Niels Zondervan

Wageningen University & Research | WUR · Department of Food Sciences and Agrotechnology

This method paper presents a template solution for text mining of scientific literature using the R tm package. Literature to be analyzed can be collected manually or automatically using the code provided with this paper. Once the literature is collected, the three steps for conducting text mining can be performed as outlined below: • loading and c...

The disruptions caused by the COVID-19 pandemic have forced many companies in the logistics sector to innovate, or even transform their business and underlying processes. Closing borders, limited supply and manpower, and continuous changes in regulations challenged many logistics firms to innovate. This study analyzes 5098 abstracts of logistics ar...

To gain insights into the genotype-phenotype relationships in Mycoplasmas, we set to investigate which Mycoplasma proteins are most predictive of tissue and host trophism and to which functional groups of proteins they belong. We retrieved and annotated 430 Mycoplasma genomes and combined their genome information with date on which host and tissue...

In this study we explored the adaptability and robustness of glycolysis and pyruvate metabolism of Mycoplasma pneumoniae (MPN). We used a dual approach, we analysed metabolomics data collected for a large number of OE and KO mutants and perturbation samples. Furthermore, we trained a dynamic model of central carbon metabolism and tested the model c...

Sustainable production of fish and seafood products contributes to achieving the economic, social, and environmental goals in fisheries. Different sustainability strategies are applied to achieve these three goals. This paper presents a meta-analysis of the status and implementation of various sustainable fishery management strategies in the Philip...

This research studies patterns in the interaction between bacterial pathogens and their human and animal host. Among the studied pathogens are the lung pathogens Mycobacterium tuberculosis, various Mycoplasma strains such as the lung pathogen M. pneumoniae, and various Staphylococcus and Streptococcus strains such as the soft tissue infecting bacte...

p>Following publication of the original article [1], it was reported that there was a missing reference in the Methods section and should have been reference [2] at the end of the following sentence: The GNU “parallel” package was used to perform all of the above steps in parallel [2]. This reference has been inserted in the original article, the s...

Background Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype. Results We compared 235 Staphylococ...

Background Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representing biomolecules as nodes and their interactions as edges. Very often the input data come from various sorts of omics analyses. Thos...

Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review r...

Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant M. tuberculosis strains makes treating tuberculosis increasingly challenging. In order to develop novel intervention strategies, detailed understanding of the molecular mechanisms behind the success of this pathogen is required. Here, we review r...