Peter J. Schaap

A metadata managed FAIR end-to-end workflow for microbial community Omics data analysis

The paper presents a metadata-managed FAIR end-to-end workflow for microbial community Omics data analysis, demonstrating its reliability and reproducibility through mock datasets.

Unraveling the metabolic interactions of a Dehalobacter-containinganaerobic mixed culture for bioremediation

The paper uses genome-resolved metagenomics and metabolic modeling to study microbial interactions in a Dehalobacter-containing community for chlorinated benzene degradation.

Metabolic modeling unveils potential probiotic roles of Flavonifractor plautii in reshaping the Western gut microbiota landscape

This study develops a genome-scale metabolic model of Flavonifractor plautii to explore its probiotic potential and ecological roles in the gut microbiota.

Comparative genomics of Rickettsiella bacteria reveal variable metabolic pathways potentially involved in symbiotic interactions with arthropods

This study sequenced Rickettsiella genomes from ticks and used comparative genomics to identify variable metabolic pathways and potential mechanisms for symbiotic interactions with arthropods.

MiGenPro: A linked data workflow for phenotype-genotype prediction of microbial traits using machine learning.

MiGenPro trains machine learning models to predict microbial traits from annotated genomes using linked data and semantic frameworks.

Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts

This study uses deep sequencing on 16 Ixodes ricinus ticks to analyze symbionts, revealing genome sequences, transmission modes, and genetic variability in Rickettsia helvetica.

Implementation of a Clostridium luticellarii genome-scale model for upgrading syngas fermentations

This paper develops a genome-scale metabolic model for Clostridium luticellarii to improve syngas fermentation, showing its potential for producing value-added biochemicals.

FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

The paper introduces FROG analysis to standardize reproducibility assessments of genome-scale metabolic models, resulting in full reproducibility of all tested models.

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

This study evaluates COBRA-based tools for microbial consortia modeling using FAIR criteria and experimental data, finding that newer, better-documented tools generally outperform older ones in quality and performance.

Identification of Aspergillus niger aquaporins involved in hydrogen peroxide signaling

The paper identifies AQPF, an aquaporin in Aspergillus niger, as facilitating hydrogen peroxide transport across the cell membrane, supporting its role as a signaling molecule in glucose oxidase induction.

FAIR Data Station for Lightweight Metadata Management & Validation of Omics Studies

The paper introduces FAIR Data Station, a tool for managing and validating metadata in omics studies to support FAIR principles through standardized workflows and metadata export.

Exploring the adaptability and robustness of the central carbon metabolism of Mycoplasma pneumoniae

This study analyzes the adaptability and robustness of Mycoplasma pneumoniae's central carbon metabolism using metabolomics data and a dynamic model, identifying key control hubs.

Comparative genome-scale constraint-based metabolic modeling reveals key lifestyle features of plant-associated Pseudomonas spp.

The paper uses metabolic modeling to compare plant-associated Pseudomonas strains and identifies metabolic differences between beneficial and pathogenic species.

Classification of the plant-associated phenotype of Pseudomonas strains using genome properties and machine learning

The paper uses genome properties and machine learning to classify Pseudomonas strains as plant-beneficial or pathogenic, identifying 28 key features that distinguish these phenotypes.

Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum

This study develops a genome-scale metabolic model for Anaerotignum neopropionicum to understand ethanol metabolism via the acrylate pathway and validate it with experimental data.

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

SALARECON links the Atlantic salmon genome to metabolic fluxes and growth, showing that marine feed efficiency can be achieved by supplementing plant- and insect-based feeds with specific amino acids.

Large scale function-based genome prospecting for industrial traits applied to 1,3-propanediol production.

The paper identifies 187 new candidate species for 1,3-propanediol production using a function-based genome mining approach.

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

This paper presents a chromosome-level genome assembly for the black tiger shrimp, enabling the identification of novel growth-associated genes through transcriptome comparison.

A protocol for adding knowledge to Wikidata, a case report

The paper describes a protocol for enhancing Wikidata with structured knowledge using Shape Expressions, demonstrating its application to SARS-CoV-2 and other coronaviruses.

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

Modeling a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to increase syngas conversion to medium-chain fatty-acids

The paper develops a genome-scale metabolic model of a co-culture of Clostridium autoethanogenum and Clostridium kluyveri to optimize syngas conversion to medium-chain fatty acids.

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

The paper identifies a fungal citrate exporter in Aspergillus niger by comparing gene expression under different citrate-producing conditions and validating its function in yeast and the fungus itself.

Consistency, Inconsistency and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome Scale Metabolic Modelling

This study examines name inconsistencies and ambiguities in biochemical databases used for genome-scale metabolic modeling, finding up to 83.1% inconsistency and proposing solutions for better mapping.

Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

The paper analyzes the correlation between 16S-rRNA phylogeny and protein domain content in bacterial genomes to assess functional diversity and its relationship with evolutionary distance.

The Rumen Metatranscriptome Landscape Reflects Dietary Adaptation and Methanogenesis in Lactating Dairy Cows

The paper examines how corn silage enhanced diets affect rumen microbiota and methanogenesis in dairy cows, finding reduced methane emissions and altered gene expression.

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining

The paper introduces GBOL, a formalized ontology for genome annotations, to improve interoperability and enable large-scale comparative analysis of functional genomic data.