OOIR: Observatory of International Research

Papers

(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.)

Article	Citations
Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii	132
Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank	88
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification	84
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible wit	71
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes	67
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores	60
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history	52
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses	52
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid	48
Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study	47
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands	46
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance	41
An assessment of genome annotation coverage across the bacterial tree of life	35
EvoMining reveals the origin and fate of natural product biosynthetic enzymes	31
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex	30
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 biofi	30
Recovery of small plasmid sequences via Oxford Nanopore sequencing	30
A comprehensive and high-quality collection of Escherichia coli genomes and their genes	29
Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes	29
Coinfinder: detecting significant associations and dissociations in pangenomes	27
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones	26
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis	26
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors	25
Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization	23
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning	23

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28	23
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex	23
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland	23