Helena B. Cooper

Genomic indicators of gene function: A systematic assessment of the human genome

The paper assesses genomic indicators of gene function in the human genome, finding that transcriptional activity and evolutionary conservation are strongest predictors of functional regions.

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports co-existence of diverse lineages

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

IS-capades of Klebsiella pneumoniae: Insertion sequences drive metabolic loss in obscure sub-lineages

The paper investigates the relationship between insertion sequences (IS) and metabolic capacity in four Klebsiella pneumoniae sub-lineages, finding higher IS loads correlate with reduced metabolic gene numbers and substrate utilisation.

Wild type domestication: loss of intrinsic metabolic traits concealed by culture in rich media

The paper identifies hidden metabolic mutations in Klebsiella pneumoniae cultures grown in rich media, showing how these mutations can persist undetected and affect auxotrophy.

A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex

This paper constructs a comprehensive pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, showing improved accuracy in growth predictions compared to previous models.

Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models

Bactabolize generates strain-specific bacterial metabolic models and growth predictions, outperforming existing tools for Klebsiella pneumoniae.

Features of Functional Human Genes.

The paper investigates genomic features associated with functional genes and finds evolutionary conservation and transcriptional activity are the strongest indicators of functionality.