| # | Title | Journal | Year | Citations |
|---|
| 1 | SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments | Microbial Genomics | 2016 | 888 |
| 2 | Completing bacterial genome assemblies with multiplex MinION sequencing | Microbial Genomics | 2017 | 559 |
| 3 | ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads | Microbial Genomics | 2017 | 478 |
| 4 | Microreact: visualizing and sharing data for genomic epidemiology and phylogeography | Microbial Genomics | 2016 | 470 |
| 5 | Identification of Klebsiella capsule synthesis loci from whole genome data | Microbial Genomics | 2016 | 372 |
| 6 | MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies | Microbial Genomics | 2018 | 349 |
| 7 | ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping | Microbial Genomics | 2018 | 307 |
| 8 | NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats | Microbial Genomics | 2016 | 237 |
| 9 | Genome-scale rates of evolutionary change in bacteria | Microbial Genomics | 2016 | 224 |
| 10 | Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii | Microbial Genomics | 2019 | 209 |
| 11 | Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data | Microbial Genomics | 2016 | 208 |
| 12 | chewBBACA: A complete suite for gene-by-gene schema creation and strain identification | Microbial Genomics | 2018 | 201 |
| 13 | On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data | Microbial Genomics | 2017 | 198 |
| 14 | Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations | Microbial Genomics | 2018 | 197 |
| 15 | The diversity of Klebsiella pneumoniae surface polysaccharides | Microbial Genomics | 2016 | 185 |
| 16 | CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community | Microbial Genomics | 2016 | 176 |
| 17 | EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens | Microbial Genomics | 2015 | 174 |
| 18 | Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes | Microbial Genomics | 2019 | 171 |
| 19 | Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification | Microbial Genomics | 2021 | 168 |
| 20 | Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes | Microbial Genomics | 2016 | 162 |
| 21 | Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1 | Microbial Genomics | 2016 | 155 |
| 22 | ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes | Microbial Genomics | 2022 | 126 |
| 23 | Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone | Microbial Genomics | 2017 | 122 |
| 24 | mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species | Microbial Genomics | 2018 | 121 |
| 25 | Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank | Microbial Genomics | 2020 | 120 |
| 26 | SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology | Microbial Genomics | 2017 | 119 |
| 27 | Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive | Microbial Genomics | 2020 | 118 |
| 28 | In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages | Microbial Genomics | 2016 | 110 |
| 29 | Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi | Microbial Genomics | 2018 | 110 |
| 30 | Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK | Microbial Genomics | 2015 | 105 |
| 31 | Trends in fluoroquinolone resistance in Campylobacter | Microbial Genomics | 2018 | 100 |
| 32 | The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer | Microbial Genomics | 2016 | 99 |
| 33 | Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages | Microbial Genomics | 2018 | 95 |
| 34 | Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence | Microbial Genomics | 2018 | 91 |
| 35 | Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26 | Microbial Genomics | 2017 | 89 |
| 36 | Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens | Microbial Genomics | 2016 | 88 |
| 37 | Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores | Microbial Genomics | 2020 | 87 |
| 38 | Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships | Microbial Genomics | 2015 | 86 |
| 39 | Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal | Microbial Genomics | 2017 | 86 |
| 40 | Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing | Microbial Genomics | 2018 | 80 |
| 41 | Quantitative assessment of insertion sequence impact on bacterial genome architecture | Microbial Genomics | 2016 | 80 |
| 42 | Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches | Microbial Genomics | 2017 | 74 |
| 43 | Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history | Microbial Genomics | 2021 | 71 |
| 44 | Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198 | Microbial Genomics | 2019 | 69 |
| 45 | Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study | Microbial Genomics | 2020 | 69 |
| 46 | Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses | Microbial Genomics | 2020 | 69 |
| 47 | SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data | Microbial Genomics | 2018 | 68 |
| 48 | Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid | Microbial Genomics | 2020 | 68 |
| 49 | Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network | Microbial Genomics | 2016 | 67 |
| 50 | Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance | Microbial Genomics | 2020 | 67 |
