Gemma Catherine Atkinson

Characterization of six environmental coli-phages isolated in Astana, Kazakhstan, during the School of Molecular and Theoretical Biology

The paper isolates and characterizes six new E. coli-infecting phages from Kazakhstan, expanding a phage collection and demonstrating phage research in high school education.

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection

This study identifies a novel bacterial defense mechanism where nucleoid-associated proteins detect phage-induced genome damage by relocating to the cytoplasm and activating immune effectors.

Characterization of five environmental phages infecting Escherichia coli K-12 isolated during a phage biology training course

The paper isolates and characterizes five Escherichia coli phages, identifies their defense system sensitivities, and highlights the educational value of phage isolation training.

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

The paper predicts structures for 27,000 viral proteins using AlphaFold2, revealing conserved folds across viruses infecting bacteria, archaea, and eukaryotes and identifying a new antiviral toxin-antitoxin system.

Systematic annotation of hyper-variability hotspots in phage genomes and plasmids

The paper introduces iLund4u, an algorithm to systematically annotate hyper-variability hotspots in phage genomes and plasmids, identifying 13.7K hotspots and 171K diverse protein families across 873K phage and 696K plasmid sequences.

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.

The paper introduces DefenseFinder, a resource for antiphage defense systems, including a web service, wiki, and databases with structure predictions.

LoVis4u: Locus Visualisation tool for comparative genomics

LoVis4u is a tool for visualizing genomic loci alignments, generating publication-ready PDFs from GenBank or GFF data, with customizable features for prokaryotic genomes.

Structural basis of Cfr-mediated antimicrobial resistance and mechanisms for its evasion

This study determines the structural basis of Cfr-mediated antimicrobial resistance and identifies mechanisms for evading it through ribosome structures with Cfr-modified 23S rRNA.

uORF4u: a tool for annotation of conserved upstream open reading frames

uORF4u annotates conserved upstream open reading frames (uORFs) in 5' upstream sequences of proteins or homologues using evolutionary conservation.

Predicting Functional Associations using Flanking Genes (FlaGs)

FlaGs predicts functional associations by analyzing gene neighborhood conservation across species, revealing new toxin-antitoxin systems in prokaryotes and bacteriophages.

ABCF ATPases involved in protein synthesis, ribosome assembly and antibiotic resistance: structural and functional diversification across the tree of life

The paper analyzes ABCF ATPases across 4505 genomes to uncover their diversity, subfamily relationships, and roles in antibiotic resistance and ribosome function.