Stefan Janssen
A5065650315- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Material Dynamics and Properties
- RNA and protein synthesis mechanisms
- Nuclear Physics and Applications
- Metabolomics and Mass Spectrometry Studies
- Dermatology and Skin Diseases
- Theoretical and Computational Physics
- Microbial Community Ecology and Physiology
- Contact Dermatitis and Allergies
- Magnetism in coordination complexes
- Skin Protection and Aging
- Atomic and Subatomic Physics Research
- RNA modifications and cancer
- Protein Structure and Dynamics
- Magnetic properties of thin films
- RNA Research and Splicing
- Rare-earth and actinide compounds
- High-pressure geophysics and materials
- X-ray Diffraction in Crystallography
- Physics of Superconductivity and Magnetism
- Scientific Computing and Data Management
- Breast Cancer Treatment Studies
- Advanced NMR Techniques and Applications
- Microstructure and mechanical properties
Justus-Liebig-Universität Gießen
2020-2025
University of California, San Diego
2016-2024
University of Lübeck
1997-2024
Universitätsklinik für Strahlentherapie
2024
Heinrich Heine University Düsseldorf
2018-2023
Düsseldorf University Hospital
2021-2023
University Hospital Bonn
2021
German Center for Infection Research
2018-2021
Helmholtz Centre for Infection Research
2017-2019
Medizinische Hochschule Hannover
2009-2017
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging integrate extent of microbial molecular diversity in stool remains unknown. Using standardized protocols Earth Microbiome Project sample contributions over 10,000 citizen-scientists, together with an open research network, we compare specimens primarily United States, Kingdom, Australia one another environmental samples. Our results show...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a de novo tree the short sequences) can provide incorrect results in human gut metagenomic studies and show phylogenetic placement new sequences SEPP resolves this problem yielding other benefits over existing methods.
Amyloids are a class of protein with unique self-aggregation properties, and their aberrant accumulation can lead to cellular dysfunctions associated neurodegenerative diseases. While genetic environmental factors influence amyloid formation, molecular triggers and/or facilitators not well defined. Growing evidence suggests that non-identical proteins may accelerate reciprocal aggregation in prion-like fashion. humans encode ~30 amyloidogenic proteins, the gut microbiome also produces...
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution individual genes. Here we build a reference phylogeny 10,575 evenly-sampled bacterial and archaeal genomes, based on comprehensive set 381 markers, using multiple strategies. Our trees indicate remarkably closer proximity between Archaea Bacteria than previous estimates that were limited to fewer "core" genes, such as ribosomal proteins. The...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Use of skin personal care products on a regular basis is nearly ubiquitous, but their effects molecular and microbial diversity the are unknown. We evaluated impact four beauty (a facial lotion, moisturizer, foot powder, deodorant) 11 volunteers over 9 weeks.Mass spectrometry 16S rRNA inventories revealed decreases in chemical as well bacterial archaeal halting deodorant use. Specific compounds from used before study remain detectable with half-lives 0.5-1.9 weeks. The powder increased...
Abstract For the past half-century, structural biologists relied on notion that similar protein sequences give rise to structures and functions. While this assumption has driven research explore certain parts of universe, it disregards spaces don’t rely assumption. Here we areas universe where functions can be achieved by different structures. We predict ~200,000 for diverse from 1,003 representative genomes across microbial tree life annotate them functionally a per-residue basis. Structure...
Abstract In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2–12]. Given this impact, carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested comparing raw Voom-SNM-corrected data per-batch, finding predictive...
Standard anti-proliferative chemotherapy is relatively ineffective against slowly proliferating androgen-independent prostate cancer cells within metastatic sites. In contrast, the lipophilic cytotoxin thapsigargin, which causes apoptosis by disrupting intracellular free Ca2+ levels, effective both proliferative and quiescent (i.e., G0-arrested) cells. However, thapsigargin's mechanism of action indicates that it unlikely to be selective for or cells.We coupled a chemically modified form...
Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and developing infant gut microbiome is directly exposed. We investigated whether environmental in breastmilk affect composition function at 1 month. measured breastmilk, fecal short-chain fatty acids (SCFAs), from 16S rRNA gene amplicon sequencing using samples 267 mother-child pairs Norwegian Microbiota Cohort (NoMIC). tested 28 chemical exposures: polychlorinated...
Abstract Motivation : shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable focusing a single structure minimal free energy. We report recent extensions this approach. Results have rebuilt original shapes as repository components that us integrate established tools for analysis: , alishapes and pknots RG, including its extension p K iss . As spin-off, we obtain heretofore unavailable functionality: e....
Various indoor, outdoor, and host-associated environments contain small quantities of microbial biomass represent a niche that is often understudied because technical constraints. Many studies attempt to evaluate these low-biomass microbiome samples are riddled with erroneous results typically false positive signals obtained during the sampling process. We have investigated various kits methods determine limit detection pipelines. Here we present KatharoSeq, high-throughput protocol...
Abstract The vitamin D receptor is highly expressed in the gastrointestinal tract where it transacts gene expression. With current limited understanding of interactions between gut microbiome and D, we conduct a cross-sectional analysis 567 older men quantifying serum metabolites using LC-MSMS defining stool sub-Operational Taxonomic Units from16S ribosomal RNA sequencing data. Faith’s Phylogenetic Diversity non-redundant covariate analyses reveal that 1,25(OH) 2 level explains 5% variance...