Søren Johannes Sørensen

This study defines the structure and mechanism of retron type IX, revealing how its DNA-scaffolded ring assembly mediates antiphage immunity through phage-encoded nuclease-triggered activation.

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.

PlasMAAG improves plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning, outperforming existing methods in accuracy and efficiency.

This paper introduces MSSM, a method for high-resolution spatial metagenomics that enables strain-level analysis of gut microbiomes at the microscale.

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

The paper uses machine learning to predict plasmid permissiveness in wastewater microbiomes from 16S rDNA sequences, showing moderate-to-strong correlations with experimental data.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

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 analyzes gut metagenomes from pigs to investigate co-occurrence patterns of antibiotic resistance genes (ARGs) with metal and biocide resistance genes, finding non-random phylogenetic associations.

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

CRISPRCasTyper is a tool that identifies and classifies CRISPR-Cas loci in prokaryotic sequences using machine learning, achieving high accuracy in subtyping and handling fragmented data.

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.

This paper introduces a method for high-throughput screening of protein variants using encapsulated E. coli micro-colonies and evaluates biophysical predictors for mutation effects on GFP fluorescence.

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.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.