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Author: A Sarah Walker

Rankings

  • All-time downloads: 209,331 (rank: 431 )
  • Categories:
    • bioinformatics: 14,475 (rank: 561 (tie) )
    • epidemiology: 1,892 (rank: 7,594 (tie) )
    • genomics: 5,228 (rank: 5,195 (tie) )
    • infectious diseases: 167,891 (rank: 190 )
    • microbiology: 18,954 (rank: 1,014 )
    • public and global health: 891 (rank: 5,377 (tie) )

Downloads per author, site-wide

Preprints

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

infectious diseases more details view paper
  • Downloaded 119,948 times
  • Download rankings, all-time:
    • Site-wide: 45
    • In infectious diseases: 20
  • Year to date:
    • Site-wide: 59
  • Since beginning of last month:
    • Site-wide: 166

Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom

infectious diseases more details view paper
  • Downloaded 19,439 times
  • Download rankings, all-time:
    • Site-wide: 468
    • In infectious diseases: 171
  • Year to date:
    • Site-wide: 139
  • Since beginning of last month:
    • Site-wide: 720

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

infectious diseases more details view paper
  • Downloaded 10,994 times
  • Download rankings, all-time:
    • Site-wide: 967
    • In infectious diseases: 312
  • Year to date:
    • Site-wide: 1,104
  • Since beginning of last month:
    • Site-wide: 2,348

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

bioinformatics more details view paper
  • Downloaded 8,601 times
  • Download rankings, all-time:
    • Site-wide: 1,313
    • In bioinformatics: 72
  • Year to date:
    • Site-wide: 27,084
  • Since beginning of last month:
    • Site-wide: 49,326

Increased infections, but not viral burden, with a new SARS-CoV-2 variant

infectious diseases more details view paper
  • Downloaded 8,497 times
  • Download rankings, all-time:
    • Site-wide: 1,327
    • In infectious diseases: 396
  • Year to date:
    • Site-wide: 355
  • Since beginning of last month:
    • Site-wide: 9,667

Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

infectious diseases more details view paper
  • Downloaded 6,187 times
  • Download rankings, all-time:
    • Site-wide: 2,003
    • In infectious diseases: 537
  • Year to date:
    • Site-wide: 723
  • Since beginning of last month:
    • Site-wide: 1,946

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

genomics more details view paper
  • Downloaded 3,321 times
  • Download rankings, all-time:
    • Site-wide: 4,745
    • In genomics: 467
  • Year to date:
    • Site-wide: 132,003
  • Since beginning of last month:
    • Site-wide: 151,620

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches

microbiology more details view paper
  • Downloaded 2,995 times
  • Download rankings, all-time:
    • Site-wide: 5,507
    • In microbiology: 352
  • Year to date:
    • Site-wide: 56,676
  • Since beginning of last month:
    • Site-wide: 42,555

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,338 times
  • Download rankings, all-time:
    • Site-wide: 7,921
    • In bioinformatics: 866
  • Year to date:
    • Site-wide: 28,776
  • Since beginning of last month:
    • Site-wide: 45,108

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
  • Download rankings, all-time:
    • Site-wide: 9,059
    • In microbiology: 537
  • Year to date:
    • Site-wide: 138,128
  • Since beginning of last month:
    • Site-wide: 152,975

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

microbiology more details view paper
  • Downloaded 1,835 times
  • Download rankings, all-time:
    • Site-wide: 11,345
    • In microbiology: 661
  • Year to date:
    • Site-wide: 22,554
  • Since beginning of last month:
    • Site-wide: 29,995

The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers

infectious diseases more details view paper
  • Downloaded 1,714 times
  • Download rankings, all-time:
    • Site-wide: 12,561
    • In infectious diseases: 1,626
  • Year to date:
    • Site-wide: 14,212
  • Since beginning of last month:
    • Site-wide: 79,534

Modelling microbiome recovery after antibiotics using a stability landscape framework

microbiology more details view paper
  • Downloaded 1,531 times
  • Download rankings, all-time:
    • Site-wide: 14,917
    • In microbiology: 860
  • Year to date:
    • Site-wide: 132,329
  • Since beginning of last month:
    • Site-wide: 162,154

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

microbiology more details view paper
  • Downloaded 1,382 times
  • Download rankings, all-time:
    • Site-wide: 17,526
    • In microbiology: 1,016
  • Year to date:
    • Site-wide: 126,845
  • Since beginning of last month:
    • Site-wide: 146,326

Severe infections emerge from the microbiome by adaptive evolution

genomics more details view paper
  • Downloaded 1,353 times
  • Download rankings, all-time:
    • Site-wide: 18,052
    • In genomics: 1,723
  • Year to date:
    • Site-wide: 148,315
  • Since beginning of last month:
    • Site-wide: 156,338

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
  • Download rankings, all-time:
    • Site-wide: 18,276
    • In microbiology: 1,060
  • Year to date:
    • Site-wide: 100,690
  • Since beginning of last month:
    • Site-wide: 152,995

Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies

bioinformatics more details view paper
  • Downloaded 1,311 times
  • Download rankings, all-time:
    • Site-wide: 18,949
    • In bioinformatics: 2,143
  • Year to date:
    • Site-wide: 12,730
  • Since beginning of last month:
    • Site-wide: 95,970

Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study

public and global health more details view paper
  • Downloaded 891 times
  • Download rankings, all-time:
    • Site-wide: 33,832
    • In public and global health: 615
  • Year to date:
    • Site-wide: 6,425
  • Since beginning of last month:
    • Site-wide: 9,994

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
  • Download rankings, all-time:
    • Site-wide: 35,089
    • In microbiology: 2,071
  • Year to date:
    • Site-wide: 132,550
  • Since beginning of last month:
    • Site-wide: 100,394

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 831 times
  • Download rankings, all-time:
    • Site-wide: 37,357
    • In bioinformatics: 4,016
  • Year to date:
    • Site-wide: 77,420
  • Since beginning of last month:
    • Site-wide: 44,794

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

microbiology more details view paper
  • Downloaded 822 times
  • Download rankings, all-time:
    • Site-wide: 38,029
    • In microbiology: 2,269
  • Year to date:
    • Site-wide: 55,790
  • Since beginning of last month:
    • Site-wide: 148,005

Estimating the effectiveness of first dose of COVID-19 vaccine against mortality in England: a quasi-experimental study

infectious diseases more details view paper
  • Downloaded 779 times
  • Download rankings, all-time:
    • Site-wide: 40,961
    • In infectious diseases: 3,000
  • Year to date:
    • Site-wide: 7,923
  • Since beginning of last month:
    • Site-wide: 4,315

Flanker: a tool for comparative genomics of gene flanking regions

bioinformatics more details view paper
  • Downloaded 740 times
  • Download rankings, all-time:
    • Site-wide: 44,121
    • In bioinformatics: 4,616
  • Year to date:
    • Site-wide: 8,614
  • Since beginning of last month:
    • Site-wide: 27,237

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

microbiology more details view paper
  • Downloaded 611 times
  • Download rankings, all-time:
    • Site-wide: 57,407
    • In microbiology: 3,570
  • Year to date:
    • Site-wide: 78,690
  • Since beginning of last month:
    • Site-wide: 48,935

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

microbiology more details view paper
  • Downloaded 570 times
  • Download rankings, all-time:
    • Site-wide: 62,455
    • In microbiology: 3,923
  • Year to date:
    • Site-wide: 162,194
  • Since beginning of last month:
    • Site-wide: 163,434

Monitoring populations at increased risk for SARS-CoV-2 infection in the community

epidemiology more details view paper
  • Downloaded 566 times
  • Download rankings, all-time:
    • Site-wide: 62,971
    • In epidemiology: 2,872
  • Year to date:
    • Site-wide: 13,126
  • Since beginning of last month:
    • Site-wide: 4,371

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
  • Download rankings, all-time:
    • Site-wide: 64,770
    • In genomics: 4,588
  • Year to date:
    • Site-wide: 95,093
  • Since beginning of last month:
    • Site-wide: 72,824

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

microbiology more details view paper
  • Downloaded 526 times
  • Download rankings, all-time:
    • Site-wide: 68,892
    • In microbiology: 4,432
  • Year to date:
    • Site-wide: 124,148
  • Since beginning of last month:
    • Site-wide: 157,079

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
  • Download rankings, all-time:
    • Site-wide: 69,552
    • In microbiology: 4,478
  • Year to date:
    • Site-wide: 92,850
  • Since beginning of last month:
    • Site-wide: 88,875

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
  • Download rankings, all-time:
    • Site-wide: 78,172
    • In microbiology: 5,169
  • Year to date:
    • Site-wide: 17,505
  • Since beginning of last month:
    • Site-wide: 8,984

Trends in Escherichia coli bloodstream infection, urinary tract infections and antibiotic susceptibilities in Oxfordshire, 1998-2016: an observational study

epidemiology more details view paper
  • Downloaded 470 times
  • Download rankings, all-time:
    • Site-wide: 78,239
    • In epidemiology: 3,436
  • Year to date:
    • Site-wide: 145,598
  • Since beginning of last month:
    • Site-wide: 113,506

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

microbiology more details view paper
  • Downloaded 449 times
  • Download rankings, all-time:
    • Site-wide: 82,247
    • In microbiology: 5,473
  • Year to date:
    • Site-wide: 146,520
  • Since beginning of last month:
    • Site-wide: 139,791

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

microbiology more details view paper
  • Downloaded 433 times
  • Download rankings, all-time:
    • Site-wide: 85,400
    • In microbiology: 5,708
  • Year to date:
    • Site-wide: 140,763
  • Since beginning of last month:
    • Site-wide: 151,208

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

microbiology more details view paper
  • Downloaded 404 times
  • Download rankings, all-time:
    • Site-wide: 91,356
    • In microbiology: 6,192
  • Year to date:
    • Site-wide: 155,032
  • Since beginning of last month:
    • Site-wide: 159,636

Genomic network analysis of an environmental and livestock IncF plasmid population

bioinformatics more details view paper
  • Downloaded 364 times
  • Download rankings, all-time:
    • Site-wide: 100,381
    • In bioinformatics: 8,616
  • Year to date:
    • Site-wide: 117,074
  • Since beginning of last month:
    • Site-wide: 128,792

Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage

microbiology more details view paper
  • Downloaded 363 times
  • Download rankings, all-time:
    • Site-wide: 100,663
    • In microbiology: 6,956
  • Year to date:
    • Site-wide: 124,569
  • Since beginning of last month:
    • Site-wide: 97,107

M. tuberculosis microvariation is common and is associated with transmission: analysis of three years prospective universal sequencing in England

microbiology more details view paper
  • Downloaded 362 times
  • Download rankings, all-time:
    • Site-wide: 100,940
    • In microbiology: 6,977
  • Year to date:
    • Site-wide: 129,374
  • Since beginning of last month:
    • Site-wide: 81,780

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

microbiology more details view paper
  • Downloaded 362 times
  • Download rankings, all-time:
    • Site-wide: 100,986
    • In microbiology: 6,989
  • Year to date:
    • Site-wide: 59,405
  • Since beginning of last month:
    • Site-wide: 109,993

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
  • Download rankings, all-time:
    • Site-wide: 103,450
    • In microbiology: 7,205
  • Year to date:
    • Site-wide: 149,811
  • Since beginning of last month:
    • Site-wide: 157,554

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

microbiology more details view paper
  • Downloaded 350 times
  • Download rankings, all-time:
    • Site-wide: 103,772
    • In microbiology: 7,220
  • Year to date:
    • Site-wide: 118,991
  • Since beginning of last month:
    • Site-wide: 92,443

An ecological comparison of hospital-level antibiotic use and mortality in 36,124,372 acute/general medicine inpatients in England

epidemiology more details view paper
  • Downloaded 296 times
  • Download rankings, all-time:
    • Site-wide: 117,365
    • In epidemiology: 4,951
  • Year to date:
    • Site-wide: 67,965
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    • Site-wide: 47,305

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
  • Download rankings, all-time:
    • Site-wide: 119,085
    • In bioinformatics: 9,718
  • Year to date:
    • Site-wide: 118,364
  • Since beginning of last month:
    • Site-wide: 122,988

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
  • Downloaded 288 times
  • Download rankings, all-time:
    • Site-wide: 119,442
    • In epidemiology: 5,070
  • Year to date:
    • Site-wide: 147,774
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    • Site-wide: 111,713

Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

microbiology more details view paper
  • Downloaded 274 times
  • Download rankings, all-time:
    • Site-wide: 123,429
    • In microbiology: 8,885
  • Year to date:
    • Site-wide: 143,160
  • Since beginning of last month:
    • Site-wide: 101,277

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

epidemiology more details view paper
  • Downloaded 272 times
  • Download rankings, all-time:
    • Site-wide: 123,824
    • In epidemiology: 5,220
  • Year to date:
    • Site-wide: 164,787
  • Since beginning of last month:
    • Site-wide: 163,975

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 202 times
  • Download rankings, all-time:
    • Site-wide: 141,718
    • In infectious diseases: 5,884
  • Year to date:
    • Site-wide: 118,145
  • Since beginning of last month:
    • Site-wide: 141,625

Strategic Treatment Optimization for HCV (STOPHCV1): a randomised controlled trial of ultrashort duration therapy for chronic hepatitis C

infectious diseases more details view paper
  • Downloaded 131 times
  • Download rankings, all-time:
    • Site-wide: 156,046
    • In infectious diseases: 6,313
  • Year to date:
    • Site-wide: 91,238
  • Since beginning of last month:
    • Site-wide: 133,925

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