenomena result in a dynamical system which may lead to complex behaviours, to self-replication, to chaotic or regular patterns, to emergent phenomena from local interactions. They give insight to the nature of the real-world phenomena which the network, and its dynamics, may approximate. To a large extent the models considered here are motivated by biological and social phenomena, where the vertices may be genes, proteins, genomes or organisms, and the links interactions of various kinds. In this, the first paper of a series, we consider the dynamics of pure reproduction models where networks grow relentlessly in a deterministic way.
Some Models of Reproducing Graphs: III Game Based Reproduction  [PDF]
Richard Southwell, Chris Cannings
Applied Mathematics (AM) , 2010, DOI: 10.4236/am.2010.15044
Abstract: Many real world networks change over time. This may arise due to individuals joining or leaving the network or due to links forming or being broken. These events may arise because of interactions between the vertices which occasion payoffs which subsequently determine the fate of the vertices, due to ageing or crowding, or perhaps due to isolation. Such phenomena result in a dynamical system which may lead to complex behaviours, to selfreplication, to chaotic or regular patterns, or to emergent phenomena from local interactions. They hopefully give insight to the nature of the real-world phenomena which the network, and its dynamics, may approximate. To a large extent the models considered here are motivated by biological and social phenomena, where the vertices may be genes, proteins, genomes or organisms, and the links interactions of various kinds. In this, the third paper of a series, we consider the vertices to be players of some game. Offspring inherit their parent’s strategies and vertices which behave poorly in games with their neighbours get destroyed. The process is analogous to the way different kinds of animals reproduce whilst unfit animals die. Some game based systems are analytically tractable, others are highly complex-causing small initial structures to grow and break into large collections of self replicating structures.
A Basis for Improving Numerical Forecasting in the Gulf Area by Assimilating Doppler Radar Radial Winds  [PDF]
Fathalla Rihan, Chris Collier
International Journal of Geosciences (IJG) , 2010, DOI: 10.4236/ijg.2010.12010
Abstract: An approach to assimilate Doppler radar radial winds into a high resolution Numerical Weather Prediction (NWP) model using 3D-Var system is described. We discuss the types of errors that occur in radar radial winds. Some related problems such as nonlinearity and sensitivity of the forecast to possible small errors in initial conditions, random observation errors, and the background states are also considered. The technique can be used to improve the model forecasts, in the Gulf area, at the local scale and under high aerosol (dust/sand/pollution) conditions.
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