Jonathan Thorsen

The paper analyzes the evolutionary history and microbial interactions of Bifidobacterium longum subspecies in infants, finding that subspecies distribution is shaped by ecological factors and cross-feeding rather than host-specific factors.

The paper introduces PARAFAC2 to model subject-specific temporal patterns in longitudinal microbiome data, outperforming CP in capturing individual variations and enabling replicable pattern discovery.

MAGinator quantifies strain-level abundance of metagenome-assembled genomes and infers their functional and phylogenetic profiles from shotgun metagenomics data.

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

The paper examines the stability of maternal vaginal microbiota during pregnancy and its impact on early infant colonization through analysis of 700 mother-child dyads.

DAtest is an R package that empirically compares statistical methods for differential expression or abundance directly on a user's own dataset across diverse omics types.