OOIR: Observatory of International Research

Papers

(The H4-Index of Microbial Genomics is 21. 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 2020-09-01 to 2024-09-01.)

Article	Citations
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification	231
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes	162
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores	77
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex	69
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance	65
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history	65
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands	57
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12	41
Recovery of small plasmid sequences via Oxford Nanopore sequencing	39
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning	33
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction	30
A comprehensive and high-quality collection of Escherichia coli genomes and their genes	30
ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data	29
From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment	27
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery	27
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147	24
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains	23
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants	23
Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction	23
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici	22
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands	22
Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology	21
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm	21