Jakob Stokholm

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.

The paper shows that boosting TCA cycle activity through nutritional strategies improves neonatal host defense against infection by enhancing disease tolerance and resistance.

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

The paper develops PHAMB, a method to bin viral genomes from bulk metagenomics data, and applies it to the HMP2 cohort to recover viral genomes and explore viral-host interactions.

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.

The paper introduces a method for integrating heterogeneous biological data using a graphical LASSO framework and applies it to study asthma and eczema risk factors in children.