Julien F. Ayroles
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View article: The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity
The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity Open
Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we invoke the analogy of a kaleidoscope: while the DNA sequence represents its core, the genome …
View article: Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations
Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations Open
Most genetic polymorphisms associated with complex traits are found in non-coding regions of the genome. Characterizing their effect presents a formidable challenge, and expression quantitative trait locus (eQTLs) mapping has been a key ap…
View article: Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia
Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia Open
Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thu…
View article: Prevalence and spatio-demographic variability of nutrition-related health issues in Kiribati
Prevalence and spatio-demographic variability of nutrition-related health issues in Kiribati Open
The nutrition transition in Small Island Developing States like Kiribati has led to a significant shift from traditional diets to processed, imported foods, resulting in a double burden of malnutrition. This study provides the first compre…
View article: Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection
Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection Open
Evolutionary adaptation to new environments likely results from a combination of selective sweeps and polygenic shifts, depending on the genetic architecture of traits under selection. While selective sweeps have been widely studied, polyg…
View article: Urbanization exacerbates age-associated declines in cardiometabolic health in Turkana and Orang Asli
Urbanization exacerbates age-associated declines in cardiometabolic health in Turkana and Orang Asli Open
Declines in cardiometabolic health among older individuals are so ubiquitous in Western, high-income countries that non-communicable diseases (NCDs) like type 2 diabetes, hypertension, and cardiovascular disease have been termed “diseases …
View article: Microbial solutions to dietary stress: experimental evolution reveals host–microbiome interplay in <i>Drosophila melanogaster</i>
Microbial solutions to dietary stress: experimental evolution reveals host–microbiome interplay in <i>Drosophila melanogaster</i> Open
Can the microbiome serve as a reservoir of adaptive potential for hosts? To address this question, we leveraged approximately 150 generations of experimental evolution in Drosophila melanogaster on a stressful, high-sugar diet. We performe…
View article: Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data
Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data Open
Animal behavior spans many timescales, from short, seconds-scale actions to daily rhythms over many hours to life-long changes during aging. To access longer timescales of behavior, we continuously recorded individual Drosophila melanogast…
View article: Unlocking the hidden dimensions of genomic diversity within species
Unlocking the hidden dimensions of genomic diversity within species Open
The missing heritability problem, defined as the failure of genetic variants to explain variance in phenotypes, has been an unsolved issue in genetics for the past two decades. A potential solution to this problem stems from the idea that …
View article: Characterizing the genetic architecture of drug response using gene-context interaction methods
Characterizing the genetic architecture of drug response using gene-context interaction methods Open
Identifying factors that affect treatment response is a central objective of clinical research, yet the role of common genetic variation remains largely unknown. Here, we develop a framework to study the genetic architecture of response to…
View article: The built environment is more predictive of cardiometabolic health than other aspects of lifestyle in two rapidly transitioning Indigenous populations
The built environment is more predictive of cardiometabolic health than other aspects of lifestyle in two rapidly transitioning Indigenous populations Open
Summary Background Many subsistence-level and Indigenous societies around the world are rapidly experiencing urbanization, nutrition transition, and integration into market-economies, resulting in marked increases in cardiometabolic diseas…
View article: Reassessing the modularity of gene co-expression networks using the Stochastic Block Model
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model Open
Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is,…
View article: Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection
Longitudinal sequencing reveals polygenic and epistatic nature of genomic response to selection Open
Evolutionary adaptation to new environments likely results from a combination of selective sweeps and polygenic shifts, depending on the genetic architecture of traits under selection. While selective sweeps have been widely studied, polyg…
View article: <i>Wolbachia</i> impacts microbiome diversity and fitness‐associated traits for <i>Drosophila melanogaster</i> in a seasonally fluctuating environment
<i>Wolbachia</i> impacts microbiome diversity and fitness‐associated traits for <i>Drosophila melanogaster</i> in a seasonally fluctuating environment Open
The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the mi…
View article: Characterizing the genetic architecture of drug response using gene-context interaction methods
Characterizing the genetic architecture of drug response using gene-context interaction methods Open
Identifying the factors responsible for variability of treatment response is a central objective of clinical research. Specially designed pharmacogenomic studies have identified a handful of individual mutations modulating the effect of sp…
View article: Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations
Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations Open
A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. …
View article: Sex differences in immune function and disease risk are not easily explained by an evolutionary mismatch
Sex differences in immune function and disease risk are not easily explained by an evolutionary mismatch Open
The Pregnancy Compensation Hypothesis (PCH) posits that sex differences in the mammalian immune system reflect the effects of selection on female immunity during pregnancy, during which increased immunomodulation is required to reduce immu…
View article: Chromatin activity identifies differential gene regulation across human ancestries
Chromatin activity identifies differential gene regulation across human ancestries Open
View article: Saturating the eQTL Map in Drosophila Melanogaster:&nbsp;Genome-Wide Patterns of CIS and Trans Regulation of Transcriptional Variation in Outbred Populations
Saturating the eQTL Map in Drosophila Melanogaster: Genome-Wide Patterns of CIS and Trans Regulation of Transcriptional Variation in Outbred Populations Open
View article: Relative abundance data can misrepresent heritability of the microbiome
Relative abundance data can misrepresent heritability of the microbiome Open
Background Host genetics can shape microbiome composition, but to what extent it does, remains unclear. Like any other complex trait, this important question can be addressed by estimating the heritability ( h 2 ) of the microbiome—the pro…
View article: Applying an evolutionary mismatch framework to understand disease susceptibility
Applying an evolutionary mismatch framework to understand disease susceptibility Open
Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of “lifestyle” diseases that were rare throughout human history but are now common. The evolutionary mism…
View article: Capturing continuous, long timescale behavioral changes in $\textit{Drosophila melanogaster}$ postural data
Capturing continuous, long timescale behavioral changes in $\textit{Drosophila melanogaster}$ postural data Open
Animal behavior spans many timescales, from short, seconds-scale actions to circadian rhythms over many hours to life-long changes during aging. Most quantitative behavior studies have focused on short-timescale behaviors such as locomotio…
View article: Characterizing the landscape of gene expression variance in humans
Characterizing the landscape of gene expression variance in humans Open
Gene expression variance has been linked to organismal function and fitness but remains a commonly neglected aspect of molecular research. As a result, we lack a comprehensive understanding of the patterns of transcriptional variance acros…
View article: Reassessing the modularity of gene co-expression networks using the Stochastic Block Model
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model Open
Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is,…
View article: From GWAS to signal validation: An approach for estimating genetic effects while preserving genomic context
From GWAS to signal validation: An approach for estimating genetic effects while preserving genomic context Open
Validating associations between genotypic and phenotypic variation remains a challenge, despite advancements in association studies. Common approaches for signal validation rely on gene-level perturbations, such as loss-of-function mutatio…
View article: Evolutionary mismatch and the role of GxE interactions in human disease.
Evolutionary mismatch and the role of GxE interactions in human disease. Open
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases th…
View article: Evolutionary mismatch and the role of GxE interactions in human disease
Evolutionary mismatch and the role of GxE interactions in human disease Open
Globally, we are witnessing the rise of complex, non-communicable diseases (NCDs) related to changes in our daily environments. Obesity, asthma, cardiovascular disease, and type 2 diabetes are part of a long list of "lifestyle" diseases th…
View article: Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations
Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations Open
A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. …
View article: Chromatin activity identifies differential gene regulation across human ancestries
Chromatin activity identifies differential gene regulation across human ancestries Open
Current evidence suggests that cis -regulatory elements controlling gene expression may be the predominant target of natural selection in humans and other species. Detecting selection acting on these elements is critical to understanding e…
View article: Chromatin activity identifies differential gene regulation across human ancestries
Chromatin activity identifies differential gene regulation across human ancestries Open
This repository contains data related to: Chromatin activity identifies differential gene regulation across human ancestries Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea, Julien Ayroles, Howard Y. Chang, Maya Kasowski, Hunter B. Fraser