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 shows ATF6 activation in colonic epithelial cells alters lipid metabolism, promoting tumor-associated microbial adaptation in mice and human colorectal cancer patients.

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 uses machine learning to meta-analyze gut microbiome data from Parkinson's disease patients, identifying microbial pathways linked to disease and potential diagnostic applications.

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.