ArticleGenetics2022
Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage.
Article in Genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- From forests to deserts: Sequencing of the giant forest hog completes the genomic history of the African suids.iScience · 2026Article
- Adaptation across an extreme elevational gradient in Andean leaf-eared mice, the world's highest-dwelling mammal.Science (New York, N.Y.) · 2026Article
- Genome-Wide Population Structure of Lake Whitefish (Evolutionary applications · 2026Article
- Seizure samples reveal complex evolutionary dynamics among Southeast Asian pangolins.Heredity · 2026Article
- Population structure and domestication history of the Javan banteng.Current biology : CB · 2026Article
- Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.Molecular ecology · 2025Article
- Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea.Molecular ecology · 2025Article
- Large Inversion Polymorphisms are Widespread in North American Songbirds.Genome biology and evolution · 2025Article
- Comparative Whole Genome Phylogeography Reveals Genetic Distinctiveness of Appalachian Populations of Boreal Songbirds.Evolutionary applications · 2025Article
- Article
- Long-distance seasonal migration to the tropics promotes genetic diversity but not gene flow in boreal birds.Nature ecology & evolution · 2025Article
- Leveraging Whole Genomes, Mitochondrial DNA and Haploblocks to Decipher Complex Demographic Histories: An Example From a Broadly Admixed Arctic Fish.Molecular ecology · 2025Article
- Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot.Molecular ecology · 2025Article
- vcfgl: a flexible genotype likelihood simulator for VCF/BCF files.Bioinformatics (Oxford, England) · 2025Article
- Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.Molecular biology and evolution · 2025Article
- Genomic Insights Into Red Squirrels in Scotland Reveal Loss of Heterozygosity Associated With Extreme Founder Effects.Evolutionary applications · 2025Article
- Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model.Systematic biology · 2024Article
- Genomic and Acoustic Biogeography of the Iconic Sulphur-crested Cockatoo Clarifies Species Limits and Patterns of Intraspecific Diversity.Molecular biology and evolution · 2024Article
- Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.Science advances · 2023Article
- Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change.Science advances · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation-maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Furthermore, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.
Indexed as
Identifiers
What OpenQuestion holds
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.