Jacques Fellay

Comparative evaluation of genotyping and low-pass sequencing for pharmacogenetic variant and phenotype inference

This study compares genotyping arrays and low-pass whole-genome sequencing for pharmacogenetic variant and phenotype inference, finding high concordance but improved variant coverage with LP-WGS.

Multi-omics integration identifies a reproducible inflammatory host-response axis in pediatric sepsis

The paper integrates multi-omics data from pediatric sepsis patients to identify a reproducible inflammatory host-response axis associated with disease severity.

Mutational bias shapes protein evolution across RNA viruses

The paper quantifies how mutational biases shape protein evolution in RNA viruses by analyzing SARS-CoV-2 and 34 other species, showing that mutational spectra predict amino acid composition changes and deviations indicate selection pressures.

Identification and Functional Characterization of Regulatory Variants in DPP9 Associated with COVID-19 Severity

The paper identifies and functionally characterizes regulatory variants in DPP9 associated with severe COVID-19 by analyzing genetic risk factors and their impact on gene expression and immune cell function.

Application of qualifying variants for genomic analysis

The paper introduces a framework for defining and reusing qualifying variants (QVs) in genomic analysis to improve transparency, reproducibility, and interoperability across pipelines.

Archipelago method for variant set association test statistics.

The paper introduces the Archipelago method to visualize variant set association test statistics by assigning genomic coordinates to P values, enabling combined visualization of set-level and individual variant associations.

PanelAppRex aggregates disease gene panels and facilitates sophisticated search

PanelAppRex aggregates and standardizes disease gene panels to enable efficient search and integration into bioinformatic workflows, recovering causal genes in all benchmarked cases.

Zygosity-Aware DNA Language Modeling Improves Ancestry and Gene Expression Prediction

This paper evaluates zygosity-aware DNA language models for ancestry and gene expression prediction, showing improved performance with diploid representations.

Interdependent Dynamics of mRNA Expression and HIV-1 Viral Load: Insights from Transcriptomics and Mendelian Randomization

The paper identifies 792 genes associated with HIV load using transcriptomics and confirms TRABD2A as a viral restriction factor through Mendelian Randomization.

Granulysin antimicrobial activity promotes dormancy in Mycobacterium tuberculosis

The paper investigates how granulysin from immune cells induces dormancy in Mycobacterium tuberculosis, revealing an immune escape mechanism.

Rare variants in infection response protein pathways associated with sepsis in children.

The paper identifies genetic pathways and variants associated with sepsis susceptibility in children through genomic analysis of a paediatric cohort.

Genome-wide association study of pediatric bacteremia and sepsis

This paper identifies a genetic locus associated with sepsis susceptibility in children using a genome-wide association study of a national cohort.

Quantifying prior probabilities for disease-causing variants reveals the top genetic contributors in inborn errors of immunity

This paper introduces a statistical framework to quantify prior probabilities of disease-causing variants in inborn errors of immunity, revealing top genetic contributors and validating results in national cohorts.

MosCoverY: a new method to estimate mosaic Loss of Y chromosome from NGS sequencing coverage data

MosCoverY estimates mosaic loss of the Y chromosome from NGS sequencing data, showing comparable performance to existing methods and replicating known associations.

Mitochondrial Deletions and Healthspan: Lessons from the Common Repeat

The paper investigates the role of mitochondrial DNA repeats in aging and healthspan, finding that disrupting the common repeat reduces somatic deletions and improves healthspan.

Human genetic ancestry, Mycobacterium tuberculosis diversity and tuberculosis disease severity in Dar es Salaam, Tanzania

This study examines the relationship between human genetic ancestry, Mycobacterium tuberculosis diversity, and TB disease severity in Dar es Salaam, Tanzania, finding no significant genetic influence on disease severity.

Mitochondrial mutation spectrum in Chordates: damage versus replication signatures, causes, and dynamics

The paper analyzes the mitochondrial mutation spectrum in chordates, identifying three main mutation signatures and their underlying causes, with implications for age-related disease prevention.

Transcriptomics and chromatin accessibility in multiple African population samples

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

Genetic features and genomic targets of human KRAB-Zinc Finger Proteins

This study examines the genetic features and genomic targets of human KRAB-Zinc Finger Proteins, revealing their role in regulating transposable elements and their evolutionary significance.

Risk of mitochondrial deletions is affected by the global secondary structure of the human mitochondrial genome

The paper identifies a contact zone in the human mitochondrial genome where deletions are more likely, linking it to aging and lifespan.

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with critical COVID-19

The paper identifies rare loss-of-function variants in type I IFN immunity genes associated with severe COVID-19, particularly in younger patients with recessive inheritance.

Associations of genetic and infectious risk factors with coronary heart disease

This study identifies high polygenic risk and infection with Fusobacterium nucleatum as independent risk factors for incident coronary heart disease in a population cohort.

G2GSnake: A Snakemake workflow for host-pathogen genomic association studies

G2GSnake provides a Snakemake workflow and R Shiny app for reproducible genome-to-genome association studies between host and pathogen genomes.

Aneuploidy in human embryos is associated with a maternal age- independent increase in mitochondrial DNA content and an enrichment of ultra-rare mitochondrial DNA variants

The paper finds that aneuploidy in human embryos is linked to higher mitochondrial DNA content and more ultra-rare mtDNA variants, independent of maternal age.

The Immune Factors Driving DNA Methylation Variation in Human Blood

This study identifies factors influencing DNA methylation variation in human blood, showing that cytomegalovirus infection and aging drive methylation changes, with cellular composition and DNA sequence as key predictors.

A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits

This paper introduces a phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits, showing improved detection of host genetic variants in simulations and applied to HIV-1 data.

A polygenic risk score to predict sudden cardiac arrest in patients with coronary artery disease

This paper develops a polygenic risk score (metaPRS) to predict sudden cardiac arrest in patients with coronary artery disease using genetic and clinical data from two cohorts.

Is competition for cellular resources a driver of complex trait heritability?

The paper models resource competition for polymerases during transcription and finds it cannot explain most of the heritability in complex traits.

Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes

The paper identifies novel genetic and non-genetic factors associated with plasma protein levels in healthy donors, highlighting their impact on immune response variability.

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

The paper improves genotype imputation in underrepresented populations by adding population-specific SNPs to existing reference panels, showing improved accuracy in a Tanzanian cohort.