Jingyuan Fu

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

GECSI predicts chromatin states from gene expression data, outperforming existing methods and providing annotations for 449 additional epigenomes.

This study compares hiPSC-derived hepatic organoids and liver-on-a-chip systems, showing that microfluidic flow enhances hepatic maturation and metabolic specialization.

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

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

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.

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

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

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.

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.

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

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

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.

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.

This study identifies 592 genetic loci associated with 184 plasma proteins in 26,494 individuals and finds causal relationships between protein levels and disease.

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.

The paper identifies 31 host genetic loci influencing gut microbiome composition through GWAS and suggests causal effects in inflammatory diseases.

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.

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

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.

The paper identifies genetic variants affecting gene expression using genotypes derived from public RNA-seq data, finding cis-eQTLs for 8,034 genes and strong ASE effects for 34 rare pathogenic variants.

The paper introduces a method for cell-specific eQTL analysis without cell sorting, showing that Crohn's disease-associated SNPs mainly affect neutrophil gene expression in whole blood data.