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References from Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent. Local targets link to admitted publications; unresolved targets remain external evidence.
Selection, recombination, and the ancestral initiation graph
10.1016/j.tpb.2021.08.001 · 2021 · External reference
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models
10.7717/peerj.786 · 2015 · External reference
Sweepstakes reproductive success via pervasive and recurrent selective sweeps
10.7554/elife.80781.sa2 · 2023 · External reference
10.24072/pcjournal.267 · 2023 · Admitted local publication
Inference of recombination maps from a single pair of genomes and its application to ancient samples
10.1371/journal.pgen.1008449 · 2019 · External reference
Predicting geographic location from genetic variation with deep neural networks
10.7554/elife.54507 · 2020 · External reference
Efficient ancestry and mutation simulation with msprime 1.0
10.1093/genetics/iyab229 · 2021 · External reference
An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution
10.1534/genetics.112.144329 · 2013 · External reference
A modified lookdown construction for the Xi-Fleming-Viot process with mutation and populations with recurrent bottlenecks
10.48550/arxiv.0808.0412 · 2008 · External reference
Coalescent results for diploid exchangeable population models
10.1214/18-ejp175 · 2018 · External reference
Sweeps in time: leveraging the joint distribution of branch lengths
10.1093/genetics/iyab119 · 2021 · External reference
The seed bank coalescent with simultaneous switching
10.1214/19-ejp401 · 2020 · External reference
Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
10.1371/journal.pgen.1005877 · 2016 · External reference
On Ruelle's probability cascades and an abstract cavity method
10.1007/s002200050450 · 1998 · External reference
Evaluation of methods for estimating coalescence times using ancestral recombination graphs
10.1093/genetics/iyac044 · 2022 · External reference
The Promise of Inferring the Past using the Ancestral Recombination Graph (ARG)
10.1093/gbe/evae005 · 2024 · External reference
Geometric Deep Learning: Going beyond Euclidean data
10.1109/msp.2017.2693418 · 2017 · External reference
Noisy traveling waves: Effect of selection on genealogies
10.1209/epl/i2006-10224-4 · 2006 · External reference
Effect of selection on ancestry: An exactly soluble case and its phenomenological generalization
10.1103/physreve.76.041104 · 2007 · External reference
Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown
10.1371/journal.pcbi.1010407 · 2022 · External reference
A Comprehensive Survey on Geometric Deep Learning
10.1109/access.2020.2975067 · 2020 · External reference
The Symmetric Coalescent and Wright-Fisher models with bottlenecks
10.48550/arxiv.1903.05642 · 2020 · External reference
Population size may shape the accumulation of functional mutations following domestication
10.1186/s12862-018-1120-6 · 2018 · External reference
Population size may shape the accumulation of functional mutations following domestication
10.1186/s12862-018-1120-6 · 2018 · External reference
Adaptive value, entropy and survivorship curves
10.1038/275213a0 · 1978 · External reference
On the length of an external branch in the Beta-coalescent
10.1016/j.spa.2012.12.010 · 2013 · External reference
Bursts of coalescence within population pedigrees whenever big families occur
10.1101/2023.10.17.562743 · 2023 · External reference
Particle representations for measure-valued population models
10.1214/aop/1022677258 · 1999 · External reference
A coalescent model for the effect of advantageous mutations on the genealogy of a population
10.1016/j.spa.2005.04.009 · 2005 · External reference
Beyond the standard coalescent: demographic inference with complete genomes and graph neural networks under the beta coalescent
10.24072/pci.evolbiol.100699 · 2024 · External reference
Coalescent processes when the distribution of offspring number among individuals is highly skewed
10.1534/genetics.105.052175 · 2006 · External reference
Can the Site-Frequency Spectrum Distinguish Exponential Population Growth from Multiple-Merger Coalescents?
10.1534/genetics.114.173807 · 2015 · External reference
Fast Graph Representation Learning with PyTorch Geometric
10.48550/arxiv.1903.02428 · 2019 · External reference
The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference
10.1093/molbev/msy224 · 2018 · External reference
Interpreting the pervasive observation of U-shaped Site Frequency Spectra
10.1371/journal.pgen.1010677 · 2023 · External reference
Inferring population size changes with sequence and SNP data: lessons from human bottlenecks
10.1038/hdy.2012.120 · 2013 · External reference
Inferring Past Effective Population Size from Distributions of Coalescent Times
10.1534/genetics.115.185058 · 2016 · External reference
Tree‐sequence recording in SLiM opens new horizons for forward‐time simulation of whole genomes
10.1111/1755-0998.12968 · 2019 · External reference
Considering Genomic Scans for Selection as Coalescent Model Choice
10.1093/gbe/evaa093 · 2020 · External reference
Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and Commentary
10.5343/bms.2010.1051 · 2011 · External reference
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph
10.1093/molbev/msab332 · 2021 · External reference
Inference of Ancestral Recombination Graphs Using ARGweaver
10.1007/978-1-0716-0199-0_10 · 2020 · External reference
Properties of a neutral allele model with intragenic recombination
10.1016/0040-5809(83)90013-8 · 1983 · External reference
Aleatoric and epistemic uncertainty in machine learning: an introduction to concepts and methods
10.1007/s10994-021-05946-3 · 2021 · External reference
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks
10.1111/1755-0998.13379 · 2021 · External reference
Recommendations for improving statistical inference in population genomics
10.1371/journal.pbio.3001669 · 2022 · External reference
Toward an Evolutionarily Appropriate Null Model: Jointly Inferring Demography and Purifying Selection
10.1534/genetics.119.303002 · 2020 · External reference
The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects
10.1093/molbev/msab050 · 2021 · External reference
Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer
10.1098/rsos.171060 · 2017 · External reference
Efficient pedigree recording for fast population genetics simulation
10.1371/journal.pcbi.1006581 · 2018 · External reference
Inferring whole-genome histories in large population datasets
10.1038/s41588-019-0483-y · 2019 · External reference
The evolving beta coalescent
10.1214/ejp.v19-3332 · 2014 · External reference
Exact decoding of the sequentially Markov coalescent
10.1101/2020.09.21.307355 · 2020 · External reference
How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories
10.1089/cmb.2019.0318 · 2020 · External reference
The Coalescent
10.1016/0304-4149(82)90011-4 · 1982 · External reference
Semi-Supervised Classification with Graph Convolutional Networks
10.48550/arxiv.1609.02907 · 2016 · External reference
Kevin Korfmann/GNNcoal: GNNcoal (PCI recommendation)
10.5281/zenodo.10781643 · 2024 · External reference
Kevin Korfmann/GNNcoal-analysis: GNNcoal-analysis (PCI recommendation)
10.5281/zenodo.10781640 · 2024 · External reference
Supplementary Information for "Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent" publication. In PCJ.
10.5281/zenodo.10792836 · 2024 · External reference
Deep Learning in Population Genetics
10.1093/gbe/evad008 · 2023 · External reference
Multi-locus data distinguishes between population growth and multiple merger coalescents
10.1515/sagmb-2017-0011 · 2018 · External reference
Robust model selection between population growth and multiple merger coalescents
10.1016/j.mbs.2019.03.004 · 2019 · External reference
Graph Classification using Structural Attention
10.1145/3219819.3219980 · 2018 · External reference
The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics
10.1371/journal.pgen.1011110 · 2024 · External reference
Inference of human population history from individual whole-genome sequences
10.1038/nature10231 · 2011 · External reference
Bayesian inference of ancestral recombination graphs
10.1371/journal.pcbi.1009960 · 2022 · External reference
A genomic history of Aboriginal Australia
10.1038/nature18299 · 2016 · External reference
Fast "coalescent" simulation
10.1186/1471-2156-7-16 · 2006 · External reference
Coalescent Processes with Skewed Offspring Distributions and Nonequilibrium Demography
10.1534/genetics.117.300499 · 2018 · External reference
Approximating the coalescent with recombination
10.1098/rstb.2005.1673 · 2005 · External reference
Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis
10.1093/molbev/msaa179 · 2020 · External reference
cggh/scikit-allel: v1.3.3
10.5281/zenodo.4759368 · 2021 · External reference
A classification of coalescent processes for haploid exchangeable population models
10.1214/aop/1015345761 · 2001 · External reference
Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution
10.1111/evo.13954 · 2020 · External reference
Genealogies of rapidly adapting populations
10.1073/pnas.1213113110 · 2013 · External reference
Accounting for long-range correlations in genome-wide simulations of large cohorts
10.1371/journal.pgen.1008619 · 2020 · External reference
Reproductive skew in Japanese sardine inferred from DNA sequences
10.1093/icesjms/fsw070 · 2016 · External reference
Automatic differentiation in PyTorch
2017 · External reference
Coalescents with multiple collisions
10.1214/aop/1022677552 · 1999 · External reference
Deciphering signatures of natural selection via deep learning
10.1101/2021.05.27.445973 · 2021 · External reference
Genome-Wide Inference of Ancestral Recombination Graphs
10.1371/journal.pgen.1004342 · 2014 · External reference
Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra
10.1101/461517 · 2018 · External reference
Linkage Disequilibrium Between Loci With Unknown Phase
10.1534/genetics.108.093153 · 2009 · External reference
Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions
10.1534/genetics.118.301684 · 2019 · External reference
Convergence to the coalescent with simultaneous multiple mergers
10.1239/jap/1067436085 · 2003 · External reference
The general coalescent with asynchronous mergers of ancestral lines
10.1239/jap/1032374759 · 1999 · External reference
Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation
10.1111/1755-0998.13224 · 2020 · External reference
Current progress and open challenges for applying deep learning across the biosciences
10.1038/s41467-022-29268-7 · 2022 · External reference
A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms
10.1016/j.tpb.2008.04.009 · 2008 · External reference
Inferring human population size and separation history from multiple genome sequences
10.1038/ng.3015 · 2014 · External reference
Modeling Relational Data with Graph Convolutional Networks
10.48550/arxiv.1703.06103 · 2017 · External reference
Coalescent processes obtained from supercritical Galton-Watson processes
10.1016/s0304-4149(03)00028-0 · 2003 · External reference
Sellinger, Thibaut/eSMC2: eSMC2 : 5.1.3
10.5281/zenodo.10782372 · 2024 · External reference
Limits and convergence properties of the sequentially Markovian coalescent
10.1111/1755-0998.13416 · 2021 · External reference
Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data
10.1371/journal.pgen.1008698 · 2020 · External reference
Deep Learning for Population Genetic Inference
10.1371/journal.pcbi.1004845 · 2016 · External reference
A method for genome-wide genealogy estimation for thousands of samples
10.1038/s41588-019-0484-x · 2019 · External reference
Analysis of DNA sequence variation within marine species using Beta-coalescents
10.1371/journal.pcbi.1010419 · 2013 · External reference
Selective Sweeps
10.1534/genetics.118.301319 · 2019 · External reference
Inference of evolutionary transitions to self-fertilization using whole-genome sequences
2022 · External reference
Coalescence 2.0: a multiple branching of recent theoretical developments and their applications
10.1111/mec.12755 · 2014 · External reference
Robust and scalable inference of population history froth hundreds of unphased whole genomes
10.1038/ng.3748 · 2017 · External reference
Robust Inference of Population Size Histories from Genomic Sequencing Data
10.1101/2021.05.22.445274 · 2021 · External reference
Tracking human population structure through time from whole genome sequences
10.1371/journal.pgen.1008552 · 2020 · External reference
Automatic inference of demographic parameters using generative adversarial networks
10.1111/1755-0998.13386 · 2021 · External reference
Tree sequences as a general-purpose tool for population genetic inference
10.1101/2024.02.20.581288 · 2024 · External reference
The SMC' Is a Highly Accurate Approximation to the Ancestral Recombination Graph
10.1534/genetics.114.173898 · 2015 · External reference
Recombination as a point process along sequences
10.1006/tpbi.1998.1403 · 1999 · External reference
A general and efficient representation of ancestral recombination graphs
10.1101/2023.11.03.565466 · 2023 · External reference
How Powerful are Graph Neural Networks?
10.48550/arxiv.1810.00826 · 2019 · External reference
Revisiting Semi-Supervised Learning with Graph Embeddings
10.48550/arxiv.1603.08861 · 2016 · External reference
Creating artificial human genomes using generative neural networks
10.1371/journal.pgen.1009303 · 2021 · External reference
Hierarchical Graph Representation Learning with Differentiable Pooling
10.48550/arxiv.1806.08804 · 2019 · External reference
Link Prediction Based on Graph Neural Networks
2018 · External reference
Graph neural networks: A review of methods and applications
10.1016/j.aiopen.2021.01.001 · 2020 · External reference
