Maarten J. M. F. Reijnders

On the state of protein function prediction: a report on the fourth CAFA challenge

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

CrowdGO: machine learning and semantic similarity guided consensus Gene Ontology annotation

CrowdGO improves gene function annotations by combining machine learning with semantic similarity to produce consensus Gene Ontology terms with high precision and recall.

Wei2GO: weighted sequence similarity-based protein function prediction

Wei2GO improves protein function prediction by using weighted sequence similarity, outperforming existing web servers and reducing computational time.

Summary visualisations of Gene Ontology terms with GO-Figure!

GO-Figure! is an open-source Python tool that generates semantic similarity scatterplots of GO term lists to aid in visualizing and comparing functional enrichment results.

Anopheles mosquitoes revealed new principles of 3D genome organization in insects

This study profiles 3D genome organization in five Anopheles mosquito species, identifying long-range looping interactions conserved over 100 million years and distinct from known chromatin mechanisms.

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

The paper improves Anopheles genome assemblies using comparative genomics methods and experimental data, resulting in more contiguous and chromosomally anchored assemblies.

Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors

The paper presents the genome of Cephus cinctus, a wheat pest, and analyzes its chemoreceptor evolution, identifying conserved and lineage-specific gene expansions.