ArticleMolecular biology and evolution2019
Localizing and Classifying Adaptive Targets with Trend Filtered Regression.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 45 citations in OpenAlex.
- Allelic gene conversion softens selective sweeps.Genetics · 2026Article
- Adaptive evolution at thyroid hormone, insulin and glycerolipid pathways improved energy metabolism in high-latitude Eurasian populations.Communications biology · 2026Article
- Soft Selective Sweeps Predominate in the Yellow Fever Mosquito Aedes aegypti.Molecular biology and evolution · 2026Article
- Summary statistics and approximate bayesian computation are comparable to convolutional neural networks for inferring times to fixation.bioRxiv : the preprint server for biology · 2026Article
- Accessible, Realistic Genome Simulation with Selection Using stdpopsim.Molecular biology and evolution · 2025Article
- Accessible, realistic genome simulation with selection using stdpopsim.bioRxiv : the preprint server for biology · 2025Article
- Signatures of soft selective sweeps predominate in the yellow fever mosquitobioRxiv : the preprint server for biology · 2025Article
- Article
- Efficient Detection and Characterization of Targets of Natural Selection Using Transfer Learning.Molecular biology and evolution · 2025Article
- Efficient detection and characterization of targets of natural selection using transfer learning.bioRxiv : the preprint server for biology · 2025Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.Genetics · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Tree Sequences as a General-Purpose Tool for Population Genetic Inference.Molecular biology and evolution · 2024Article
- Tree sequences as a general-purpose tool for population genetic inference.bioRxiv : the preprint server for biology · 2024Article
- Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations.bioRxiv : the preprint server for biology · 2024Article
- Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle.Animals : an open access journal from MDPI · 2024Article
- A Novel Approach Utilizing Domain Adversarial Neural Networks for the Detection and Classification of Selective Sweeps.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- IntroUNET: Identifying introgressed alleles via semantic segmentation.PLoS genetics · 2024Article
- IntroUNET: identifying introgressed alleles via semantic segmentation.bioRxiv : the preprint server for biology · 2024Article
- Tensor Decomposition-based Feature Extraction and Classification to Detect Natural Selection from Genomic Data.Molecular biology and evolution · 2023Article
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2 authors at 1 institution in 1 country.
Funding
Abstract
Identifying genomic locations of natural selection from sequence data is an ongoing challenge in population genetics. Current methods utilizing information combined from several summary statistics typically assume no correlation of summary statistics regardless of the genomic location from which they are calculated. However, due to linkage disequilibrium, summary statistics calculated at nearby genomic positions are highly correlated. We introduce an approach termed Trendsetter that accounts for the similarity of statistics calculated from adjacent genomic regions through trend filtering, while reducing the effects of multicollinearity through regularization. Our penalized regression framework has high power to detect sweeps, is capable of classifying sweep regions as either hard or soft, and can be applied to other selection scenarios as well. We find that Trendsetter is robust to both extensive missing data and strong background selection, and has comparable power to similar current approaches. Moreover, the model learned by Trendsetter can be viewed as a set of curves modeling the spatial distribution of summary statistics in the genome. Application to human genomic data revealed positively selected regions previously discovered such as LCT in Europeans and EDAR in East Asians. We also identified a number of novel candidates and show that populations with greater relatedness share more sweep signals.
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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.