Mathias Kuhring
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View article: Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19 Open
View article: Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19 Open
The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome…
View article: SODAR: managing multiomics study data and metadata
SODAR: managing multiomics study data and metadata Open
Scientists employing omics in life science studies face challenges such as the modeling of multiassay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are …
View article: Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19
Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19 Open
The clinical course of the 2019 coronavirus disease (COVID-19) is variable and to a substantial degree still unpredictable, especially in persons who have neither been vaccinated nor recovered from previous infection. We hypothesized that …
View article: SODAR: managing multi-omics study data and metadata
SODAR: managing multi-omics study data and metadata Open
Scientists employing omics in life science studies face challenges such as the modeling of multi assay studies, recording of all relevant parameters, and managing many samples with their metadata. They must manage many large files that are…
View article: Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance
Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance Open
Background CKD is characterized by a sustained proinflammatory response of the immune system, promoting hypertension and cardiovascular disease. The underlying mechanisms are incompletely understood but may be linked to gut dysbiosis. Dysb…
View article: Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance
Inflammation in children with chronic kidney disease linked to gut dysbiosis and metabolite imbalance Open
Chronic kidney disease (CKD) is characterized by a sustained pro-inflammatory response. The underlying mechanisms are incompletely understood, but may be linked to gut dysbiosis. Dysbiosis has been described in adults with CKD; however, co…
View article: An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples
An iterative and automated computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic samples Open
Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. How…
View article: AltamISA: a Python API for ISA-Tab files
AltamISA: a Python API for ISA-Tab files Open
View article: Computational Methods for Omics Sequence Data with Focus on Non-Model Organisms
Computational Methods for Omics Sequence Data with Focus on Non-Model Organisms Open
Sequence data are the backbone for many biological research areas including but not limited to genomics, proteomics as well as proteogenomics. Sequence acquisition is facilitated by a wide selection of advanced technologies such as Next Ge…
View article: Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation
Parasitic Nematodes Exert Antimicrobial Activity and Benefit From Microbiota-Driven Support for Host Immune Regulation Open
Intestinal parasitic nematodes live in intimate contact with the host microbiota. Changes in the microbiome composition during nematode infection affect immune control of the parasites and shifts in the abundance of bacterial groups have b…
View article: Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development
Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development Open
Gastrointestinal nematodes are among the most prevalent parasites infecting humans and livestock worldwide. Infective larvae of the soil-transmitted nematode Ascaris spp. enter the host and start tissue migration by crossing the intestinal…
View article: SuRankCo: supervised ranking of contigs in de novo assemblies
SuRankCo: supervised ranking of contigs in de novo assemblies Open
SuRankCo analyzes the reliability of de novo assemblies on the contig level and thereby allows quality control and ranking prior to further downstream and validation experiments.