Sophie S. Abby

UbiB proteins mediate an ATP-dependent decarboxylation step in bacterial ubiquinone biosynthesis

This study identifies UbiB as an ATP-dependent decarboxylase in bacterial ubiquinone biosynthesis, showing it can replace the UbiX/UbiD system in Escherichia coli.

Isoprenoid quinone profiling using a novel semi-quantitative HPLC-MS/MS method: application to wastewater sludges

This paper introduces a semi-quantitative HPLC-MS/MS method for detecting isoprenoid quinones in wastewater sludges, identifying 57 quinones across treatment stages.

COCOA-Tree: Phylogenetic visualization and comparative analysis of coevolving residues

COCOA-Tree reanalyzes coevolution datasets to uncover evolutionary properties of coevolving residues and shows different metrics identify distinct groups.

Global distribution of isoprenoid quinones across Bacteria

This study maps the distribution of isoprenoid quinones in Bacteria using genomic data and phylogenetic analysis, revealing new insights into their evolutionary history and metabolic adaptations.

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes

The paper analyzes insertion sequences (ISs) in prokaryotic genomes using transposon ecology to uncover general principles and niche specificities shaping their distribution and activity.

A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism

The paper identifies a novel ancestral high redox potential quinone, methyl-plastoquinone, and shows its evolutionary origin predates the Great Oxygenation Event.

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

MacSyFinder v2 improves molecular system detection in microbial genomes with enhanced modeling, search engine, and updated models.