相关论文: Viral population estimation using pyrosequencing
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a…
Background. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they…
Capture-recapture methods aim to estimate the size of a closed population on the basis of multiple incomplete enumerations of individuals. In many applications, the individual probability of being recorded is heterogeneous in the…
Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…
Infection can spread easily on networks with heterogeneous degree distribution. Here, we considered targeted immunization on such networks, wherein a fraction of individuals with the highest connectivity are immunized. To quantify the…
The multivariate hypergeometric distribution describes sampling without replacement from a discrete population of elements divided into multiple categories. Addressing a gap in the literature, we tackle the challenge of estimating discrete…
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
We consider the estimation of densities in multiple subpopulations, where the available sample size in each subpopulation greatly varies. This problem occurs in epidemiology, for example, where different diseases may share similar…
Because of its relevance to everyday life, the spreading of viral infections has been of central interest in a variety of scientific communities involved in fighting, preventing and theoretically interpreting epidemic processes. Recent…
Capturing the structured mixing within a population is key to the reliable projection of infectious disease dynamics and hence informed control. Both heterogeneity in the number of contacts and age-structured mixing have been repeatedly…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Estimates of population size for hidden and hard-to-reach individuals are of particular interest to health officials when health problems are concentrated in such populations. Efforts to derive these estimates are often frustrated by a…
Phylodynamics seeks to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. One way to accomplish this task formulates an observed sequence data likelihood exploiting…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…