ArticleGenetics2009
Detecting selective sweeps: a new approach based on hidden markov models.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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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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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.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Meta-Assembly of Selection Signatures in Cattle.PloS one · 2016Pooled it
- Bovine Genome Database: new curated collection of selective sweeps in bovine populations across the world.Nucleic acids research · 2026Article
- Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina.Genome biology and evolution · 2022Article
- Uncovering ecological state dynamics with hidden Markov models.Ecology letters · 2020Review
- Detecting Selection from Linked Sites Using anGenetics · 2020Article
- Selective Sweeps Under Dominance and Inbreeding.G3 (Bethesda, Md.) · 2020Article
- Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps.PLoS computational biology · 2019Article
- A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes.Molecular ecology resources · 2019Article
- Genomic divergence and adaptive convergence inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference.Molecular biology and evolution · 2019Article
- Selective Sweeps.Genetics · 2019Review
- Supervised Machine Learning for Population Genetics: A New Paradigm.Trends in genetics : TIG · 2018Review
- Whole-Genome Sequencing Reveals Genetic Variation in the Asian House Rat.G3 (Bethesda, Md.) · 2016Article
- Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds.Genetics · 2016Article
- Detecting recent selective sweeps while controlling for mutation rate and background selection.Molecular ecology · 2016Article
- Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms.Molecular biology and evolution · 2015Article
- Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.Proceedings. Biological sciences · 2015Article
- Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation.G3 (Bethesda, Md.) · 2015Article
- Detecting signatures of selection through haplotype differentiation among hierarchically structured populations.Genetics · 2013Article
- Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.Molecular ecology resources · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Detecting and localizing selective sweeps on the basis of SNP data has recently received considerable attention. Here we introduce the use of hidden Markov models (HMMs) for the detection of selective sweeps in DNA sequences. Like previously published methods, our HMMs use the site frequency spectrum, and the spatial pattern of diversity along the sequence, to identify selection. In contrast to earlier approaches, our HMMs explicitly model the correlation structure between linked sites. The detection power of our methods, and their accuracy for estimating the selected site location, is similar to that of competing methods for constant size populations. In the case of population bottlenecks, however, our methods frequently showed fewer false positives.
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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.