Microbial Genomics

(The H4-Index of Microbial Genomics is 23. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 500 papers]. The publications cover those that have been published in the past four years, i.e., from 2019-10-01 to 2023-10-01.)
Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii132
Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank88
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification84
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible wit71
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes67
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores60
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history52
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses52
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid48
Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study47
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands46
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance41
An assessment of genome annotation coverage across the bacterial tree of life35
EvoMining reveals the origin and fate of natural product biosynthetic enzymes31
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex30
Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofi30
Recovery of small plasmid sequences via Oxford Nanopore sequencing30
A comprehensive and high-quality collection of Escherichia coli genomes and their genes29
Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes29
Coinfinder: detecting significant associations and dissociations in pangenomes27
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones26
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis26
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors25
Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization23
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning23
Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H2823
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex23
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland23