Jakob Wirbel

This study compares the effects of two GVHD prophylaxis regimens on the gut microbiome in allo-HCT recipients and finds that while PTCy reduces microbiome diversity and bile acid metabolism, it is linked to better clinical outcomes.

This study characterizes the crAssphage lifestyle as a phage-plasmid, demonstrating its persistence in the gut microbiome without causing host lysis or chromosomal integration.

The paper uses long-read metagenomics to study prophage integration dynamics in gut microbiota, finding dynamic phage-host interactions and a new class of phages.

This study expands the human gut microbiome atlas of Africa by analyzing 1,803 women from four countries, revealing geographic and lifestyle-associated taxa and novel microbial genomes.

The paper benchmarks differential abundance methods in microbiome studies, showing that only a few methods control false discoveries well and that confounding variables can lead to spurious associations.

MEFISTO enables spatio-temporal dimensionality reduction and pattern separation in multi-modal genomic data, revealing conserved and diverged developmental programs and microbiome heterogeneity.

The paper predicts combination therapies for MS by modeling patient-specific signaling networks using phosphoproteomics data and identifies TAK1 as a co-druggable target.

The paper introduces mOTUs3, a tool for reference genome-independent taxonomic profiling of metagenomes, improving accuracy and coverage for underexplored microbiomes.

The paper introduces SIAMCAT, a machine-learning toolbox for metagenomics analysis, showing it can identify disease-specific and shared biomarkers across studies.