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View article: Methods for inferring coalescent tree topologies from genomic data: a comparison based on the transmission of reproductive success
Methods for inferring coalescent tree topologies from genomic data: a comparison based on the transmission of reproductive success Open
iInferring coalescent trees from genomic data has become a major subject in population genetics, particularly with the recent advances in tree sequence reconstruction methods. Yet, how well these methods perform under imbalanced genealogie…
View article: PRIVET: Privacy Metric Based on Extreme Value Theory
PRIVET: Privacy Metric Based on Extreme Value Theory Open
Deep generative models are often trained on sensitive data, such as genetic sequences, health data, or more broadly, any copyrighted, licensed or protected content. This raises critical concerns around privacy-preserving synthetic data, an…
View article: Ancient genomic insights into <i>Salmonella enterica</i> Paratyphi C from Central Mexico
Ancient genomic insights into <i>Salmonella enterica</i> Paratyphi C from Central Mexico Open
Salmonella enterica is a widespread pathogen of major global health relevance, with over 2,500 serovars classified into non-typhoidal and typhoidal groups. Within the typhoidal group, S. enterica Paratyphi C causes paratyphoid fever in hum…
View article: Archaic ancestry inference in imputed ancient human genomes
Archaic ancestry inference in imputed ancient human genomes Open
When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This groundbreaking discovery, made in part possible through the genomic analysis of archaic remains, reshaped …
View article: Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean
Out-of-Anatolia: Cultural and genetic interactions during the Neolithic expansion in the Aegean Open
West Anatolia has been a crucial yet elusive element in the Neolithic expansion from the Fertile Crescent to Europe. In this work, we describe the changing genetic and cultural landscapes of early Holocene West Anatolia using 30 new paleog…
View article: Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data
Assessing simulation-based supervised machine learning for demographic parameter inference from genomic data Open
The ever-increasing availability of high-throughput DNA sequences and the development of numerous computational methods have led to considerable advances in our understanding of the evolutionary and demographic history of populations. Seve…
View article: Imputing missing minimum inhibitory concentration (MIC) values for <i>Pseudomonas aeruginosa</i> strains with a Denoising AutoEncoder
Imputing missing minimum inhibitory concentration (MIC) values for <i>Pseudomonas aeruginosa</i> strains with a Denoising AutoEncoder Open
Pseudomonas aeruginosa is a problematic pathogen with complex antibiotic resistance patterns. In clinical practice, minimum inhibitory concentration (MIC) tests typically focus on a limited subset of antibiotics, hindering a comprehensive …
View article: An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes
An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes Open
Admixture between populations is a common feature of human history. Admixture events introduce new genetic variation that can fuel evolution. Characterizing the significance of admixture events on the evolution of a population across vario…
View article: Diffusion-based artificial genomes and their usefulness for local ancestry inference
Diffusion-based artificial genomes and their usefulness for local ancestry inference Open
The creation of synthetic data through generative modeling has emerged as a significant area of research in genomics, offering versatile applications from tailoring functional sequences with specific attributes to generating high-quality, …
View article: Interpreting artificial neural networks to detect genome-wide association signals for complex traits
Interpreting artificial neural networks to detect genome-wide association signals for complex traits Open
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousand…
View article: Simulation-based benchmarking of ancient haplotype inference fordetecting population structure
Simulation-based benchmarking of ancient haplotype inference fordetecting population structure Open
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other homi…
View article: Simulation-based benchmarking of ancient haplotype inference fordetecting population structure
Simulation-based benchmarking of ancient haplotype inference fordetecting population structure Open
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other homi…
View article: GRUPS-rs, a high-performance ancient DNA genetic relatednessestimation software relying on pedigree simulations
GRUPS-rs, a high-performance ancient DNA genetic relatednessestimation software relying on pedigree simulations Open
Background: The study of fine-grain genetic kinship ties (parents, siblings, cousins, etc.) from ancient remains is now gaining significant interest within the field of paleogenetics, as a means of deciphering the social organization of pa…
View article: Towards creating longer genetic sequences with GANs: Generation in principal component space
Towards creating longer genetic sequences with GANs: Generation in principal component space Open
International audience
View article: Deep convolutional and conditional neural networks for large-scale genomic data generation
Deep convolutional and conditional neural networks for large-scale genomic data generation Open
Applications of generative models for genomic data have gained significant momentum in the past few years, with scopes ranging from data characterization to generation of genomic segments and functional sequences. In our previous study, we…
View article: Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure
Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure Open
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other homi…
View article: The <i>MUC19</i> Gene: An Evolutionary History of Recurrent Introgression and Natural Selection
The <i>MUC19</i> Gene: An Evolutionary History of Recurrent Introgression and Natural Selection Open
We study the gene MUC19 , for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants for the Denisovan-like MUC19 haplotype…
View article: A Quantitative Theory for Genomic Offset Statistics
A Quantitative Theory for Genomic Offset Statistics Open
Genomic offset statistics predict the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics h…
View article: Demographic history and genetic structure in pre-Hispanic Central Mexico
Demographic history and genetic structure in pre-Hispanic Central Mexico Open
Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward b…
View article: Deep convolutional and conditional neural networks for large-scale genomic data generation
Deep convolutional and conditional neural networks for large-scale genomic data generation Open
Applications of generative models for genomic data have gained significant momentum in the past few years, with scopes ranging from data characterization to generation of genomic segments and functional sequences. In our previous study, we…
View article: Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies, and demographic inferences Open
Cultural transmission of reproductive success has been observed in many human populations as well as other animals. Cultural transmission of reproductive success consists of a positive correlation of nongenetic origin between the progeny s…
View article: A quantitative theory for genomic offset statistics
A quantitative theory for genomic offset statistics Open
Genomic offset statistics predict the maladaptation of populations to rapid habitat alteration based on association of genotypes with environmental variation. Despite substantial evidence for empirical validity, genomic offset statistics h…
View article: <tt>dnadna</tt>: a deep learning framework for population genetics inference
dnadna: a deep learning framework for population genetics inference Open
Motivation We present dnadna, a flexible python-based software for deep learning inference in population genetics. It is task-agnostic and aims at facilitating the development, reproducibility, dissemination and re-usability of neural netw…
View article: Towards a genetic theory of island biogeography: Inferring processes from multidimensional community‐scale data
Towards a genetic theory of island biogeography: Inferring processes from multidimensional community‐scale data Open
Background MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically…
View article: Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences
Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences Open
Cultural Transmission of Reproductive Success (CTRS) has been observed in many human populations as well as other animals. It consists in a positive correlation of non-genetic origin between the progeny size of parents and children. This c…
View article: Simulation of bacterial populations with SLiM
Simulation of bacterial populations with SLiM Open
International audience
View article: Creating artificial human genomes using generative neural networks
Creating artificial human genomes using generative neural networks Open
Generative models have shown breakthroughs in a wide spectrum of domains due to recent advancements in machine learning algorithms and increased computational power. Despite these impressive achievements, the ability of generative models t…