Christopher L. Dupont

Upper respiratory tract bacterial microbiome features associated with Streptococcus pneumoniae colonisation, environmental and demographic factors among older children in a rural setting in The Gambia

The study examines URT microbiome features linked to S. pneumoniae colonisation in older children in The Gambia, identifying microbial associations and environmental factors influencing colonisation.

Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics

Leviathan provides fast, memory-efficient, and scalable taxonomic and functional profiling for metagenomics and metatranscriptomics using (pan)genome-resolved references.

Benchmarking single cell transcriptome matching methods for incremental growth of cell atlases

The paper benchmarks seven computational tools for matching cell types across cell atlases, finding variations in accuracy and proposing a framework for incremental growth of cell atlases.

Blood cultures contain populations of genetically diverse Candida albicans strains that may differ in echinocandin tolerance and virulence

The paper identifies genetically diverse Candida albicans strains in blood cultures that differ in echinocandin tolerance and virulence, with implications for antifungal treatment.

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing

VEBA 2.0 is a modular bioinformatics suite that enables genome-resolved analysis of prokaryotes, microeukaryotes, and viruses from short- or long-read sequencing data, with applications in diverse environments.

Efficient Formation of Single-copy Human Artificial Chromosomes

This paper describes a method to efficiently form single-copy human artificial chromosomes by using a large construct and yeast spheroplast fusion to avoid multimerization.

METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

METATRYP v2 identifies shared peptides across organisms in metaproteomics to improve taxonomic attribution, showing low peptide sharing among marine microbes and coronaviruses.

Development of an Ocean Protein Portal for Interactive Discovery and Education

The paper develops the Ocean Protein Portal (OPP) to address big-data challenges in marine microbial proteomics by enabling data sharing, discovery, and educational use through interactive visualizations and metadata links.

Universal Loop assembly (uLoop): open, efficient, and species-agnostic DNA fabrication

The paper introduces uLoop, a DNA assembly method that enables efficient, hierarchical fabrication of large DNA constructs across any organism.

Diatom Centromeres Suggest a Novel Mechanism for Nuclear Gene Acquisition

The paper identifies diatom centromeres and shows that non-native DNA sequences can function as centromeres, suggesting a mechanism for foreign DNA acquisition.