Geert van Geest

Community needs for FAIR pathogen data: a cross-sectional survey of infectious-disease researchers and educators

This paper surveys infectious-disease stakeholders to identify barriers to FAIR pathogen data and prioritize training and infrastructure needs.

Characterization of heterogeneous bioinformatics training needs in the AI era

The paper introduces a network-based clustering method to identify distinct learner profiles from training-needs surveys, revealing heterogeneous bioinformatics training needs in the AI era.

Lineage-specific macrophage programs dictate metabolic suppression and stress responses associated with VBNC-like states in Listeria monocytogenes

This study shows that lineage-specific macrophage environments shape Listeria monocytogenes' metabolic and stress responses, leading to different intracellular survival strategies.

Using Glittr.org to find, compare and re-use online materials for training and education

Glittr.org curates Git repositories for computational life sciences education, enabling search and comparison based on topic, author, and engagement metrics.

Molecular characterization of cell types in the squid Loligo vulgaris

This study uses single-cell transcriptomics to characterize cell types in the squid Loligo vulgaris and identifies key markers for major nervous system components.

Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR

The paper introduces polyqtlR, a tool for QTL analysis in polyploid crops, enabling detection of QTL, exploration of allelic composition, and analysis of meiotic processes.

polymapR: linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

polymapR is an R package for genetic linkage analysis and map construction in polyploid crops, handling triploid, tetraploid, and hexaploid data with preferential pairing correction.