Alexandra Zhernakova

Comprehensive profiling of infant gut virome assembly reveals associations with eczema and wheeze

This study profiles the infant gut virome using dual methods and finds associations with eczema and wheeze.

Pregnancy and Early-Life Gut Virome in the Lifelines NEXT cohort:Origin, Persistence, Influencing Factors and Health Implications

The paper analyzes the gut virome in mother-infant pairs to identify factors influencing its development and persistence, finding that delivery mode and breastmilk shape the infant virome and that viral diversity is linked to food allergies.

Prophages of infant-derived Bifidobacterium longum subspecies employ antagonistic and synergistic strategies to persist in their host

The paper identifies and analyzes prophages in infant-derived Bifidobacterium longum subspecies, revealing their antagonistic and synergistic strategies for persistence in the gut.

Lactobacillus iners dominates the vaginal microbiota of healthy Italian women of reproductive age.

This study tracks vaginal microbiota changes in Italian women across menstrual phases, finding Lactobacillus iners as dominant and highlighting population-specific patterns and hormonal associations.

Negativeome in Early-Life Virome Studies: Characterization and Decontamination

The paper identifies viral contaminants in early-life gut viromes and shows the effectiveness of strain-aware decontamination to preserve biological signals.

Discovery, functionality and global dynamics of Bifidobacterium longum subsp. nexti : a novel starch-degrading subspecies in the infant gut

The paper identifies a novel subspecies of Bifidobacterium longum, BL. nexti, in infant gut microbiomes, showing its association with formula feeding and vertical transmission.

Dynamics and determinants of the gut mobilome in early life

The paper analyzes the gut mobilome in mother-infant dyads, finding increased infant mobilome richness over time, formula feeding effects, and antibiotic resistance gene presence in plasmids.

Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data

The paper develops interpretable neural networks for multi-omics data to predict smoking status, age, and LDL levels, showing improved performance and generalizability across cohorts.

High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation

This study analyzes the gut microbiome of treated coeliac disease patients at strain level, revealing increased interindividual variation and specific microbial associations.

The gut microbiome across the cardiovascular risk spectrum

The paper examines gut microbiome changes across different cardiovascular risk levels and in STEMI patients, identifying microbial species and pathways associated with cardiovascular risk and disease.

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

This study identifies two CpGs associated with the gut microbiome genus Eggerthella and shows microbiome mediates environmental effects on DNA methylation.

Genome-wide characterization of circulating metabolic biomarkers reveals substantial pleiotropy and novel disease pathways

This study identifies 400+ genetic loci associated with circulating metabolic traits and highlights pleiotropy and novel disease pathways.

Unbiased identification of unknown cellular and environmental factors that mediate eQTLs using principal interaction component analysis

This paper introduces PICALO, a method to identify unknown contexts influencing eQTLs, finding 31 and 21 PICs in blood and brain datasets, respectively, associated with cell type, RNA quality, and environmental factors.

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project

The paper identifies host genetic loci associated with gut microbiome composition and function in a large cohort, finding significant associations near LCT and ABO genes.

A systematic analysis of metabolic pathways in the human gut microbiota

This study systematically profiles primary metabolic genes in the human gut microbiota, revealing pathway differences among phyla and showing limited correlation between gene abundance and metabolite levels in plasma.

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference

The paper identifies 818 genes influencing DNA methylation in blood using genetic anchors and causal inference, revealing both transcription factors and non-DNA-binding proteins with regulatory roles.

Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes

This study investigates genetic variants in ACE2 and TMPRSS2 genes for associations with quantitative phenotypes and medication use in a population cohort, finding suggestive links with hypertension and inflammation-related drugs.

Genomic evaluation of circulating proteins for drug target characterisation and precision medicine

The paper identifies pQTLs for cardiovascular proteins and uses them to evaluate drug targets and suggest new candidates for precision medicine.

Genome-wide identification of directed gene networks using large-scale population genomics data

The paper identifies 49 gene drivers of downstream transcriptional changes using population genomics data and RNA-sequencing from 3,072 individuals.

Environmental factors dominate over host genetics in shaping human gut microbiota composition

This study shows environmental factors have a greater impact on human gut microbiota than host genetics, with microbiome data adding significant predictive value to phenotypes.

Disease variants alter transcription factor levels and methylation of their binding sites

The paper identifies trans-meQTLs linking disease variants to methylation changes at transcription factor binding sites, revealing eight-fold more downstream effects than trans-eQTLs.

Hypothesis-free identification of modulators of genetic risk factors

The paper identifies context-dependent eQTLs in peripheral blood RNA-seq data from Dutch individuals using a hypothesis-free approach, revealing gene expression influenced by cell type and signaling pathways.

An introduction to LifeLines DEEP: study design and baseline characteristics

This paper introduces LifeLines DEEP, a sub-cohort with extensive biological samples and data layers, and describes its baseline characteristics and potential for studying genetic and metabolic variation in gastrointestinal health.