Luis Bruno Barreiro

A 4,000-year genomic history of Bantu speakers from the Congo rainforest

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.

Genetic ancestry shapes context-dependent immune regulation across Indigenous South American populations

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

Evolutionary Histories and Environments Shape Ugandan and Global Oral Microbiomes

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

Widespread gene-environment interactions shape the immune response to SARS-CoV-2 infection in hospitalized COVID-19 patients

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

Continuous antiretroviral therapy induces progressive senescence-like reprogramming of alveolar macrophages

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

Adaptive immune responses to vaccination reflect social status at first exposure in female rhesus macaques

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

Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis

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.

Impact of disease-associated chromatin accessibility QTLs across immune cell types and contexts

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.

β-Glucan Reprograms Neutrophils to Induce Disease Tolerance Against Influenza A Virus

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.

Ancient tree-topologies and gene-flow processes among human lineages in Africa

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.

EpiVar Browser: advanced exploration of epigenomics data under controlled access

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

DNA methylation-environment interactions in the human genome

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.

Genome graphs detect human polymorphisms in active epigenomic states during influenza infection

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.

Reply to Barton et al: signatures of natural selection during the Black Death

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.

Developmental role of macrophages modelled in human pluripotent stem cell derived intestinal tissue

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.

Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection

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

Agonism and grooming behavior explain social status effects on physiology and gene regulation in rhesus macaques

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

Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV

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

Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection

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

Transposable elements have contributed human regulatory regions that are activated upon bacterial infection

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.

Social history and exposure to pathogen signals modulate social status effects on gene regulation in rhesus macaques

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.

Gene activation precedes DNA demethylation in response to infection in human dendritic cells

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

Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques

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.

Polygenic adaptation and convergent evolution across both growth and cardiac genetic pathways in African and Asian rainforest hunter-gatherers

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

α7 nicotinic acetylcholine receptor signaling modulates the inflammatory and iron homeostasis in fetal brain microglia

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.

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations

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

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells

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

Genome-wide quantification of the effects of DNA methylation on human gene regulation

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