Author: Nicole Stoesser
- ORCiD: http://orcid.org/0000-0002-4508-7969
- Most recently observed institution: University of Oxford
Rankings
- All-time downloads: 150,142 (rank: 985 )
- Categories:
- bioinformatics: 14,410 (rank: 596 )
- epidemiology: 36,584 (rank: 699 )
- evolutionary biology: 392 (rank: 20,707 (tie) )
- genomics: 1,954 (rank: 14,786 (tie) )
- infectious diseases: 80,632 (rank: 871 )
- microbiology: 8,843 (rank: 2,320 )
Downloads per author, site-wide
Preprints
Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK
epidemiology more details view paper- Downloaded 34,750 times
- Download rankings, all-time:
- Site-wide: 287
- In epidemiology: 62
- Year to date:
- Site-wide: 220
- Since beginning of last month:
- Site-wide: 1,476
Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom
infectious diseases more details view paper- Downloaded 20,469 times
- Download rankings, all-time:
- Site-wide: 524
- In infectious diseases: 193
- Year to date:
- Site-wide: 2,862
- Since beginning of last month:
- Site-wide: 3,140
The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom
infectious diseases more details view paper- Downloaded 15,471 times
- Download rankings, all-time:
- Site-wide: 725
- In infectious diseases: 257
- Year to date:
- Site-wide: 8,804
- Since beginning of last month:
- Site-wide: 9,469
Virus detection and identification in minutes using single-particle imaging and deep learning
infectious diseases more details view paper- Downloaded 11,712 times
- Download rankings, all-time:
- Site-wide: 1,048
- In infectious diseases: 340
- Year to date:
- Site-wide: 4,753
- Since beginning of last month:
- Site-wide: 8,478
Increased infections, but not viral burden, with a new SARS-CoV-2 variant
infectious diseases more details view paper- Downloaded 8,955 times
- Download rankings, all-time:
- Site-wide: 1,469
- In infectious diseases: 442
- Year to date:
- Site-wide: 9,674
- Since beginning of last month:
- Site-wide: 13,393
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
bioinformatics more details view paper- Downloaded 8,752 times
- Download rankings, all-time:
- Site-wide: 1,512
- In bioinformatics: 75
- Year to date:
- Site-wide: 50,071
- Since beginning of last month:
- Site-wide: 118,952
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 7,053 times
- Download rankings, all-time:
- Site-wide: 1,989
- In infectious diseases: 565
- Year to date:
- Site-wide: 4,013
- Since beginning of last month:
- Site-wide: 11,769
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 4,463 times
- Download rankings, all-time:
- Site-wide: 3,698
- In infectious diseases: 862
- Year to date:
- Site-wide: 1,701
- Since beginning of last month:
- Site-wide: 24,625
SARS-CoV-2 RNA detected in blood samples from patients with COVID-19 is not associated with infectious virus
infectious diseases more details view paper- Downloaded 2,809 times
- Download rankings, all-time:
- Site-wide: 7,166
- In infectious diseases: 1,251
- Year to date:
- Site-wide: 46,068
- Since beginning of last month:
- Site-wide: 101,542
Genomic diversity affects the accuracy of bacterial SNP calling pipelines
bioinformatics more details view paper- Downloaded 2,423 times
- Download rankings, all-time:
- Site-wide: 8,903
- In bioinformatics: 892
- Year to date:
- Site-wide: 58,762
- Since beginning of last month:
- Site-wide: 66,450
OMICRON-ASSOCIATED CHANGES IN SARS-COV-2 SYMPTOMS IN THE UNITED KINGDOM
epidemiology more details view paper- Downloaded 2,198 times
- Download rankings, all-time:
- Site-wide: 10,263
- In epidemiology: 1,196
- Year to date:
- Site-wide: 567
- Since beginning of last month:
- Site-wide: 2,192
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 2,111 times
- Download rankings, all-time:
- Site-wide: 10,945
- In infectious diseases: 1,768
- Year to date:
- Site-wide: 2,637
- Since beginning of last month:
- Site-wide: 14,795
A haemagglutination test for rapid detection of antibodies to SARS-CoV-2
infectious diseases more details view paper- Downloaded 1,811 times
- Download rankings, all-time:
- Site-wide: 13,717
- In infectious diseases: 1,983
- Year to date:
- Site-wide: 7,501
- Since beginning of last month:
- Site-wide: 4,860
The duration, dynamics and determinants of SARS-CoV-2 antibody responses in individual healthcare workers
infectious diseases more details view paper- Downloaded 1,798 times
- Download rankings, all-time:
- Site-wide: 13,877
- In infectious diseases: 1,805
- Year to date:
- Site-wide: 68,791
- Since beginning of last month:
- Site-wide: 42,709
Anti-spike antibody response to natural SARS-CoV-2 infection in the general population
infectious diseases more details view paper- Downloaded 1,790 times
- Download rankings, all-time:
- Site-wide: 13,973
- In infectious diseases: 1,855
- Year to date:
- Site-wide: 12,833
- Since beginning of last month:
- Site-wide: 45,044
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 1,501 times
- Download rankings, all-time:
- Site-wide: 18,248
- In infectious diseases: 2,054
- Year to date:
- Site-wide: 124,597
- Since beginning of last month:
- Site-wide: 180,325
Optimised use of Oxford Nanopore Flowcells for Hybrid Assemblies
bioinformatics more details view paper- Downloaded 1,399 times
- Download rankings, all-time:
- Site-wide: 20,341
- In bioinformatics: 2,205
- Year to date:
- Site-wide: 63,062
- Since beginning of last month:
- Site-wide: 42,556
The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples
microbiology more details view paper- Downloaded 1,358 times
- Download rankings, all-time:
- Site-wide: 21,308
- In microbiology: 1,149
- Year to date:
- Site-wide: 177,817
- Since beginning of last month:
- Site-wide: 172,894
Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance
infectious diseases more details view paper- Downloaded 1,354 times
- Download rankings, all-time:
- Site-wide: 21,407
- In infectious diseases: 3,494
- Year to date:
- Site-wide: 1,084
- Since beginning of last month:
- Site-wide: 3,543
Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli
microbiology more details view paper- Downloaded 1,296 times
- Download rankings, all-time:
- Site-wide: 22,915
- In microbiology: 1,240
- Year to date:
- Site-wide: 155,288
- Since beginning of last month:
- Site-wide: 160,206
Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131
genomics more details view paper- Downloaded 956 times
- Download rankings, all-time:
- Site-wide: 36,341
- In genomics: 2,816
- Year to date:
- Site-wide: 128,053
- Since beginning of last month:
- Site-wide: 114,365
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 890 times
- Download rankings, all-time:
- Site-wide: 40,410
- In microbiology: 2,216
- Year to date:
- Site-wide: 174,095
- Since beginning of last month:
- Site-wide: 130,356
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae
microbiology more details view paper- Downloaded 873 times
- Download rankings, all-time:
- Site-wide: 41,547
- In microbiology: 2,410
- Year to date:
- Site-wide: 93,292
- Since beginning of last month:
- Site-wide: 98,461
Flanker: a tool for comparative genomics of gene flanking regions
bioinformatics more details view paper- Downloaded 865 times
- Download rankings, all-time:
- Site-wide: 42,160
- In bioinformatics: 4,461
- Year to date:
- Site-wide: 47,984
- Since beginning of last month:
- Site-wide: 32,703
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 864 times
- Download rankings, all-time:
- Site-wide: 42,188
- In bioinformatics: 4,168
- Year to date:
- Site-wide: 129,998
- Since beginning of last month:
- Site-wide: 173,098
Increasing test specificity without impairing sensitivity - lessons learned from SARS-CoV-2 serology
infectious diseases more details view paper- Downloaded 718 times
- Download rankings, all-time:
- Site-wide: 55,193
- In infectious diseases: 3,726
- Year to date:
- Site-wide: 32,165
- Since beginning of last month:
- Site-wide: 47,208
Transmission dynamics and between-species interactions of multidrug-resistant Enterobacteriaceae
epidemiology more details view paper- Downloaded 678 times
- Download rankings, all-time:
- Site-wide: 59,931
- In epidemiology: 2,715
- Year to date:
- Site-wide: 147,873
- Since beginning of last month:
- Site-wide: 94,251
Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients
microbiology more details view paper- Downloaded 650 times
- Download rankings, all-time:
- Site-wide: 63,368
- In microbiology: 3,646
- Year to date:
- Site-wide: 119,239
- Since beginning of last month:
- Site-wide: 140,489
Novel blaKPC-carrying species identified in the hospital environment
microbiology more details view paper- Downloaded 616 times
- Download rankings, all-time:
- Site-wide: 67,931
- In microbiology: 3,918
- Year to date:
- Site-wide: 170,426
- Since beginning of last month:
- Site-wide: 119,556
Dynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study
microbiology more details view paper- Downloaded 604 times
- Download rankings, all-time:
- Site-wide: 69,805
- In microbiology: 4,066
- Year to date:
- Site-wide: 131,577
- Since beginning of last month:
- Site-wide: 120,406
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 580 times
- Download rankings, all-time:
- Site-wide: 73,399
- In genomics: 4,752
- Year to date:
- Site-wide: 141,228
- Since beginning of last month:
- Site-wide: 159,219
Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli
microbiology more details view paper- Downloaded 565 times
- Download rankings, all-time:
- Site-wide: 75,791
- In microbiology: 4,565
- Year to date:
- Site-wide: 124,992
- Since beginning of last month:
- Site-wide: 162,581
Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study
microbiology more details view paper- Downloaded 543 times
- Download rankings, all-time:
- Site-wide: 79,572
- In microbiology: 4,734
- Year to date:
- Site-wide: 167,486
- Since beginning of last month:
- Site-wide: 150,581
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction
genomics more details view paper- Downloaded 509 times
- Download rankings, all-time:
- Site-wide: 85,791
- In genomics: None
- Year to date:
- Site-wide: 4,842
- Since beginning of last month:
- Site-wide: 1,164
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 488 times
- Download rankings, all-time:
- Site-wide: 90,022
- In epidemiology: 3,680
- Year to date:
- Site-wide: 170,459
- Since beginning of last month:
- Site-wide: 177,325
Metrics for Public Health Perspective Surveillance of Bacterial Antibiotic Resistance in Low- and Middle-Income Countries
genomics more details view paper- Downloaded 483 times
- Download rankings, all-time:
- Site-wide: 91,026
- In genomics: 5,544
- Year to date:
- Site-wide: 115,768
- Since beginning of last month:
- Site-wide: 76,014
Molecular epidemiology of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire (UK) 2008-2018
infectious diseases more details view paper- Downloaded 454 times
- Download rankings, all-time:
- Site-wide: 97,470
- In infectious diseases: 4,887
- Year to date:
- Site-wide: 90,774
- Since beginning of last month:
- Site-wide: 65,002
Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399
evolutionary biology more details view paper- Downloaded 421 times
- Download rankings, all-time:
- Site-wide: 105,253
- In evolutionary biology: 4,969
- Year to date:
- Site-wide: 79,722
- Since beginning of last month:
- Site-wide: 111,812
The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm
microbiology more details view paper- Downloaded 398 times
- Download rankings, all-time:
- Site-wide: 110,852
- In microbiology: 7,221
- Year to date:
- Site-wide: 119,718
- Since beginning of last month:
- Site-wide: 128,460
Genomic network analysis of an environmental and livestock IncF plasmid population
bioinformatics more details view paper- Downloaded 395 times
- Download rankings, all-time:
- Site-wide: 111,656
- In bioinformatics: 9,018
- Year to date:
- Site-wide: 127,763
- Since beginning of last month:
- Site-wide: 92,302
The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates
microbiology more details view paper- Downloaded 375 times
- Download rankings, all-time:
- Site-wide: 116,891
- In microbiology: 7,455
- Year to date:
- Site-wide: 178,512
- Since beginning of last month:
- Site-wide: 184,977
Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment
microbiology more details view paper- Downloaded 370 times
- Download rankings, all-time:
- Site-wide: 118,247
- In microbiology: 7,528
- Year to date:
- Site-wide: 182,258
- Since beginning of last month:
- Site-wide: 184,725
The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination
infectious diseases more details view paper- Downloaded 353 times
- Download rankings, all-time:
- Site-wide: 123,110
- In infectious diseases: 5,926
- Year to date:
- Site-wide: 18,290
- Since beginning of last month:
- Site-wide: 41,294
Molecular epidemiology of paediatric bloodstream infections caused by Gram-negative bacteria in Oxfordshire, UK
infectious diseases more details view paper- Downloaded 340 times
- Download rankings, all-time:
- Site-wide: 126,492
- In infectious diseases: 6,578
- Year to date:
- Site-wide: 27,809
- Since beginning of last month:
- Site-wide: 40,752
Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia
microbiology more details view paper- Downloaded 309 times
- Download rankings, all-time:
- Site-wide: 135,674
- In microbiology: 9,066
- Year to date:
- Site-wide: 170,243
- Since beginning of last month:
- Site-wide: 130,277
The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study
infectious diseases more details view paper- Downloaded 303 times
- Download rankings, all-time:
- Site-wide: 137,625
- In infectious diseases: None
- Year to date:
- Site-wide: 10,690
- Since beginning of last month:
- Site-wide: 20,587
Transmission patterns of hyper-endemic multi-drug resistant Klebsiella pneumoniae in a Cambodian neonatal unit: a longitudinal study with whole genome sequencing
epidemiology more details view paper- Downloaded 297 times
- Download rankings, all-time:
- Site-wide: 139,266
- In epidemiology: 5,502
- Year to date:
- Site-wide: 155,646
- Since beginning of last month:
- Site-wide: 177,327
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli
microbiology more details view paper- Downloaded 291 times
- Download rankings, all-time:
- Site-wide: 141,121
- In microbiology: 10,865
- Year to date:
- Site-wide: 44,870
- Since beginning of last month:
- Site-wide: 37,619
Plasmid overlap and evolution between Enterobacterales isolates from bloodstream infections and non-human compartments
genomics more details view paper- Downloaded 263 times
- Download rankings, all-time:
- Site-wide: 149,259
- In genomics: None
- Year to date:
- Site-wide: 13,227
- Since beginning of last month:
- Site-wide: 1,748
Antimicrobial resistance surveillance: can we estimate resistance in bloodstream infections from other types of specimen?
infectious diseases more details view paper- Downloaded 240 times
- Download rankings, all-time:
- Site-wide: 156,114
- In infectious diseases: 6,484
- Year to date:
- Site-wide: 111,558
- Since beginning of last month:
- Site-wide: 100,249
Mortality risks associated with empirical antibiotic activity in E. coli bacteraemia: an analysis of electronic health records
infectious diseases more details view paper- Downloaded 239 times
- Download rankings, all-time:
- Site-wide: 156,225
- In infectious diseases: 6,932
- Year to date:
- Site-wide: 15,209
- Since beginning of last month:
- Site-wide: 43,225
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 231 times
- Download rankings, all-time:
- Site-wide: 158,521
- In infectious diseases: 6,507
- Year to date:
- Site-wide: 151,677
- Since beginning of last month:
- Site-wide: 170,374
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- Downloaded 211 times
- Download rankings, all-time:
- Site-wide: 163,834
- In epidemiology: 6,785
- Year to date:
- Site-wide: 53,725
- Since beginning of last month:
- Site-wide: 60,594
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- Downloaded 181 times
- Download rankings, all-time:
- Site-wide: 171,428
- In infectious diseases: 6,954
- Year to date:
- Site-wide: 84,201
- Since beginning of last month:
- Site-wide: 74,181
Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples
genomics more details view paper- Downloaded 116 times
- Download rankings, all-time:
- Site-wide: 183,675
- In genomics: None
- Year to date:
- Site-wide: 39,715
- Since beginning of last month:
- Site-wide: 6,633
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