Microbial Genomics

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. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-04-01 to 2024-04-01.)
ArticleCitations
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification160
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes127
Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank95
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores75
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses68
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history60
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance58
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid54
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands53
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex50
Recovery of small plasmid sequences via Oxford Nanopore sequencing35
A comprehensive and high-quality collection of Escherichia coli genomes and their genes33
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland33
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis31
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors29
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones28
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-1228
Genomic characterization of Salmonella Uzaramo for human invasive infection27
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning27
Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes25
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex24
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery24
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains23
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