Neil Hall

This study compares the transcriptional profiles of two closely related fungi during early wheat root colonization, revealing differences in gene expression that underlie their distinct lifestyles.

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

The paper uses single-cell sequencing to reveal genetic diversity in Bodo flagellates and their bacterial endosymbionts, showing SSU rDNA is insufficient for species classification.

This paper develops a population sequencing pipeline to estimate mutation rates in E. coli under varying population densities, finding a strong negative association between density and mutation rates.

This paper improves gene model annotations across 82 Fusarium genomes by combining existing annotations with de novo predictions, enhancing consistency and quality for comparative genomics.

This study generates high-quality genome assemblies for Gaeumannomyces species, revealing virulence lineage variation and genomic features linked to pathogenicity and lifestyle.

The paper identifies multiple independent reassignments of the UAG stop codon to encode amino acids in Phyllopharyngean ciliates, showing UAG as a sense codon and UAA as the fixed stop codon.

This study analyzes 836 Salmonella Panama genomes to reveal population structure, antimicrobial resistance, and genetic markers of invasiveness across global regions.

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

The paper uses single-cell genomics to analyze bacterial population structures in antibiotic stress experiments, revealing sub-populations and resistance development not detectable with bulk sequencing.

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

The paper analyzes recombination patterns in hexaploid wheat, identifies genes controlling recombination and gene conversion, and highlights a novel RecQ helicase gene involved in gene conversion.

The paper analyzes genomic and phylogenetic data of Salmonella Typhimurium and monophasic variants from Colombia to understand their population structure, evolution, and antibiotic resistance.

The paper identifies hidden genetic and epigenetic variation in polyploid wheat that contributes to local adaptation and suggests using methylation and transposon diversity for breeding.

The paper analyzes the genetic diversity of Hymenoscyphus fraxineus, showing the European population was founded by two divergent haplotypes with adaptive potential.

The paper introduces a modified sequence capture method that enables simultaneous analysis of genotype and methylation from the same genomic DNA sample in wheat.