Luis Bruno Barreiro

This study uses genomic data from ancient and present-day individuals to trace the 4,000-year demographic history of Bantu speakers in the Congo rainforest, revealing early dispersals and a population crisis.

The paper generates a single-cell transcriptional atlas of Indigenous South American populations and shows genetic ancestry influences immune gene expression, particularly after stimulation.

This study compares oral microbiomes of Ugandan hunter-gatherers and farmers with global populations, finding that geography and industrialization shape microbial diversity and composition.

This study identifies gene-environment interactions influencing immune response to SARS-CoV-2 in hospitalized patients using single-cell RNA-sequencing and eQTL analysis.

This study shows that continuous ART causes senescence-like changes in alveolar macrophages, increasing inflammation and impairing immune responses to SARS-CoV-2.

This study shows that social status at first exposure, but not secondary exposure, influences antibody responses and gene expression in vaccinated female rhesus macaques.

This study shows neonatal BCG vaccination expands IL-17/IL-22-producing γδ T cells, mediates protection against TB, and induces a microbiome signature linked to gut-lung axis immunity.

The paper identifies chromatin accessibility QTLs (caQTLs) in immune cells and finds they colocalize more with GWAS loci than eQTLs, but often lack downstream gene expression effects.

This study shows β-glucan reprograms neutrophils to induce disease tolerance against Influenza A virus by promoting a unique subset of neutrophils that limit tissue damage and enhance survival.

This study shows BCG vaccination changes gene expression and chromatin accessibility in human bone marrow progenitor cells, linking these changes to innate immune responses.

The paper identifies a female-biased gene expression signature of dominance in meerkats, showing differential gene expression in females but not males, with implications for social status and life history trade-offs.

This study uses whole-genome sequencing and machine learning to reconstruct demographic history and gene-flow patterns among African populations, finding that tree-like histories with gene-flow pulses better explain genetic diversity than continuous gene-flow.

The paper introduces EpiVar Browser, a tool for exploring epigenomics data under controlled access, enabling genotype-chromatin phenotype analysis without releasing identifiable information.

The paper uses mSTARR-seq to show DNA methylation interacts with environmental factors like IFNA and influenza virus in human macrophages, but not for early life adversity sites.

The paper uses genome graphs to detect polymorphic mobile elements in active epigenomic states during influenza infection, revealing novel peaks and modifying quantitative trait loci estimates.

The paper addresses statistical concerns about detecting natural selection during the Black Death using ancient genomic data, reaffirming findings related to immune loci and the ERAP2 variant.

The paper develops a human intestinal organoid model with macrophages to study their role in development, finding that macrophages regulate metabolism and growth without affecting tissue architecture.

The paper shows ancestry-related differences in transcriptional response to influenza are driven by epigenetic variation and genetic control of enhancer activity.

The paper investigates how social status in rhesus macaques affects gene regulation, glucocorticoid physiology, and mitochondrial DNA phenotypes through specific behavioral interactions.

The paper investigates how HIV and antiretroviral therapy affect the transcriptional and epigenetic response of alveolar macrophages to Mycobacterium tuberculosis.

The paper uses single-cell RNA-sequencing to show genetic ancestry affects gene expression during viral infection, with effects varying by cell type.

The paper identifies transposable elements (TEs) contributing to regulatory regions in human immune responses, showing their activation during bacterial infection through chromatin accessibility and transcription factor binding.

This study shows that social status affects gene expression in immune cells of rhesus macaques, with effects modulated by pathogen exposure, type, and social history.

The paper shows that gene expression changes precede DNA demethylation in human dendritic cells during infection with Mycobacterium tuberculosis.

This study shows that social status affects chromatin accessibility and gene regulation in response to glucocorticoids in rhesus macaques, with stable effects on chromatin accessibility and reduced gene expression effects after treatment.

The paper identifies convergent positive selection in growth and cardiac pathways between African and Asian rainforest hunter-gatherers, suggesting convergent adaptation to rainforest environments.

This study shows that 7nAChR agonists reverse LPS-induced pro-inflammatory microglial phenotype in fetal sheep, while antagonists enhance it, suggesting therapeutic potential for neuroinflammation.

The paper identifies response eQTLs that modify genetic regulation during immune activation and shows their enrichment in autoimmune disease GWAS signals.

The paper uses gene expression in dendritic cells to predict tuberculosis susceptibility, finding differentially expressed genes and genetic polymorphisms associated with TB risk.

The paper develops mSTARR-seq to quantify DNA methylation effects on regulatory elements, identifies MD regulatory elements, and predicts methylation-gene expression correlations.