User profiles for Jakob Wirbel

Jakob Wirbel

Postdoctoral Fellow, Stanford School of Medicine
Verified email at stanford.edu
Cited by 2665

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

J Wirbel, PT Pyl, E Kartal, K Zych, A Kashani… - Nature medicine, 2019 - nature.com
Association studies have linked microbiome alterations with many human diseases.
However, they have not always reported consistent results, thereby necessitating cross-study …

[HTML][HTML] Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox

J Wirbel, K Zych, M Essex, N Karcher, E Kartal… - Genome biology, 2021 - Springer
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers
using machine learning (ML). However, metagenomics-specific software is scarce, and …

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

…, S Shiba, T Shibata, S Yachida, T Yamada, J Wirbel… - Nature medicine, 2019 - nature.com
Several studies have investigated links between the gut microbiome and colorectal cancer (CRC),
but questions remain about the replicability of biomarkers across cohorts and …

Unravelling the collateral damage of antibiotics on gut bacteria

L Maier, CV Goemans, J Wirbel, M Kuhn, C Eberl… - Nature, 2021 - nature.com
Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the
composition of gut microbiota and causing dysbiosis and disease 1 . Despite this well-known …

[HTML][HTML] A faecal microbiota signature with high specificity for pancreatic cancer

…, E Molina-Montes, S Rodríguez-Perales, J Wirbel… - Gut, 2022 - gut.bmj.com
Background Recent evidence suggests a role for the microbiome in pancreatic ductal
adenocarcinoma (PDAC) aetiology and progression. Objective To explore the faecal and salivary …

Extensive transmission of microbes along the gastrointestinal tract

…, LP Coelho, SS Li, PI Costea, AY Voigt, J Wirbel… - elife, 2019 - elifesciences.org
10.7554/eLife.42693.001 The gastrointestinal tract is abundantly colonized by microbes, yet
the translocation of oral species to the intestine is considered a rare aberrant event, and a …

[PDF][PDF] Commensal Clostridiales strains mediate effective anti-cancer immune response against solid tumors

…, E Katkeviciute, P Busenhart, A Bircher, J Wirbel… - Cell host & …, 2021 - cell.com
Despite overall success, T cell checkpoint inhibitors for cancer treatment are still only efficient
in a minority of patients. Recently, intestinal microbiota was found to critically modulate anti-…

[HTML][HTML] Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments

…, L Paoli, N Karcher, Q Clayssen, MI Keller, J Wirbel… - Microbiome, 2022 - Springer
Background Taxonomic profiling is a fundamental task in microbiome research that aims to
detect and quantify the relative abundance of microorganisms in biological samples. …

[HTML][HTML] Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

…, JM Braunger, R Argelaguet, D Arnol, J Wirbel… - Nature …, 2022 - nature.com
Factor analysis is a widely used method for dimensionality reduction in genome biology, with
applications from personalized health to single-cell biology. Existing factor analysis models …

[HTML][HTML] Depression and fatigue in active IBD from a microbiome perspective—a Bayesian approach to faecal metagenomics

AK Thomann, T Wüstenberg, J Wirbel, LL Knoedler… - BMC medicine, 2022 - Springer
Background Extraintestinal symptoms are common in inflammatory bowel diseases (IBD)
and include depression and fatigue. These are highly prevalent especially in active disease, …