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Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A new data structure for cumulative frequency tables
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Recombination as a Point Process along Sequences
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An Ancestral Recombination Graph
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A Novel Approach for Compressing Phylogenetic Trees
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On the two-locus sampling distribution
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On the Combinatorics of Rooted Binary Phylogenetic Trees
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Properties of Subtree-Prune-and-Regraft Operations on Totally-Ordered Phylogenetic Trees
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Properties of a neutral allele model with intragenic recombination
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The use of sample genealogies for studying a selectively neutral m-loci model with recombination
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GCTA: A Tool for Genome-wide Complex Trait Analysis
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Sequential Markov coalescent algorithms for population models with demographic structure
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Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks
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Coalescent simulation in continuous space: Algorithms for large neighbourhood size
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Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank
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The general coalescent with asynchronous mergers of ancestral lines
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A sequential coalescent algorithm for chromosomal inversions
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Proportionally more deleterious genetic variation in European than in African populations
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Genes mirror geography within Europe
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Inference of human population history from individual whole-genome sequences
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The UK10K project identifies rare variants in health and disease
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A global reference for human genetic variation
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Differential confounding of rare and common variants in spatially structured populations
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Inferring human population size and separation history from multiple genome sequences
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Whole-genome sequence variation, population structure and demographic history of the Dutch population
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Large-scale whole-genome sequencing of the Icelandic population
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The effects of human population structure on large genetic association studies
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A new multipoint method for genome-wide association studies by imputation of genotypes
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Efficient genotype compression and analysis of large genetic-variation data sets
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Genome-wide association studies for complex traits: consensus, uncertainty and challenges
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Computer simulations: tools for population and evolutionary genetics
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Bringing genome-wide association findings into clinical use
inferredcites →https://doi.org/10.1073/pnas.1322709111openalex-snapshot
Distortion of genealogical properties when the sample is very large
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Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Modelling evolution in a spatial continuum
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An Overview of Population Genetic Data Simulation
inferredcites →https://doi.org/10.1093/bioinformatics/17.4.383openalex-snapshot
ATV: display and manipulation of annotated phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot
Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/bth264openalex-snapshot
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
inferredcites →https://doi.org/10.1093/bioinformatics/bth417openalex-snapshot
SelSim: a program to simulate population genetic data with natural selection and recombination
inferredcites →https://doi.org/10.1093/bioinformatics/bti154openalex-snapshot
Serial SimCoal: A population genetics model for data from multiple populations and points in time
inferredcites →https://doi.org/10.1093/bioinformatics/btl191openalex-snapshot
N et G en : generating phylogenetic networks with diploid hybrids
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Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
inferredcites →https://doi.org/10.1093/bioinformatics/btl622openalex-snapshot
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
inferredcites →https://doi.org/10.1093/bioinformatics/btm138openalex-snapshot
GENOME: a rapid coalescent-based whole genome simulator
inferredcites →https://doi.org/10.1093/bioinformatics/btm549openalex-snapshot
GWAsimulator: a rapid whole-genome simulation program
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
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DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/btq322openalex-snapshot
MSMS : a coalescent simulation program including recombination, demographic structure and selection at a single locus
inferredcites →https://doi.org/10.1093/bioinformatics/btr124openalex-snapshot
fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
inferredcites →https://doi.org/10.1093/bioinformatics/btr341openalex-snapshot
HAPGEN2: simulation of multiple disease SNPs
inferredcites →https://doi.org/10.1093/bioinformatics/btt067openalex-snapshot
Coalescent simulation in continuous space
inferredcites →https://doi.org/10.1093/bioinformatics/btu014openalex-snapshot
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT)
inferredcites →https://doi.org/10.1093/bioinformatics/btu562openalex-snapshot
Cosi2: an efficient simulator of exact and approximate coalescent with selection
inferredcites →https://doi.org/10.1093/bioinformatics/btu861openalex-snapshot
scrm: efficiently simulating long sequences using the approximated coalescent with recombination
inferredcites →https://doi.org/10.1093/bioinformatics/btv613openalex-snapshot
BGT: efficient and flexible genotype query across many samples
inferredcites →https://doi.org/10.1093/genetics/111.1.147openalex-snapshot
STATISTICAL PROPERTIES OF THE NUMBER OF RECOMBINATION EVENTS IN THE HISTORY OF A SAMPLE OF DNA SEQUENCES
inferredcites →https://doi.org/10.1093/genetics/151.3.1217openalex-snapshot
The Ancestry of a Sample of Sequences Subject to Recombination
inferredcites →https://doi.org/10.1093/genetics/155.1.451openalex-snapshot
The Coalescent With Gene Conversion
inferredcites →https://doi.org/10.1093/genetics/155.2.981openalex-snapshot
Detecting Bottlenecks and Selective Sweeps From DNA Sequence Polymorphism
inferredcites →https://doi.org/10.1093/jhered/91.6.506openalex-snapshot
Computer note. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography
inferredcites →https://doi.org/10.1093/molbev/msg024openalex-snapshot
Gene Genealogies When the Sample Size Exceeds the Effective Size of the Population
inferredcites →https://doi.org/10.1093/molbev/msq331openalex-snapshot
Recovering Population Parameters from a Single Gene Genealogy: An Unbiased Estimator of the Growth Rate
inferredcites →https://doi.org/10.1093/schbul/syp004openalex-snapshot
Coalescent Theory: An Introduction
inferredcites →https://doi.org/10.1093/sysbio/46.4.590openalex-snapshot
NEXUS: An Extensible File Format for Systematic Information
inferredcites →https://doi.org/10.1093/sysbio/sys025openalex-snapshot
NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata
inferredcites →https://doi.org/10.1098/rstb.2005.1673openalex-snapshot
Approximating the coalescent with recombination
inferredcites →https://doi.org/10.1101/gr.083634.108openalex-snapshot
Fast and flexible simulation of DNA sequence data
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
inferredcites →https://doi.org/10.1101/gr.361602openalex-snapshot
The Bioperl Toolkit: Perl Modules for the Life Sciences
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Calibrating a coalescent simulation of human genome sequence variation
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TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01019.xopenalex-snapshot
A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY
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O3-5.2 UK biobank: the need for large prospective epidemiological studies
inferredcites →https://doi.org/10.1177/117693430700300020openalex-snapshot
Mlcoalsim: Multilocus Coalescent Simulations
inferredcites →https://doi.org/10.1186/1471-2105-10-166openalex-snapshot
mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
inferredcites →https://doi.org/10.1186/1471-2105-10-356openalex-snapshot
phyloXML: XML for evolutionary biology and comparative genomics
inferredcites →https://doi.org/10.1186/1471-2105-11-24openalex-snapshot
ETE: a python Environment for Tree Exploration
inferredcites →https://doi.org/10.1186/1471-2105-12-265openalex-snapshot
phenosim - A software to simulate phenotypes for testing in genome-wide association studies
inferredcites →https://doi.org/10.1186/1471-2105-14-199openalex-snapshot
SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies
inferredcites →https://doi.org/10.1186/1471-2105-14-356openalex-snapshot
Processing genome scale tabular data with wormtable
inferredcites →https://doi.org/10.1186/1471-2105-14-40openalex-snapshot
ACG: rapid inference of population history from recombining nucleotide sequences
inferredcites →https://doi.org/10.1186/1471-2105-15-273openalex-snapshot
A new method for modeling coalescent processes with recombination
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Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences
inferredcites →https://doi.org/10.1186/1471-2105-6-252openalex-snapshot
CoaSim: A flexible environment for simulating genetic data under coalescent models
inferredcites →https://doi.org/10.1186/1471-2105-8-458openalex-snapshot
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography
inferredcites →https://doi.org/10.1186/1471-2105-9-322openalex-snapshot
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
inferredcites →https://doi.org/10.1186/1471-2105-9-532openalex-snapshot
Extended Newick: it is time for a standard representation of phylogenetic networks
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A survey of genetic simulation software for population and epidemiological studies
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Softwares and methods for estimating genetic ancestry in human populations
inferredcites →https://doi.org/10.1186/s12859-015-0721-yopenalex-snapshot
Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees
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Particle Representations for Measure-Valued Population Models
inferredcites →https://doi.org/10.1214/aop/1022677552openalex-snapshot
Coalescents With Multiple Collisions
inferredcites →https://doi.org/10.1214/aop/1022874819openalex-snapshot
Coalescents With Multiple Collisions
inferredcites →https://doi.org/10.1214/ejp.v15-741openalex-snapshot
A New Model for Evolution in a Spatial Continuum
inferredcites →https://doi.org/10.1214/lnms/1215459289openalex-snapshot
The Two-Locus Ancestral Graph
inferredcites →https://doi.org/10.1239/jap/1032374759openalex-snapshot
The general coalescent with asynchronous mergers of ancestral lines
inferredcites →https://doi.org/10.1371/journal.pbio.1001555openalex-snapshot
The Geography of Recent Genetic Ancestry across Europe
inferredcites →https://doi.org/10.1371/journal.pbio.1002195openalex-snapshot
Big Data: Astronomical or Genomical?
inferredcites →https://doi.org/10.1371/journal.pcbi.1002495openalex-snapshot
Simulation of Molecular Data under Diverse Evolutionary Scenarios
inferredcites →https://doi.org/10.1371/journal.pcbi.1003060openalex-snapshot
Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
inferredcites →https://doi.org/10.1371/journal.pgen.1000477openalex-snapshot
Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip
inferredcites →https://doi.org/10.1371/journal.pgen.1000695openalex-snapshot
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1002453openalex-snapshot
Inference of Population Structure using Dense Haplotype Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003521openalex-snapshot
Inferring Demographic History from a Spectrum of Shared Haplotype Lengths
inferredcites →https://doi.org/10.1371/journal.pgen.1004342openalex-snapshot
Genome-Wide Inference of Ancestral Recombination Graphs
inferredcites →https://doi.org/10.1371/journal.pgen.1004379openalex-snapshot
The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits
inferredcites →https://doi.org/10.1371/journal.pgen.1004528openalex-snapshot
Demography and the Age of Rare Variants
inferredcites →https://doi.org/10.1534/genetics.109.109736openalex-snapshot
Coalescent Simulation of Intracodon Recombination
inferredcites →https://doi.org/10.1534/genetics.114.162362openalex-snapshot
The Lengths of Admixture Tracts
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Simulation of Genomes: A Review
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GraphML specializations to codify ancestral recombinant graphs
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Gene Genealogies in Haploid Populations Evolving According to Sweepstakes Reproduction
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Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations
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Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits
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The Indian Ocean slave trade and colonial expansion resulted in strong sex-biased admixture in South Africa
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Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals
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Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes
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Human inbreeding has decreased in time through the Holocene
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Philippine Ayta possess the highest level of Denisovan ancestry in the world
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Ancestral genomic contributions to complex traits in contemporary Europeans
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How to choose sets of ancestry informative markers: A supervised feature selection approach
inferred← citeshttps://doi.org/10.1016/j.fsigen.2021.102593openalex-snapshot
Inference of recent admixture using genotype data
inferred← citeshttps://doi.org/10.1016/j.gde.2018.07.002openalex-snapshot
Inference of population history using coalescent HMMs: review and outlook
inferred← citeshttps://doi.org/10.1016/j.gde.2018.10.001openalex-snapshot
Genomic inference using diffusion models and the allele frequency spectrum
inferred← citeshttps://doi.org/10.1016/j.gde.2020.06.003openalex-snapshot
Human adaptation over the past 40,000 years
inferred← citeshttps://doi.org/10.1016/j.isci.2023.106130openalex-snapshot
Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations
inferred← citeshttps://doi.org/10.1016/j.neures.2024.10.002openalex-snapshot
Bayesian estimation of trunk-leg coordination during walking using phase oscillator models
inferred← citeshttps://doi.org/10.1016/j.patter.2021.100212openalex-snapshot
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
inferred← citeshttps://doi.org/10.1016/j.pt.2025.03.012openalex-snapshot
Potential and pitfalls of using identity-by-descent for malaria genomic surveillance
inferred← citeshttps://doi.org/10.1016/j.softx.2018.09.003openalex-snapshot
SimPrily: A Python framework to simplify high-throughput genomic simulations
inferred← citeshttps://doi.org/10.1016/j.tig.2019.12.008openalex-snapshot
From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection
inferred← citeshttps://doi.org/10.1016/j.tpb.2019.03.005openalex-snapshot
An empirical approach to demographic inference with genomic data
inferred← citeshttps://doi.org/10.1016/j.tpb.2020.02.002openalex-snapshot
Developments in coalescent theory from single loci to chromosomes
inferred← citeshttps://doi.org/10.1016/j.tpb.2020.03.004openalex-snapshot
Testing for population decline using maximal linkage disequilibrium blocks
inferred← citeshttps://doi.org/10.1016/j.tpb.2021.06.003openalex-snapshot
The distribution of waiting distances in ancestral recombination graphs
inferred← citeshttps://doi.org/10.1016/j.tpb.2023.09.002openalex-snapshot
Estimating the Lambda measure in multiple-merger coalescents
inferred← citeshttps://doi.org/10.1016/j.xgen.2025.100782openalex-snapshot
A highland-adaptation variant near MCUR1 reduces its transcription and attenuates erythrogenesis in Tibetans
inferred← citeshttps://doi.org/10.1016/j.xgen.2025.101072openalex-snapshot
Leveraging ancestral recombination graphs for scalable mixed-model analysis of complex traits
inferred← citeshttps://doi.org/10.1016/j.xhgg.2020.100017openalex-snapshot
Inclusion of variants discovered from diverse populations improves polygenic risk score transferability
inferred← citeshttps://doi.org/10.1016/j.ympev.2022.107505openalex-snapshot
Phylogenetics in space: How continuous spatial structure impacts tree inference
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107724openalex-snapshot
Comparing inference under the multispecies coalescent with and without recombination
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108142openalex-snapshot
Tracing the genealogy origin of geographic populations based on genomic variation and deep learning
inferred← citeshttps://doi.org/10.1038/s10038-024-01249-2openalex-snapshot
Heritability of complex traits in sub-populations experiencing bottlenecks and growth
inferred← citeshttps://doi.org/10.1038/s41431-020-0639-3openalex-snapshot
The exhaustive genomic scan approach, with an application to rare-variant association analysis
inferred← citeshttps://doi.org/10.1038/s41431-020-0699-4openalex-snapshot
Differences in local population history at the finest level: the case of the Estonian population
inferred← citeshttps://doi.org/10.1038/s41437-021-00471-4openalex-snapshot
Rank-invariant estimation of inbreeding coefficients
inferred← citeshttps://doi.org/10.1038/s41437-021-00475-0openalex-snapshot
The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial
inferred← citeshttps://doi.org/10.1038/s41437-025-00773-xopenalex-snapshot
Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data
inferred← citeshttps://doi.org/10.1038/s41467-018-04963-6openalex-snapshot
The origin and remolding of genomic islands of differentiation in the European sea bass
inferred← citeshttps://doi.org/10.1038/s41467-020-18335-6openalex-snapshot
Factor analysis of ancient population genomic samples
inferred← citeshttps://doi.org/10.1038/s41467-021-25435-4openalex-snapshot
Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans
inferred← citeshttps://doi.org/10.1038/s41467-021-25524-4openalex-snapshot
Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures
inferred← citeshttps://doi.org/10.1038/s41467-022-28800-zopenalex-snapshot
Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
inferred← citeshttps://doi.org/10.1038/s41467-022-29584-yopenalex-snapshot
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks
inferred← citeshttps://doi.org/10.1038/s41467-022-31581-0openalex-snapshot
Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference
inferred← citeshttps://doi.org/10.1038/s41467-022-34461-9openalex-snapshot
Prioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection
inferred← citeshttps://doi.org/10.1038/s41467-023-36167-yopenalex-snapshot
Inversions maintain differences between migratory phenotypes of a songbird
inferred← citeshttps://doi.org/10.1038/s41467-023-38930-7openalex-snapshot
Optimal strategies for learning multi-ancestry polygenic scores vary across traits
inferred← citeshttps://doi.org/10.1038/s41467-023-40052-zopenalex-snapshot
The genomic footprint of whaling and isolation in fin whale populations
inferred← citeshttps://doi.org/10.1038/s41467-023-43522-6openalex-snapshot
Haplotype-based inference of recent effective population size in modern and ancient DNA samples
inferred← citeshttps://doi.org/10.1038/s41467-023-43717-xopenalex-snapshot
Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations
inferred← citeshttps://doi.org/10.1038/s41467-024-46161-7openalex-snapshot
The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
inferred← citeshttps://doi.org/10.1038/s41467-024-47618-5openalex-snapshot
Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck
inferred← citeshttps://doi.org/10.1038/s41467-024-55477-3openalex-snapshot
Leveraging haplotype information in heritability estimation and polygenic prediction
inferred← citeshttps://doi.org/10.1038/s41467-025-56273-3openalex-snapshot
STICI: Split-Transformer with integrated convolutions for genotype imputation
inferred← citeshttps://doi.org/10.1038/s41467-025-59936-3openalex-snapshot
Tracing human genetic histories and natural selection with precise local ancestry inference
inferred← citeshttps://doi.org/10.1038/s41467-025-61574-8openalex-snapshot
SimOutbreakSelection: a simulation-based tool to optimise sampling design and analysis strategies for detecting epidemic-driven selection
inferred← citeshttps://doi.org/10.1038/s41559-018-0735-8openalex-snapshot
Multiple episodes of interbreeding between Neanderthal and modern humans
inferred← citeshttps://doi.org/10.1038/s41559-019-0807-4openalex-snapshot
Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa
inferred← citeshttps://doi.org/10.1038/s41559-019-0881-7openalex-snapshot
Ancient admixture from an extinct ape lineage into bonobos
inferred← citeshttps://doi.org/10.1038/s41559-022-01753-8openalex-snapshot
A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears
inferred← citeshttps://doi.org/10.1038/s41559-023-02145-2openalex-snapshot
Ghost admixture in eastern gorillas
inferred← citeshttps://doi.org/10.1038/s41559-024-02591-6openalex-snapshot
Ignoring population structure in hominin evolutionary models can lead to the inference of spurious admixture events
inferred← citeshttps://doi.org/10.1038/s41559-025-02919-wopenalex-snapshot
Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism
inferred← citeshttps://doi.org/10.1038/s41576-020-0269-1openalex-snapshot
Host–parasite co-evolution and its genomic signature
inferred← citeshttps://doi.org/10.1038/s41576-024-00772-4openalex-snapshot
Inference and applications of ancestral recombination graphs
inferred← citeshttps://doi.org/10.1038/s41586-019-1279-zopenalex-snapshot
The population history of northeastern Siberia since the Pleistocene
inferred← citeshttps://doi.org/10.1038/s41586-020-2302-0openalex-snapshot
A positively selected FBN1 missense variant reduces height in Peruvian individuals
inferred← citeshttps://doi.org/10.1038/s41586-020-2930-4openalex-snapshot
Drivers and dynamics of a massive adaptive radiation in cichlid fishes
inferred← citeshttps://doi.org/10.1038/s41586-021-03205-yopenalex-snapshot
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
inferred← citeshttps://doi.org/10.1038/s41586-023-06055-yopenalex-snapshot
A weakly structured stem for human origins in Africa
inferred← citeshttps://doi.org/10.1038/s41586-023-06831-wopenalex-snapshot
Indigenous Australian genomes show deep structure and rich novel variation
inferred← citeshttps://doi.org/10.1038/s41586-024-07312-4openalex-snapshot
Network of large pedigrees reveals social practices of Avar communities
inferred← citeshttps://doi.org/10.1038/s41586-024-07881-4openalex-snapshot
Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas
inferred← citeshttps://doi.org/10.1038/s41586-024-08275-2openalex-snapshot
High-resolution genomic history of early medieval Europe
inferred← citeshttps://doi.org/10.1038/s41586-025-09103-xopenalex-snapshot
Ancient DNA reveals a two-clanned matrilineal community in Neolithic China
inferred← citeshttps://doi.org/10.1038/s41588-018-0101-4openalex-snapshot
Signatures of negative selection in the genetic architecture of human complex traits
inferred← citeshttps://doi.org/10.1038/s41588-019-0483-yopenalex-snapshot
Inferring whole-genome histories in large population datasets
inferred← citeshttps://doi.org/10.1038/s41588-019-0484-xopenalex-snapshot
A method for genome-wide genealogy estimation for thousands of samples
inferred← citeshttps://doi.org/10.1038/s41588-023-01379-xopenalex-snapshot
Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits
inferred← citeshttps://doi.org/10.1038/s41588-023-01487-8openalex-snapshot
Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies
inferred← citeshttps://doi.org/10.1038/s41588-025-02129-xopenalex-snapshot
A likelihood-based framework for demographic inference from genealogical trees
inferred← citeshttps://doi.org/10.1038/s41588-025-02317-9openalex-snapshot
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
inferred← citeshttps://doi.org/10.1038/s41598-019-43320-5openalex-snapshot
Possible activation of NRF2 by Vitamin E/Curcumin against altered thyroid hormone induced oxidative stress via NFĸB/AKT/mTOR/KEAP1 signalling in rat heart
inferred← citeshttps://doi.org/10.1038/s41598-020-61216-7openalex-snapshot
A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm
inferred← citeshttps://doi.org/10.1038/s41598-023-28927-zopenalex-snapshot
Genetic and demographic consequences of range contraction patterns during biological annihilation
inferred← citeshttps://doi.org/10.1038/s43588-024-00739-9openalex-snapshot
Enabling efficient analysis of biobank-scale data with genotype representation graphs
inferred← citeshttps://doi.org/10.1073/pnas.1800334115openalex-snapshot
Whole-genome data reveal the complex history of a diverse ecological community
inferred← citeshttps://doi.org/10.1073/pnas.1814338116openalex-snapshot
Limits of long-term selection against Neandertal introgression
inferred← citeshttps://doi.org/10.1073/pnas.1905060116openalex-snapshot
Inference of complex population histories using whole-genome sequences from multiple populations
inferred← citeshttps://doi.org/10.1073/pnas.2013798118openalex-snapshot
Nonparametric coalescent inference of mutation spectrum history and demography
inferred← citeshttps://doi.org/10.1073/pnas.2102914118openalex-snapshot
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao , the chocolate tree
inferred← citeshttps://doi.org/10.1073/pnas.2200858119openalex-snapshot
Estimating bonobo ( Pan paniscus ) and chimpanzee ( Pan troglodytes ) evolutionary history from nucleotide site patterns
inferred← citeshttps://doi.org/10.1073/pnas.2315780121openalex-snapshot
Detecting inbreeding depression in structured populations
inferred← citeshttps://doi.org/10.1073/pnas.2504461122openalex-snapshot
A general framework for branch length estimation in Ancestral Recombination Graphs
inferred← citeshttps://doi.org/10.1073/pnas.2514371123openalex-snapshot
Large future genetic diversity losses are predicted from conservation indicators even with habitat protection
inferred← citeshttps://doi.org/10.1073/pnas.2514614122openalex-snapshot
Evolutionary histories of functional mutations during the domestication and spread of japonica rice in Asia
inferred← citeshttps://doi.org/10.1073/pnas.2600483123openalex-snapshot
Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone
inferred← citeshttps://doi.org/10.1080/00071668.2023.2249840openalex-snapshot
Genome-wide association analysis of neck ring traits in NongHua ma male ducks
inferred← citeshttps://doi.org/10.1080/01621459.2019.1635482openalex-snapshot
Efficiently Inferring the Demographic History of Many Populations With Allele Count Data
inferred← citeshttps://doi.org/10.1080/10618600.2019.1647215openalex-snapshot
Efficient Construction of Test Inversion Confidence Intervals Using Quantile Regression
inferred← citeshttps://doi.org/10.1086/710022openalex-snapshot
The Origin and Spread of Locally Adaptive Seasonal Camouflage in Snowshoe Hares
inferred← citeshttps://doi.org/10.1086/733456openalex-snapshot
Genetic Architecture, Spatial Heterogeneity, and the Arms Race between Newts and Snakes: Exploring Coevolution with Simulations
inferred← citeshttps://doi.org/10.1086/741060openalex-snapshot
Asymmetric Gene Flow Maintains Range Edges in a Marine Invertebrate
inferred← citeshttps://doi.org/10.1088/1742-6596/1740/1/012031openalex-snapshot
Deep learning based methods for estimating distribution of coalescence rates from genome-wide data
inferred← citeshttps://doi.org/10.1089/cmb.2023.0086openalex-snapshot
A Clonal Evolution Simulator for Planning Somatic Evolution Studies
inferred← citeshttps://doi.org/10.1093/aob/mcag277openalex-snapshot
Novel Arctic colonization origin of the Arctic lineage in Phyllodoce (Ericaceae)
inferred← citeshttps://doi.org/10.1093/bib/bbab093openalex-snapshot
eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects
inferred← citeshttps://doi.org/10.1093/bib/bbab300openalex-snapshot
Local ancestry inference in heterogeneous populations—Are recent recombination events more relevant?
inferred← citeshttps://doi.org/10.1093/bioadv/vbac045openalex-snapshot
P-smoother: efficient PBWT smoothing of large haplotype panels
inferred← citeshttps://doi.org/10.1093/bioadv/vbad163openalex-snapshot
link-ancestors: fast simulation of local ancestry with tree sequence software
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf205openalex-snapshot
IGD: a simple, efficient genotype data format
inferred← citeshttps://doi.org/10.1093/bioadv/vbag040openalex-snapshot
Fast phenotype simulation for genotype representation graphs
inferred← citeshttps://doi.org/10.1093/bioadv/vbag078openalex-snapshot
RaPID2: a parallel scalable framework for identity-by-descent segment detection via parallel PBWT
inferred← citeshttps://doi.org/10.1093/bioadv/vbag125openalex-snapshot
EGGS: Empirical Genotype Generalizer for Samples
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa486openalex-snapshot
ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab261openalex-snapshot
GSpace: an exact coalescence simulator of recombining genomes under isolation by distance
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab351openalex-snapshot
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab489openalex-snapshot
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac012openalex-snapshot
An accurate method for identifying recent recombinants from unaligned sequences
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad312openalex-snapshot
RaPID-Query for fast identity by descent search and genealogical analysis
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad535openalex-snapshot
HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae334openalex-snapshot
tstrait : a quantitative trait simulator for ancestral recombination graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf393openalex-snapshot
Tsbrowse: an interactive browser for Ancestral Recombination Graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag438openalex-snapshot
ARGformer: learning on ancestral recombination graphs with transformers
inferred← citeshttps://doi.org/10.1093/bioinformatics/btag511openalex-snapshot
Faster inference of complex demographic models from large allele frequency spectra
inferred← citeshttps://doi.org/10.1093/bioinformatics/btw355openalex-snapshot
ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty184openalex-snapshot
POPdemog: visualizing population demographic history from simulation scripts
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty197openalex-snapshot
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty840openalex-snapshot
MetaSMC: a coalescent-based shotgun sequence simulator for evolving microbial populations
inferred← citeshttps://doi.org/10.1093/evlett/qraf053openalex-snapshot
Genomic analyses in Drosophila do not support the classic allopatric model of speciation
inferred← citeshttps://doi.org/10.1093/evolut/qpac013openalex-snapshot
The efficacy of selection may increase or decrease with selfing depending upon the recombination environment
inferred← citeshttps://doi.org/10.1093/g3journal/jkaa036openalex-snapshot
Visualizing population structure with variational autoencoders
inferred← citeshttps://doi.org/10.1093/g3journal/jkac012openalex-snapshot
Predicting the genomic resolution of bulk segregant analysis
inferred← citeshttps://doi.org/10.1093/g3journal/jkac029openalex-snapshot
The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean
inferred← citeshttps://doi.org/10.1093/g3journal/jkad165openalex-snapshot
Identity-by-descent-based estimation of the X chromosome effective population size with application to sex-specific demographic history
inferred← citeshttps://doi.org/10.1093/g3journal/jkae058openalex-snapshot
Estimating between-country migration in pneumococcal populations
inferred← citeshttps://doi.org/10.1093/g3journal/jkaf088openalex-snapshot
Allele age estimators designed for whole-genome datasets show only a moderate reduction in performance when applied to whole-exome datasets
inferred← citeshttps://doi.org/10.1093/g3journal/jkaf172openalex-snapshot
Estimating allele frequencies, ancestry proportions and genotype likelihoods in the presence of mapping bias
inferred← citeshttps://doi.org/10.1093/g3journal/jkag100openalex-snapshot
High-resolution analysis of recent population structure using rare variants
inferred← citeshttps://doi.org/10.1093/g3journal/jkag114openalex-snapshot
On the use of generative models for demographic inference in malaria vectors from genomic data
inferred← citeshttps://doi.org/10.1093/g3journal/jkag140openalex-snapshot
diempy: fast and reference-free genome polarization and chromosome painting
inferred← citeshttps://doi.org/10.1093/gbe/evab025openalex-snapshot
A Chromosome-Painting-Based Pipeline to Infer Local Ancestry under Limited Source Availability
inferred← citeshttps://doi.org/10.1093/gbe/evab115openalex-snapshot
Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture
inferred← citeshttps://doi.org/10.1093/gbe/evac016openalex-snapshot
Controlling for Variable Transposition Rate with an Age-Adjusted Site Frequency Spectrum
inferred← citeshttps://doi.org/10.1093/gbe/evad040openalex-snapshot
Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing
inferred← citeshttps://doi.org/10.1093/gbe/evad223openalex-snapshot
Novel Insights into the Landscape of Crossover and Noncrossover Events in Rhesus Macaques ( Macaca mulatta )
inferred← citeshttps://doi.org/10.1093/gbe/evae050openalex-snapshot
Background Selection From Unlinked Sites Causes Nonindependent Evolution of Deleterious Mutations
inferred← citeshttps://doi.org/10.1093/gbe/evaf097openalex-snapshot
Parameter Scaling in Population Genetics Simulations may Introduce Unintended Background Selection: Considerations for Scaled Simulation Design
inferred← citeshttps://doi.org/10.1093/genetics/iyaa045openalex-snapshot
Assessing the performance of qpAdm: a statistical tool for studying population admixture
inferred← citeshttps://doi.org/10.1093/genetics/iyab052openalex-snapshot
The timing of human adaptation from Neanderthal introgression
inferred← citeshttps://doi.org/10.1093/genetics/iyab119openalex-snapshot
Sweeps in time: leveraging the joint distribution of branch lengths
inferred← citeshttps://doi.org/10.1093/genetics/iyab229openalex-snapshot
Efficient ancestry and mutation simulation with msprime 1.0
inferred← citeshttps://doi.org/10.1093/genetics/iyac038openalex-snapshot
Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples
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