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Inferring the landscape of recombination using recurrent neural networks

https://doi.org/10.1101/662247
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-540-71021-9openalex-snapshot
Molecular Genetics of Recombination
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ImageNet Large Scale Visual Recognition Challenge
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Animal cytology and evolution
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Variation in Recombination Rate: Adaptive or Not?
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Supervised Machine Learning for Population Genetics: A New Paradigm
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On the minimum number of topologies explaining a sample of DNA sequences
inferredcites →https://doi.org/10.1016/s0169-5347(01)02187-5openalex-snapshot
Chromosomal rearrangements and speciation
inferredcites →https://doi.org/10.1016/s0959-437x(98)80142-1openalex-snapshot
Recombination at work for meiosis
inferredcites →https://doi.org/10.1016/s0960-9822(01)00131-2openalex-snapshot
Meiotic recombination: Breaking the genome to save it
inferredcites →https://doi.org/10.1017/s0016672300002391openalex-snapshot
Development of associative overdominance through linkage disequilibrium in finite populations
inferredcites →https://doi.org/10.1017/s001667230000272xopenalex-snapshot
Linkage disequilibrium due to random genetic drift
inferredcites →https://doi.org/10.1017/s0016672300010156openalex-snapshot
The effect of linkage on limits to artificial selection
inferredcites →https://doi.org/10.1017/s0016672300014634openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1017/s0016672300023776openalex-snapshot
Estimating the recombination parameter of a finite population model without selection
inferredcites →https://doi.org/10.1017/s0016672300033140openalex-snapshot
A general model for the evolution of recombination
inferredcites →https://doi.org/10.1017/s0016672301004967openalex-snapshot
Why is there so little intragenic linkage disequilibrium in humans ?
inferredcites →https://doi.org/10.1017/s0016672301005407openalex-snapshot
Chromosomal inversion polymorphism in Afrotropical populations of Drosophila melanogaster
inferredcites →https://doi.org/10.1017/s001667230800949xopenalex-snapshot
The effect of linkage on limits to artificial selection
inferredcites →https://doi.org/10.1017/s0016672308009579openalex-snapshot
The hitch-hiking effect of a favourable gene
inferredcites →https://doi.org/10.1017/s0016672396002571openalex-snapshot
Using the variance of pairwise differences to estimate the recombination rate
inferredcites →https://doi.org/10.1038/nature09525openalex-snapshot
Fine-scale recombination rate differences between sexes, populations and individuals
inferredcites →https://doi.org/10.1038/nature10336openalex-snapshot
The landscape of recombination in African Americans
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/ng.3015openalex-snapshot
Inferring human population size and separation history from multiple genome sequences
inferredcites →https://doi.org/10.1038/ng.3211openalex-snapshot
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
inferredcites →https://doi.org/10.1038/ng.3254openalex-snapshot
Exploring population size changes using SNP frequency spectra
inferredcites →https://doi.org/10.1038/ng.3748openalex-snapshot
Robust and scalable inference of population history from hundreds of unphased whole genomes
inferredcites →https://doi.org/10.1038/ng1001-217openalex-snapshot
Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex
inferredcites →https://doi.org/10.1038/ng1287openalex-snapshot
Intense and highly localized gene conversion activity in human meiotic crossover hot spots
inferredcites →https://doi.org/10.1073/pnas.1019276108openalex-snapshot
Demographic history and rare allele sharing among human populations
inferredcites →https://doi.org/10.1073/pnas.221274498openalex-snapshot
Chromosomal inversions and the reproductive isolation of species
inferredcites →https://doi.org/10.1073/pnas.34.4.137openalex-snapshot
The Suppression of Crossing Over in Inversion Heterozygotes of Drosophila Pseudoobscura
inferredcites →https://doi.org/10.1073/pnas.7.8.235openalex-snapshot
A Case of Rearrangement of Genes in Drosophila
inferredcites →https://doi.org/10.1086/280418openalex-snapshot
Some Genetic Aspects of Sex
inferredcites →https://doi.org/10.1093/aibsbulletin/2.2.14-bopenalex-snapshot
Genetics and the Origin of Species
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Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/btw556openalex-snapshot
Discoal: flexible coalescent simulations with selection
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/137.1.331openalex-snapshot
Linkage disequilibrium in growing and stable populations.
inferredcites →https://doi.org/10.1093/genetics/137.4.1019openalex-snapshot
Meiotic gene conversion tract length distribution within the rosy locus of Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/147.2.879openalex-snapshot
The Evolution of Recombination: Removing the Limits to Natural Selection
inferredcites →https://doi.org/10.1093/genetics/159.2.647openalex-snapshot
Patterns of DNA Sequence Variation Suggest the Recent Action of Positive Selection in the janus-ocnus Region of Drosophila simulans
inferredcites →https://doi.org/10.1093/genetics/160.3.1231openalex-snapshot
A Coalescent-Based Method for Detecting and Estimating Recombination From Gene Sequences
inferredcites →https://doi.org/10.1093/genetics/163.1.375openalex-snapshot
Bounds on the Minimum Number of Recombination Events in a Sample History
inferredcites →https://doi.org/10.1093/genetics/165.4.2213openalex-snapshot
Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data
inferredcites →https://doi.org/10.1093/genetics/39.2.197openalex-snapshot
AN ANALYSIS OF CROSSING OVER WITHIN A HETEROZYGOUS INVERSION IN DROSOPHILA MELANOGASTER
inferredcites →https://doi.org/10.1093/genetics/78.1.205openalex-snapshot
CHROMOSOME SEGREGATION MECHANISMS
inferredcites →https://doi.org/10.1093/genetics/83.1.181openalex-snapshot
RECOMBINATION MODIFICATION IN A FLUCTUATING ENVIRONMENT
inferredcites →https://doi.org/10.1093/molbev/msy224openalex-snapshot
The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026228openalex-snapshot
A Comparison of Estimators of the Population Recombination Rate
inferredcites →https://doi.org/10.1101/267211openalex-snapshot
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks
inferredcites →https://doi.org/10.1101/504126openalex-snapshot
Extensive recombination suppression and chromosome-wide differentiation of a segregation distorter in Drosophila
inferredcites →https://doi.org/10.1101/cshperspect.a016626openalex-snapshot
Recombination, Pairing, and Synapsis of Homologs during Meiosis
inferredcites →https://doi.org/10.1101/gr.067181.107openalex-snapshot
Confounding between recombination and selection, and the Ped/Pop method for detecting selection
inferredcites →https://doi.org/10.1101/sqb.1951.016.01.015openalex-snapshot
INTERCHROMOSOMAL EFFECTS ON CROSSING OVER IN DROSOPHILA
inferredcites →https://doi.org/10.1109/5.726791openalex-snapshot
Gradient-based learning applied to document recognition
inferredcites →https://doi.org/10.1109/asru.2013.6707742openalex-snapshot
Hybrid speech recognition with Deep Bidirectional LSTM
inferredcites →https://doi.org/10.1109/cvpr.2015.7298594openalex-snapshot
Going deeper with convolutions
inferredcites →https://doi.org/10.1109/msp.2012.2205597openalex-snapshot
Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups
inferredcites →https://doi.org/10.1111/j.0014-3820.2000.tb00038.xopenalex-snapshot
PERSPECTIVE: SEX, RECOMBINATION, AND THE EFFICACY OF SELECTION?WAS WEISMANN RIGHT?
inferredcites →https://doi.org/10.1111/j.1558-5646.1960.tb03113.xopenalex-snapshot
THE EVOLUTIONARY DYNAMICS OF COMPLEX POLYMORPHISMS,,
inferredcites →https://doi.org/10.1111/j.1558-5646.2012.01836.xopenalex-snapshot
REPRODUCTIVE ISOLATION AND LOCAL ADAPTATION QUANTIFIED FOR A CHROMOSOME INVERSION IN A MALARIA MOSQUITO
inferredcites →https://doi.org/10.1111/mec.13932openalex-snapshot
Recombination rate variation in mice from an isolated island
inferredcites →https://doi.org/10.1126/science.1105322openalex-snapshot
Comparison of Fine-Scale Recombination Rates in Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1117196openalex-snapshot
A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome
inferredcites →https://doi.org/10.1126/science.1190371openalex-snapshot
Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
inferredcites →https://doi.org/10.1126/science.1219240openalex-snapshot
Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
inferredcites →https://doi.org/10.1126/science.aar3684openalex-snapshot
Natural selection interacts with recombination to shape the evolution of hybrid genomes
inferredcites →https://doi.org/10.1145/1390156.1390294openalex-snapshot
Extracting and composing robust features with denoising autoencoders
inferredcites →https://doi.org/10.1145/3065386openalex-snapshot
ImageNet classification with deep convolutional neural networks
inferredcites →https://doi.org/10.1146/annurev.ecolsys.32.081501.113958openalex-snapshot
Sex Chromosome Meiotic Drive
inferredcites →https://doi.org/10.1371/journal.pbio.1000501openalex-snapshot
How and Why Chromosome Inversions Evolve
inferredcites →https://doi.org/10.1371/journal.pcbi.1004842openalex-snapshot
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
inferredcites →https://doi.org/10.1371/journal.pgen.1000519openalex-snapshot
Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations
inferredcites →https://doi.org/10.1371/journal.pgen.1000550openalex-snapshot
The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing
inferredcites →https://doi.org/10.1371/journal.pgen.1002660openalex-snapshot
The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
inferredcites →https://doi.org/10.1371/journal.pgen.1002905openalex-snapshot
The Many Landscapes of Recombination in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1003090openalex-snapshot
Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1004410openalex-snapshot
Speciation and Introgression between Mimulus nasutus and Mimulus guttatus
inferredcites →https://doi.org/10.1371/journal.pgen.1006130openalex-snapshot
A Genomic Map of the Effects of Linked Selection in Drosophila
inferredcites →https://doi.org/10.1371/journal.pgen.1007341openalex-snapshot
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia
inferredcites →https://doi.org/10.1371/journal.pone.0048588openalex-snapshot
LDx: Estimation of Linkage Disequilibrium from High-Throughput Pooled Resequencing Data
inferredcites →https://doi.org/10.1534/g3.116.028233openalex-snapshot
New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era
inferredcites →https://doi.org/10.1534/g3.116.029330openalex-snapshot
Third Chromosome Balancer Inversions Disrupt Protein-Coding Genes and Influence Distal Recombination Events inDrosophila melanogaster
inferredcites →https://doi.org/10.1534/g3.118.200262openalex-snapshot
diploS/HIC: An Updated Approach to Classifying Selective Sweeps
inferredcites →https://doi.org/10.1534/genetics.103.025387openalex-snapshot
Linkage Disequilibrium as a Signature of Selective Sweeps
inferredcites →https://doi.org/10.1534/genetics.105.047985openalex-snapshot
Chromosome Inversions, Local Adaptation and Speciation
inferredcites →https://doi.org/10.1534/genetics.107.078907openalex-snapshot
Estimating Meiotic Gene Conversion Rates From Population Genetic Data
inferredcites →https://doi.org/10.1534/genetics.112.142018openalex-snapshot
Genomic Variation in Natural Populations ofDrosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.112.146746openalex-snapshot
Fine-Scale Heterogeneity in Crossover Rate in thegarnet-scallopedRegion of theDrosophila melanogasterX Chromosome
inferredcites →https://doi.org/10.1534/genetics.113.150201openalex-snapshot
A Fast Estimate for the Population Recombination Rate Based on Regression
inferredcites →https://doi.org/10.1534/genetics.114.166454openalex-snapshot
How Population Growth Affects Linkage Disequilibrium
inferredcites →https://doi.org/10.1534/genetics.115.174664openalex-snapshot
The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population
inferredcites →https://doi.org/10.1534/genetics.115.174912openalex-snapshot
Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps
inferredcites →https://doi.org/10.5962/bhl.title.27468openalex-snapshot
The genetical theory of natural selection

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cub.2020.03.053openalex-snapshot
Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura
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/10.1101/2021.01.13.426571openalex-snapshot
Using image-based haplotype alignments to map global adaptation of SARS-CoV-2
inferred← citeshttps://doi.org/10.1111/1755-0998.13224openalex-snapshot
Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation
inferred← citeshttps://doi.org/10.1111/mec.16841openalex-snapshot
Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008449openalex-snapshot
Inference of recombination maps from a single pair of genomes and its application to ancient samples
inferred← citeshttps://doi.org/10.1371/journal.pgen.1009303openalex-snapshot
Creating artificial human genomes using generative neural networks
inferred← citeshttps://doi.org/10.24072/pcjournal.267openalex-snapshot
The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
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