ArticleGenetics2007
Sequence-level population simulations over large genomic regions.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
70 citing papers in PubMed.
- The rights and wrongs of rescaling in population genetics simulations.PLoS genetics · 2026Review
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
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- Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.Genetics · 2025Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.bioRxiv : the preprint server for biology · 2024Article
- Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.Molecular biology and evolution · 2024Article
- Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations.Genome biology and evolution · 2024Article
- On the prospect of achieving accurate joint estimation of selection with population history.Genome biology and evolution · 2022Article
- Article
- Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.Molecular biology and evolution · 2021Article
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- The impact of purifying and background selection on the inference of population history: problems and prospects.bioRxiv : the preprint server for biology · 2021Article
- Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection.Genetics · 2020Article
- Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years.Human molecular genetics · 2020Article
- Weak Epistasis May Drive Adaptation in Recombining Bacteria.Genetics · 2018Article
- Weighted likelihood inference of genomic autozygosity patterns in dense genotype data.BMC genomics · 2017Article
- Detecting Long-Term Balancing Selection Using Allele Frequency Correlation.Molecular biology and evolution · 2017Article
- cophesim: a comprehensive phenotype simulator for testing novel association methods.F1000Research · 2017Article
- Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants.Genome research · 2016Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Simulation is an invaluable tool for investigating the effects of various population genetics modeling assumptions on resulting patterns of genetic diversity, and for assessing the performance of statistical techniques, for example those designed to detect and measure the genomic effects of selection. It is also used to investigate the effectiveness of various design options for genetic association studies. Backward-in-time simulation methods are computationally efficient and have become widely used since their introduction in the 1980s. The forward-in-time approach has substantial advantages in terms of accuracy and modeling flexibility, but at greater computational cost. We have developed flexible and efficient simulation software and a rescaling technique to aid computational efficiency that together allow the simulation of sequence-level data over large genomic regions in entire diploid populations under various scenarios for demography, mutation, selection, and recombination, the latter including hotspots and gene conversion. Our forward evolution of genomic regions (FREGENE) software is freely available from www.ebi.ac.uk/projects/BARGEN together with an ancillary program to generate phenotype labels, either binary or quantitative. In this article we discuss limitations of coalescent-based simulation, introduce the rescaling technique that makes large-scale forward-in-time simulation feasible, and demonstrate the utility of various features of FREGENE, many not previously available.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.