Nicholas J. Croucher

The paper identifies invasion-associated genetic variants in pneumococcal lineages by separating serotype and lineage effects, highlighting candidate determinants for experimental investigation.

This study examines capsule switching in Streptococcus pneumoniae using whole-genome sequences, finding that switching is limited to specific capsule-type pairs and influenced by genetic and ecological factors.

The paper develops a mathematical model to predict vaccine replacement dynamics in Streptococcus pneumoniae and identifies optimal genomic surveillance strategies.

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

This study sequenced 4,475 H. influenzae isolates from Thailand and combined them with global data to show pervasive recombination and purifying selection, with MDR lineages widespread and not restricted to disease-causing subpopulations.

The paper investigates how prophage and bacterial competence machinery engage in an evolutionary arms race through chromosomal curing and transformation mechanisms.

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

PopPIPE clusters bacterial populations and detects transmission events using reference-free methods, outperforming traditional approaches in nosocomial outbreak analysis.

This paper introduces ska lo, a reference-free variant calling tool that uses a coloured De Bruijn graph to detect SNPs, insertions, deletions, and recombination events in pathogen genomes.

This paper compares four clustering methods for S. pneumoniae genomes to assess their accuracy in reflecting population structure and highlights the need for standardized nomenclature.

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

This paper introduces SKA2, a method for rapid and accurate genotyping of bacterial populations, showing superior variant recall and no false positives in outbreak simulations.

GNASTy improves pneumococcal serotyping by using a pangenome graph algorithm with Nanopore Adaptive Sampling, enhancing sensitivity for novel serotypes in complex samples.

ggCaller provides a fast and accurate method for pangenome annotation and clustering by integrating gene prediction, annotation, and clustering using de Bruijn Graphs, outperforming existing tools in speed and accuracy.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

This paper applies genome-wide association, prediction, and heritability analyses to bacterial data, identifying genetic factors influencing antibiotic resistance and within-host survival in Streptococcus pneumoniae.

The paper reconstructs the evolutionary histories of antibiotic-resistant pneumococcal lineages PMEN3 and PMEN9, showing how interspecies recombination contributes to antibiotic resistance and serotype switching.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

The paper uses genome-wide association studies to show human and pneumococcal genetic variation influences susceptibility and severity of pneumococcal meningitis.

PopPUNK provides fast, scalable clustering of bacterial genomes using k-mer analysis, enabling real-time outbreak detection and stable cluster naming across species and datasets.

This study identifies negative frequency-dependent selection in Escherichia coli ST131 as a key driver of its evolutionary success and adaptation to different ecological niches.

The paper introduces a Bayesian method for dating bacterial phylogenies, leveraging precomputed phylogenetic relationships to improve speed and scalability.

SuperDCA enables genome-wide epistasis analysis in bacteria by efficiently modeling interactions among polymorphisms, revealing novel biological insights in Streptococcus pneumoniae.

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.

Phandango provides an interactive web tool for exploring large-scale bacterial population genomics datasets by integrating multiple analysis outputs.

This paper identifies genomic variation associated with pneumococcal carriage duration using longitudinal data and genome-wide association studies.

The paper introduces fastGEAR, an algorithm for detecting both recent and ancestral recombination in bacterial populations, demonstrating its effectiveness on Streptococcus pneumoniae genomes.

The paper analyzes genetic data to show that pneumococcal capsule recombination generates novel serotypes, highlighting risks for vaccine efficacy.