Biology subjects

de Vries, F.

Publications and source records attributed to de Vries, F..

2 recordsLinked to original sources

bioRxiv2025

PanVA: a visual analytics tool for pangenomic variant analysis

SummaryThe growing number of sequences and increasing proof that single references create reference bias have driven the development of pangenomes to represent the genomic diversity of species. To leverage this complex diversity information for biological insights, analysis and visualization support are needed to explore the variants in the context of metadata and phylogenies. We developed PanVA, an interactive visual analytics tool for exploring sequence variants in groups of homologous sequences in their biological context. PanVA is a web application that allows users to explore existing instances or create new ones to visualize their own data. Availability and ImplementationThe PanVA source code is available on GitHub at https://github.com/PanBrowse/PanVA under the GPLv3 License. Documentation and and public demo instances showcasing examples can be accessed at https://panbrowse.github.io/PanVA/.

bioinformatics↗

bioRxiv2023

A fast-slow trait continuum at the level of entire communities

Across the tree of life, organismal functional strategies form a continuum from slow-to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above-and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a slow-fast axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that slow and fast strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.

ecology↗