Topic
Generation time
About: Generation time is a research topic. Over the lifetime, 112 publications have been published within this topic receiving 4388 citations.
Papers published on a yearly basis
Papers
TL;DR: A new statistical approach to analyse epidemic time-series data and introduces a diffusion process that mimicks the susceptible–infectious–removed (SIR) epidemic process, but that is more tractable analytically.
Abstract: We present a new statistical approach to analyse epidemic time-series data. A major difficulty for inference is that (i) the latent transmission process is partially observed and (ii) observed quantities are further aggregated temporally. We develop a data augmentation strategy to tackle these problems and introduce a diffusion process that mimicks the susceptible–infectious–removed (SIR) epidemic process, but that is more tractable analytically. While methods based on discrete-time models require epidemic and data collection processes to have similar time scales, our approach, based on a continuous-time model, is free of such constraint. Using simulated data, we found that all parameters of the SIR model, including the generation time, were estimated accurately if the observation interval was less than 2.5 times the generation time of the disease. Previous discrete-time TSIR models have been unable to estimate generation times, given that they assume the generation time is equal to the observation interval. However, we were unable to estimate the generation time of measles accurately from historical data. This indicates that simple models assuming homogenous mixing (even with age structure) of the type which are standard in mathematical epidemiology miss key features of epidemics in large populations.
171 citations
TL;DR: A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age, and the effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described.
Abstract: A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.
165 citations
TL;DR: The experimental observations of Prescott concerning the generation time distribution and population growth of Tetrahymena geleii HS cells appear to support best the theoretical formulation of the maturity-time representation, which suggests that memory of the maturation velocity or generation time of a given cell tends to persist from parent to daughter for several generations at least.
145 citations
TL;DR: A new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time is described, strengthening confidence in estimates of a short viral generation time.
Abstract: The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here, we describe a new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time. The method is applied to sequences obtained from a long-term nonprogressing individual at five sampling occasions. The estimate of viral generation time using the coalescent method is 1.2 days per generation and is close to that obtained by mathematical modeling (1.8 days per generation), thus strengthening confidence in estimates of a short viral generation time. Apart from the estimation of relevant parameters relating to viral dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.
134 citations
TL;DR: The Ne/N calculated for clonally reproducing organisms in this paper seem to be substantially smaller than published values for organisms lacking clonal reproduction.
127 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2025 | 2 |
| 2024 | 8 |
| 2023 | 10 |
| 2022 | 25 |
| 2021 | 7 |
| 2020 | 8 |