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Author: Derrick W Crook

Rankings

  • All-time downloads: 263,657 (rank: 201 )
  • Categories:
    • bioinformatics: 14,475 (rank: 560 (tie) )
    • epidemiology: 28,331 (rank: 714 )
    • genomics: 5,674 (rank: 4,630 (tie) )
    • infectious diseases: 168,038 (rank: 189 )
    • microbiology: 47,139 (rank: 324 )

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Preprints

Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting

epidemiology more details view paper

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Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays

infectious diseases more details view paper
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    • Site-wide: 45
    • In infectious diseases: 20
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    • Site-wide: 59
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Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK

epidemiology more details view paper
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    • Site-wide: 307
    • In epidemiology: 59
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Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

microbiology more details view paper
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    • Site-wide: 340
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Virus detection and identification in minutes using single-particle imaging and deep learning

infectious diseases more details view paper
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    • Site-wide: 948
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Antibodies to SARS-CoV-2 are associated with protection against reinfection

infectious diseases more details view paper
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    • Site-wide: 966
    • In infectious diseases: 312
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    • Site-wide: 1,101
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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

bioinformatics more details view paper
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    • Site-wide: 1,311
    • In bioinformatics: 72
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Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

infectious diseases more details view paper
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    • Site-wide: 1,726
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    • Site-wide: 7,713
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Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study

infectious diseases more details view paper
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    • Site-wide: 2,880
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An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status

infectious diseases more details view paper
  • Downloaded 3,676 times
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    • Site-wide: 4,093
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Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

genomics more details view paper
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    • Site-wide: 4,743
    • In genomics: 466
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Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing

infectious diseases more details view paper
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    • Site-wide: 4,762
    • In infectious diseases: 943
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Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status

infectious diseases more details view paper
  • Downloaded 3,245 times
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    • Site-wide: 4,896
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Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches

microbiology more details view paper
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    • Site-wide: 5,505
    • In microbiology: 351
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Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis

microbiology more details view paper
  • Downloaded 2,720 times
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    • Site-wide: 6,326
    • In microbiology: 398
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Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
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    • Site-wide: 7,916
    • In bioinformatics: 865
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Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

microbiology more details view paper
  • Downloaded 2,133 times
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    • Site-wide: 9,054
    • In microbiology: 536
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MinION Nanopore Sequencing of Multiple Displacement Amplified Mycobacteria DNA Direct from Sputum

microbiology more details view paper
  • Downloaded 1,835 times
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    • Site-wide: 11,341
    • In microbiology: 660
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Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell

infectious diseases more details view paper
  • Downloaded 1,448 times
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    • Site-wide: 16,291
    • In infectious diseases: 1,854
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Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

microbiology more details view paper
  • Downloaded 1,382 times
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    • Site-wide: 17,528
    • In microbiology: 1,014
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Severe infections emerge from the microbiome by adaptive evolution

genomics more details view paper
  • Downloaded 1,353 times
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    • Site-wide: 18,060
    • In genomics: 1,725
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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

microbiology more details view paper
  • Downloaded 1,342 times
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    • Site-wide: 18,269
    • In microbiology: 1,059
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    • Site-wide: 100,944
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    • Site-wide: 153,681

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

bioinformatics more details view paper
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    • Site-wide: 18,951
    • In bioinformatics: 2,142
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Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis

microbiology more details view paper
  • Downloaded 1,279 times
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    • Site-wide: 19,658
    • In microbiology: 1,147
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    • Site-wide: 89,401
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SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 and correlates of protection in the UK general population

infectious diseases more details view paper
  • Downloaded 1,190 times
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    • Site-wide: 21,901
    • In infectious diseases: 2,153
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    • Site-wide: 4,134
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    • Site-wide: 1,114

High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families

microbiology more details view paper
  • Downloaded 867 times
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    • Site-wide: 35,109
    • In microbiology: 2,067
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TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data

bioinformatics more details view paper
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    • In bioinformatics: 4,012
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Flanker: a tool for comparative genomics of gene flanking regions

bioinformatics more details view paper
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    • In bioinformatics: 4,612
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    • Site-wide: 8,594
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Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

microbiology more details view paper
  • Downloaded 611 times
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    • Site-wide: 57,313
    • In microbiology: 3,567
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Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC

microbiology more details view paper
  • Downloaded 570 times
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    • Site-wide: 62,478
    • In microbiology: 3,934
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    • Site-wide: 162,081
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Genomic epidemiology of a complex, multi-species plasmid-borne blaKPC carbapenemase outbreak in Enterobacterales in the UK, 2009-2014

genomics more details view paper
  • Downloaded 554 times
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    • Site-wide: 64,650
    • In genomics: 4,588
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    • Site-wide: 95,118
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Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

microbiology more details view paper
  • Downloaded 526 times
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    • In microbiology: 4,427
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Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers

infectious diseases more details view paper
  • Downloaded 523 times
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    • Site-wide: 69,349
    • In infectious diseases: 3,868
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DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

microbiology more details view paper
  • Downloaded 522 times
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    • Site-wide: 69,452
    • In microbiology: 4,476
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    • Site-wide: 92,912
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Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

microbiology more details view paper
  • Downloaded 521 times
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BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.

microbiology more details view paper
  • Downloaded 470 times
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    • In microbiology: 5,169
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Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

microbiology more details view paper
  • Downloaded 460 times
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    • Site-wide: 80,125
    • In microbiology: 5,295
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Identifying mixed Mycobacterium tuberculosis infection and laboratory cross-contamination during Mycobacterial sequencing programs

microbiology more details view paper
  • Downloaded 449 times
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    • Site-wide: 82,199
    • In microbiology: 5,466
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Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

genomics more details view paper
  • Downloaded 446 times
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A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

microbiology more details view paper
  • Downloaded 433 times
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    • Site-wide: 85,264
    • In microbiology: 5,708
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Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing

microbiology more details view paper
  • Downloaded 426 times
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    • Site-wide: 86,770
    • In microbiology: 5,818
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Hash-based core genome multi-locus sequencing typing for Clostridium difficile

microbiology more details view paper
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Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the hospital environment: a bacterial genome-wide association study

infectious diseases more details view paper
  • Downloaded 386 times
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Genomic network analysis of an environmental and livestock IncF plasmid population

bioinformatics more details view paper
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    • Site-wide: 100,463
    • In bioinformatics: 8,609
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The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

microbiology more details view paper
  • Downloaded 362 times
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    • Site-wide: 100,840
    • In microbiology: 6,967
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The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

microbiology more details view paper
  • Downloaded 358 times
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Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline

microbiology more details view paper
  • Downloaded 351 times
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    • Site-wide: 103,497
    • In microbiology: 7,190
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Phenotypically distinct human sequence is widespread in publicly archived microbial reads: an evaluation of methods for its detection

bioinformatics more details view paper
  • Downloaded 290 times
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    • Site-wide: 118,948
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When do big problems far away become smaller than the problems closer to home: Lessons for antimicrobial resistance from Father Ted

epidemiology more details view paper
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Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopaedic Device Infection

infectious diseases more details view paper
  • Downloaded 276 times
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    • Site-wide: 122,835
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Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

microbiology more details view paper
  • Downloaded 274 times
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    • Site-wide: 123,169
    • In microbiology: 8,879
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Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting

epidemiology more details view paper
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Ten years of population-level genomic Escherichia coli and Klebsiella pneumoniae serotype surveillance informs vaccine development for invasive infections

infectious diseases more details view paper
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Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.

infectious diseases more details view paper
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