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Author: Derrick Crook

Rankings

  • All-time downloads: 197,982 (rank: 288 )
  • Categories:
    • bioinformatics: 13,290 (rank: 502 )
    • epidemiology: 496 (rank: 15,445 (tie) )
    • genomics: 5,423 (rank: 4,252 )
    • infectious diseases: 138,400 (rank: 152 )
    • microbiology: 40,373 (rank: 269 )

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Preprints

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: 48
    • In infectious diseases: 18
  • Year to date:
    • Site-wide: 43
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    • Site-wide: 20

Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

microbiology more details view paper
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    • Site-wide: 325
    • In microbiology: 34
  • Year to date:
    • Site-wide: 40
  • Since beginning of last month:
    • Site-wide: 26

Virus detection and identification in minutes using single-particle imaging and deep learning

infectious diseases more details view paper
  • Downloaded 10,581 times
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    • Site-wide: 777
    • In infectious diseases: 240
  • Year to date:
    • Site-wide: 2,110
  • Since beginning of last month:
    • Site-wide: 4,060

Antibodies to SARS-CoV-2 are associated with protection against reinfection

infectious diseases more details view paper
  • Downloaded 10,065 times
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    • Site-wide: 837
    • In infectious diseases: 253
  • Year to date:
    • Site-wide: 579
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    • Site-wide: 2,140

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

bioinformatics more details view paper
  • Downloaded 8,396 times
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    • Site-wide: 1,047
    • In bioinformatics: 62
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    • Site-wide: 22,759
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    • Site-wide: 28,026

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
  • Downloaded 6,454 times
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    • Site-wide: 1,463
    • In infectious diseases: 388
  • Year to date:
    • Site-wide: 6,367
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    • Site-wide: 7,752

Differential occupational risks to healthcare workers from SARS-CoV-2: A prospective observational study

infectious diseases more details view paper
  • Downloaded 4,401 times
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    • Site-wide: 2,491
    • In infectious diseases: 537
  • Year to date:
    • Site-wide: 7,448
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    • Site-wide: 21,429

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis.

genomics more details view paper
  • Downloaded 3,275 times
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    • Site-wide: 3,809
    • In genomics: 419
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    • Site-wide: 87,284
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Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches

microbiology more details view paper
  • Downloaded 2,866 times
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    • Site-wide: 4,576
    • In microbiology: 291
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    • Site-wide: 46,604
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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
  • Downloaded 2,707 times
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    • Site-wide: 4,990
    • In infectious diseases: 840
  • Year to date:
    • Site-wide: 5,831
  • Since beginning of last month:
    • Site-wide: 8,161

Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis

microbiology more details view paper
  • Downloaded 2,374 times
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    • Site-wide: 6,073
    • In microbiology: 358
  • Year to date:
    • Site-wide: 12,104
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    • Site-wide: 11,997

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,164 times
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    • Site-wide: 6,941
    • In bioinformatics: 818
  • Year to date:
    • Site-wide: 19,957
  • Since beginning of last month:
    • Site-wide: 23,629

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

microbiology more details view paper
  • Downloaded 2,096 times
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    • Site-wide: 7,281
    • In microbiology: 417
  • Year to date:
    • Site-wide: 83,691
  • Since beginning of last month:
    • Site-wide: 99,964

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 1,633 times
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    • Site-wide: 10,521
    • In infectious diseases: 1,291
  • Year to date:
    • Site-wide: 831
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    • Site-wide: 493

MinION Nanopore Sequencing of Multiple Displacement Amplified Mycobacteria DNA Direct from Sputum

microbiology more details view paper
  • Downloaded 1,605 times
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    • Site-wide: 10,799
    • In microbiology: 612
  • Year to date:
    • Site-wide: 19,252
  • Since beginning of last month:
    • Site-wide: 16,849

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

microbiology more details view paper
  • Downloaded 1,329 times
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    • Site-wide: 14,320
    • In microbiology: 821
  • Year to date:
    • Site-wide: 91,139
  • Since beginning of last month:
    • Site-wide: 98,420

Severe infections emerge from the microbiome by adaptive evolution

genomics more details view paper
  • Downloaded 1,314 times
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    • Site-wide: 14,559
    • In genomics: 1,515
  • Year to date:
    • Site-wide: 114,648
  • Since beginning of last month:
    • Site-wide: 105,993

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 1,303 times
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    • Site-wide: 14,746
    • In infectious diseases: 1,507
  • Year to date:
    • Site-wide: 11,819
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    • Site-wide: 15,189

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

microbiology more details view paper
  • Downloaded 1,282 times
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    • Site-wide: 15,120
    • In microbiology: 871
  • Year to date:
    • Site-wide: 59,239
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    • Site-wide: 88,234

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 1,206 times
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    • Site-wide: 16,568
    • In microbiology: 953
  • Year to date:
    • Site-wide: 55,772
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    • Site-wide: 79,182

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

bioinformatics more details view paper
  • Downloaded 1,050 times
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    • Site-wide: 20,332
    • In bioinformatics: 2,395
  • Year to date:
    • Site-wide: 8,332
  • Since beginning of last month:
    • Site-wide: 15,525

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 1,046 times
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    • Site-wide: 20,450
    • In infectious diseases: 1,758
  • Year to date:
    • Site-wide: 1,459
  • Since beginning of last month:
    • Site-wide: 518

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 794 times
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    • Site-wide: 30,318
    • In microbiology: 1,793
  • Year to date:
    • Site-wide: 138,570
  • Since beginning of last month:
    • Site-wide: 137,749

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
  • Downloaded 717 times
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    • Site-wide: 34,853
    • In bioinformatics: 3,867
  • Year to date:
    • Site-wide: 76,963
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    • Site-wide: 71,985

Nested Russian Doll-like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC

microbiology more details view paper
  • Downloaded 550 times
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    • Site-wide: 48,987
    • In microbiology: 3,067
  • Year to date:
    • Site-wide: 125,831
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    • Site-wide: 137,754

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

microbiology more details view paper
  • Downloaded 505 times
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    • Site-wide: 54,167
    • In microbiology: 3,462
  • Year to date:
    • Site-wide: 70,509
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    • Site-wide: 52,864

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

microbiology more details view paper
  • Downloaded 477 times
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    • Site-wide: 57,789
    • In microbiology: 3,741
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    • Site-wide: 79,740
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    • Site-wide: 85,105

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 466 times
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    • Site-wide: 59,178
    • In genomics: 4,381
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    • Site-wide: 83,248
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    • Site-wide: 103,575

Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

microbiology more details view paper
  • Downloaded 452 times
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    • Site-wide: 61,164
    • In microbiology: 3,998
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    • Site-wide: 120,915
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    • Site-wide: 137,336

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

microbiology more details view paper
  • Downloaded 434 times
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    • Site-wide: 63,750
    • In microbiology: 4,223
  • Year to date:
    • Site-wide: 78,527
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    • Site-wide: 56,440

Flanker: a tool for comparative genomics of gene flanking regions

bioinformatics more details view paper
  • Downloaded 423 times
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    • Site-wide: 65,534
    • In bioinformatics: 6,360
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    • Site-wide: 5,442
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    • Site-wide: 6,559

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

microbiology more details view paper
  • Downloaded 408 times
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    • Site-wide: 68,020
    • In microbiology: 4,549
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    • Site-wide: 119,940
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    • Site-wide: 101,749

Identifying mixed Mycobacterium tuberculosis infection and laboratory cross-contamination during Mycobacterial sequencing programs

microbiology more details view paper
  • Downloaded 399 times
  • Download rankings, all-time:
    • Site-wide: 69,331
    • In microbiology: 4,671
  • Year to date:
    • Site-wide: 131,993
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    • Site-wide: 132,628

Molecular diagnosis of orthopaedic device infection direct from sonication fluid by metagenomic sequencing

microbiology more details view paper
  • Downloaded 394 times
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    • Site-wide: 70,299
    • In microbiology: 4,733
  • Year to date:
    • Site-wide: 130,852
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    • Site-wide: 130,402

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

microbiology more details view paper
  • Downloaded 388 times
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    • Site-wide: 71,357
    • In microbiology: 4,815
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    • Site-wide: 105,019
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    • Site-wide: 122,458

Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries

genomics more details view paper
  • Downloaded 368 times
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    • Site-wide: 74,742
    • In genomics: 5,078
  • Year to date:
    • Site-wide: 59,515
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    • Site-wide: 94,318

Hash-based core genome multi-locus sequencing typing for Clostridium difficile

microbiology more details view paper
  • Downloaded 367 times
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    • Site-wide: 75,032
    • In microbiology: 5,111
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    • Site-wide: 132,186
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    • Site-wide: 113,258

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

microbiology more details view paper
  • Downloaded 314 times
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    • Site-wide: 85,281
    • In microbiology: 5,962
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    • Site-wide: 112,700

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline

microbiology more details view paper
  • Downloaded 312 times
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    • Site-wide: 85,568
    • In microbiology: 5,994
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    • Site-wide: 118,312
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    • Site-wide: 84,989

Genomic network analysis of an environmental and livestock IncF plasmid population

bioinformatics more details view paper
  • Downloaded 311 times
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    • Site-wide: 85,822
    • In bioinformatics: 7,713
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    • Site-wide: 72,365
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    • Site-wide: 91,957

Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting

epidemiology more details view paper
  • Downloaded 262 times
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    • Site-wide: 96,616
    • In epidemiology: 3,962
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    • Site-wide: 131,548

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

microbiology more details view paper
  • Downloaded 253 times
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    • Site-wide: 98,595
    • In microbiology: 7,111
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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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    • Site-wide: 102,851
    • In epidemiology: 4,218
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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
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    • Site-wide: 103,943
    • In bioinformatics: 8,847
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    • Site-wide: 88,311
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Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

microbiology more details view paper
  • Downloaded 220 times
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    • Site-wide: 106,202
    • In microbiology: 7,779
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    • Site-wide: 132,760
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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 147 times
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    • Site-wide: 122,287
    • In infectious diseases: 4,529
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    • Site-wide: 22,942
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    • Site-wide: 38,954

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
  • Downloaded 144 times
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    • Site-wide: 122,974
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    • Site-wide: 82,911
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