Tim Downing

Insights into goatpox virus and sheeppox virus genomes from pangenome graphs

This study compares the genomic diversity and evolution of goatpox and sheeppox viruses using pangenome graphs, revealing structural variation at inverted terminal repeats as a key driver of diversity.

Using pangenome variation graphs to improve mutation detection in a large DNA virus

This paper demonstrates that pangenome variation graphs improve SNP detection in lumpy skin disease virus by capturing more genetic diversity and identifying variants missed by linear reference mapping.

Pathogenesis and immune responses to Eurasian avian like H1N1 and influenza D virus in pigs.

This study compares the pathogenesis and immune responses of EAavH1N1 and IDV in pigs, finding distinct viral kinetics and immune activation profiles.

A high-quality telomere-to-telomere LSDV genome assembly

The paper presents a high-quality telomere-to-telomere assembly of the LSDV genome using long-read sequencing, resolving structural ambiguities and improving genomic analysis.

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

The paper reconstructs 3,500 years of sheeppox virus evolution using ancient genomes from archaeological and medieval parchment sources, showing divergence events and gene inactivation.

Panalyze: automated virus pangenome variation graph construction, analysis and annotation

Panalyze constructs, analyzes, and annotates virus pangenome variation graphs, offering scalability and automation for viral genomic diversity studies.

Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks

This study compares protein-protein interactions of plasmid-encoded and chromosomal genes in bacteria, finding plasmid genes have more interactions but limited network impact.

Informing plasmid compatibility with bacterial hosts using protein-protein interaction data

The paper assesses plasmid-host compatibility by analyzing protein-protein interactions across 4,363 bacterial hosts, identifying species with high interaction rates with specific plasmids like pOXA-48.

High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria

The paper analyzes genomic variation in Leishmania tropica isolates to reveal mechanisms of genetic exchange and genome plasticity associated with treatment failure and relapse.

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

The paper examines the AMR gene diversity in ST131 E. coli using a preterm infant resistome, showing that plasmids drive AMR gene composition through conjugation and recombination.

Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones

The paper analyzes global E. coli ST131 genomes to trace the evolution and spread of antibiotic-resistant subclones, identifying a C2 lineage that displaced a C1 strain in an Irish LTCF.

Global genome diversity of the Leishmania donovani complex

The paper presents a comprehensive genome-wide study of Leishmania donovani complex isolates, revealing genetic diversity and structural variation across species and geographical regions.

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

The paper uses population genomics to analyze 4,071 E. coli ST131 isolates, revealing population structure, evolutionary relationships, and dynamics of AMR genes across three main clades and their subclades.

Complete assembly of Escherichia coli ST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

This study uses long-read sequencing to assemble E. coli ST131 genomes, revealing diverse plasmid and chromosomal contexts of antibiotic resistance genes.

Protein-protein interaction network topology as a measure of bacterial plasmid-chromosome co-evolution

The paper examines plasmid-chromosome gene interactions in E. coli to identify a new invariant of bacterial protein-protein interaction networks related to co-evolution.

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

This paper assembles and annotates reference genomes for Leishmania naiffi and Leishmania guyanensis, revealing genomic traits and evolutionary patterns in the Viannia subgenus.