Publications

You can also find my articles on my Google Scholar profile for a more up-to-date list.

Some highlights

• Wirbel, Pyl et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer Nature Medicine 25; pages 679–689 (2019)
  Machine learning meta-analysis for associations between colorectal cancer and the gut microbiome

• Wirbel et al. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox Genome Biology 22, 93 (2021)
  Machine learning toolbox for comparative metagenomics

• Wirbel, Essex et al. A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies Genome Biology 25, 247 (2024)
  Benchmark for association testing methods with microbiome data

Preprints

• Wirbel, Hickey et al. Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics bioRxiv (2025)

Peer-reviewed publications

• Coleman, Sorbie et al. ATF6 activation alters colonic lipid metabolism causing tumour-associated microbial adaptation Nat Metab (2025)
• Schmidtke et al. The prototypic crAssphage is a linear phage-plasmid Cell Host & Microbe, 33, 8, 1347 - 1362.e5 (2025)
• Wirbel et al. Accurate prediction of absolute prokaryotic abundance from DNA concentration Cell Reports Methods, 5, 5, 101030 (2025)
• Romano et al. Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease Nat Commun 16, 4227 (2025)
• Maghini, Oduaran et al. Expanding the human gut microbiome atlas of Africa Nature 638, 718–728 (2025)
• Chanin, West et al. Intragenic DNA inversions expand bacterial coding capacity Nature 634, 234–242 (2024)
• Wirbel, Essex et al. A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies Genome Biology 25, 247 (2024)
• Ferretti et al. C. difficile may be overdiagnosed in adults and is a prevalent commensal in infants eLife 12:RP90111 (2023)
• Sambrunin et al. Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data Genome Medicine 15, 32 (2023)
• Ruscheweyh, Milanese et al. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments Microbiome 10, 212 (2022)
• Thomann et al. Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics BMC Medicine 20, 366 (2022)
• Sowah, Milanese et al. Calorie restriction improves metabolic state independently of gut microbiome composition: a randomized dietary intervention trial Genome Medicine 14, 30 (2022)
• Kartal et al. A faecal microbiota signature with high specificity for pancreatic cancer Gut 71:1359-1372 (2022)
• Peuker et al. Microbiota-dependent activation of the myeloid calcineurin-NFAT pathway inhibits B7H3-and B7H4-dependent anti-tumor immunity in colorectal cancer Immunity 55, 701-717 (2022)
• Velten et al. Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO Nature Methods 19, 179-186 (2022)
• Wirbel et al. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox Genome Biology 22, 93 (2021)
• Bernardo-Faura et al. Prediction of combination therapies based on topological modeling of the immune signaling network in Multiple Sclerosis Genome Medicine 13, 117 (2021)
• Maier, Goemans et al. Unravelling the collateral damage of antibiotics on gut bacteria Nature 599, 120-124 (2021)
• Montalban-Arques et al. Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors Cell Host & Microbe 29, 1573-1588 (2021)
• Garza et al. Metabolic models predict bacterial passengers in colorectal cancer Cancer & Metabolism 8, 1-13 (2020)
• Thomas, Manghi et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation Nature Medicine 25; pages 667-678 (2019)
• Wirbel, Pyl et al. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer Nature Medicine 25; pages 679–689 (2019)
• Schmidt, Hayward et al. Extensive transmission of microbes along the gastrointestinal tract eLife 8:e42693 (2019)
• Wirbel et al. Phosphoproteomics-Based Profiling of Kinase Activities in Cancer Cells. Cancer Systems Biology pp 103-132 (2018)
• Gaudreault et al. Red Blood Cells Preconditioned with Hemin Are Less Permissive to Plasmodium Invasion In Vivo and In Vitro PLoS ONE 10(10): e0140805 (2015)

Comments

• Wirbel, Bhatt, & Probst The journey to understand previously unknown microbial genes Nature 626, 267-269 (2024)