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Author: Alex Greninger

Rankings

  • All-time downloads: 119,839 (rank: 883 )
  • Categories:
    • bioinformatics: 1,803 (rank: 8,979 (tie) )
    • epidemiology: 11,367 (rank: 1,403 )
    • genomics: 6,616 (rank: 3,464 )
    • infectious diseases: 52,775 (rank: 1,004 )
    • microbiology: 45,505 (rank: 271 )
    • pathology: 1,773 (rank: 761 (tie) )

Downloads per author, site-wide

Preprints

Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate

infectious diseases more details view paper
  • Downloaded 26,493 times
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    • Site-wide: 281
    • In infectious diseases: 103
  • Year to date:
    • Site-wide: 1,451
  • Since beginning of last month:
    • Site-wide: 4,815

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

microbiology more details view paper
  • Downloaded 21,272 times
  • Download rankings, all-time:
    • Site-wide: 368
    • In microbiology: 41
  • Year to date:
    • Site-wide: 2,101
  • Since beginning of last month:
    • Site-wide: 6,100

A human coronavirus evolves antigenically to escape antibody immunity

microbiology more details view paper
  • Downloaded 14,329 times
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    • Site-wide: 583
    • In microbiology: 67
  • Year to date:
    • Site-wide: 347
  • Since beginning of last month:
    • Site-wide: 7,592

Point-of-care testing for COVID-19 using SHERLOCK diagnostics

infectious diseases more details view paper
  • Downloaded 9,729 times
  • Download rankings, all-time:
    • Site-wide: 979
    • In infectious diseases: 306
  • Year to date:
    • Site-wide: 1,703
  • Since beginning of last month:
    • Site-wide: 9,983

Cryptic transmission of SARS-CoV-2 in Washington State

epidemiology more details view paper
  • Downloaded 9,523 times
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    • Site-wide: 1,006
    • In epidemiology: 132
  • Year to date:
    • Site-wide: 8,262
  • Since beginning of last month:
    • Site-wide: 32,731

Variants of concern are overrepresented among post-vaccination breakthrough infections of SARS-CoV-2 in Washington State

infectious diseases more details view paper
  • Downloaded 7,135 times
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    • Site-wide: 1,448
    • In infectious diseases: 400
  • Year to date:
    • Site-wide: 274
  • Since beginning of last month:
    • Site-wide: 19,669

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

genomics more details view paper
  • Downloaded 3,261 times
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    • Site-wide: 4,297
    • In genomics: 446
  • Year to date:
    • Site-wide: 74,738
  • Since beginning of last month:
    • Site-wide: 72,645

A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance

infectious diseases more details view paper
  • Downloaded 2,151 times
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    • Site-wide: 7,855
    • In infectious diseases: 1,184
  • Year to date:
    • Site-wide: 1,115
  • Since beginning of last month:
    • Site-wide: 16,509

In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age

microbiology more details view paper
  • Downloaded 1,988 times
  • Download rankings, all-time:
    • Site-wide: 8,834
    • In microbiology: 527
  • Year to date:
    • Site-wide: 14,906
  • Since beginning of last month:
    • Site-wide: 30,792

Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics

infectious diseases more details view paper
  • Downloaded 1,823 times
  • Download rankings, all-time:
    • Site-wide: 10,019
    • In infectious diseases: 1,360
  • Year to date:
    • Site-wide: 26,243
  • Since beginning of last month:
    • Site-wide: 29,703

Anti-SARS-CoV-2 antibody levels are concordant across multiple platforms but are not fully predictive of sterilizing immunity

infectious diseases more details view paper
  • Downloaded 1,802 times
  • Download rankings, all-time:
    • Site-wide: 10,215
    • In infectious diseases: 1,378
  • Year to date:
    • Site-wide: 1,413
  • Since beginning of last month:
    • Site-wide: 773

Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories

pathology more details view paper
  • Downloaded 1,773 times
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    • Site-wide: 10,469
    • In pathology: 56
  • Year to date:
    • Site-wide: 49,989
  • Since beginning of last month:
    • Site-wide: 28,240

Validation and Implementation of CLIA-Compliant Whole Genome Sequencing (WGS) in Public Health Laboratory

microbiology more details view paper
  • Downloaded 1,380 times
  • Download rankings, all-time:
    • Site-wide: 15,141
    • In microbiology: 891
  • Year to date:
    • Site-wide: 54,037
  • Since beginning of last month:
    • Site-wide: None

Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load

infectious diseases more details view paper
  • Downloaded 1,206 times
  • Download rankings, all-time:
    • Site-wide: 18,516
    • In infectious diseases: 1,832
  • Year to date:
    • Site-wide: 32,308
  • Since beginning of last month:
    • Site-wide: 33,190

Discovery of a persistent Zika virus lineage in Bahia, Brazil

epidemiology more details view paper
  • Downloaded 1,202 times
  • Download rankings, all-time:
    • Site-wide: 18,619
    • In epidemiology: 1,188
  • Year to date:
    • Site-wide: 110,940
  • Since beginning of last month:
    • Site-wide: 82,366

SARS-CoV-2 ORF6 disrupts nucleocytoplasmic transport through interactions with Rae1 and Nup98

microbiology more details view paper
  • Downloaded 1,183 times
  • Download rankings, all-time:
    • Site-wide: 19,046
    • In microbiology: 1,108
  • Year to date:
    • Site-wide: 10,105
  • Since beginning of last month:
    • Site-wide: 3,050

Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies

infectious diseases more details view paper
  • Downloaded 1,172 times
  • Download rankings, all-time:
    • Site-wide: 19,344
    • In infectious diseases: 1,868
  • Year to date:
    • Site-wide: 16,884
  • Since beginning of last month:
    • Site-wide: 14,661

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

bioinformatics more details view paper
  • Downloaded 910 times
  • Download rankings, all-time:
    • Site-wide: 27,924
    • In bioinformatics: 3,179
  • Year to date:
    • Site-wide: 61,979
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    • Site-wide: None

Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the critical need for reference strain sequencing

genomics more details view paper
  • Downloaded 850 times
  • Download rankings, all-time:
    • Site-wide: 30,744
    • In genomics: 2,710
  • Year to date:
    • Site-wide: 92,156
  • Since beginning of last month:
    • Site-wide: 62,976

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei With Increased Virulence or Fluoroquinolone Resistance

microbiology more details view paper
  • Downloaded 649 times
  • Download rankings, all-time:
    • Site-wide: 44,439
    • In microbiology: 2,743
  • Year to date:
    • Site-wide: 105,533
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    • Site-wide: None

SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy

microbiology more details view paper
  • Downloaded 632 times
  • Download rankings, all-time:
    • Site-wide: 45,999
    • In microbiology: 2,841
  • Year to date:
    • Site-wide: 6,044
  • Since beginning of last month:
    • Site-wide: 929

Standard Issue: Copy number heterogeneity of JC virus standards discovered through next-generation sequencing

microbiology more details view paper
  • Downloaded 623 times
  • Download rankings, all-time:
    • Site-wide: 46,741
    • In microbiology: 2,915
  • Year to date:
    • Site-wide: 130,920
  • Since beginning of last month:
    • Site-wide: None

VAPiD: a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank

bioinformatics more details view paper
  • Downloaded 608 times
  • Download rankings, all-time:
    • Site-wide: 48,176
    • In bioinformatics: 5,008
  • Year to date:
    • Site-wide: 95,469
  • Since beginning of last month:
    • Site-wide: 8,022

Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection

genomics more details view paper
  • Downloaded 523 times
  • Download rankings, all-time:
    • Site-wide: 58,047
    • In genomics: 4,295
  • Year to date:
    • Site-wide: 101,994
  • Since beginning of last month:
    • Site-wide: None

Genomic and proteomic analysis of Human herpesvirus 6 reveals distinct clustering of acute versus inherited forms and reannotation of reference strain

microbiology more details view paper
  • Downloaded 515 times
  • Download rankings, all-time:
    • Site-wide: 59,039
    • In microbiology: 3,822
  • Year to date:
    • Site-wide: 136,360
  • Since beginning of last month:
    • Site-wide: 38,728

A novel qacA allele results in an elevated chlorhexidine gluconate minimum inhibitory concentration in cutaneous Staphylococcus epidermidis isolates

microbiology more details view paper
  • Downloaded 508 times
  • Download rankings, all-time:
    • Site-wide: 59,986
    • In microbiology: 3,882
  • Year to date:
    • Site-wide: 100,154
  • Since beginning of last month:
    • Site-wide: 5,960

Pre-Procedural Surveillance Testing for SARS-CoV-2 in an Asymptomatic Population Shows Low Rates of Positivity

infectious diseases more details view paper
  • Downloaded 483 times
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    • Site-wide: 63,342
    • In infectious diseases: 3,388
  • Year to date:
    • Site-wide: 122,570
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    • Site-wide: None

The impact of interspecies recombination on human herpes simplex virus evolution and host immune recognition

genomics more details view paper
  • Downloaded 468 times
  • Download rankings, all-time:
    • Site-wide: 65,719
    • In genomics: 4,664
  • Year to date:
    • Site-wide: 103,602
  • Since beginning of last month:
    • Site-wide: 43,240

Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors

epidemiology more details view paper
  • Downloaded 410 times
  • Download rankings, all-time:
    • Site-wide: 75,138
    • In epidemiology: 3,231
  • Year to date:
    • Site-wide: 97,228
  • Since beginning of last month:
    • Site-wide: 80,445

Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections

microbiology more details view paper
  • Downloaded 395 times
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    • Site-wide: 77,869
    • In microbiology: 5,344
  • Year to date:
    • Site-wide: 134,469
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    • Site-wide: None

Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture

genomics more details view paper
  • Downloaded 387 times
  • Download rankings, all-time:
    • Site-wide: 79,434
    • In genomics: 5,248
  • Year to date:
    • Site-wide: 124,022
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    • Site-wide: None

Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples

microbiology more details view paper
  • Downloaded 374 times
  • Download rankings, all-time:
    • Site-wide: 81,751
    • In microbiology: 5,653
  • Year to date:
    • Site-wide: 150,055
  • Since beginning of last month:
    • Site-wide: None

Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

infectious diseases more details view paper
  • Downloaded 366 times
  • Download rankings, all-time:
    • Site-wide: 83,391
    • In infectious diseases: 3,859
  • Year to date:
    • Site-wide: 13,352
  • Since beginning of last month:
    • Site-wide: 49,698

Divergent In vitro MIC Characteristics and underlying isogenic mutations in host-specialized Pseudomonas aeruginosa

microbiology more details view paper
  • Downloaded 348 times
  • Download rankings, all-time:
    • Site-wide: 87,077
    • In microbiology: 6,086
  • Year to date:
    • Site-wide: 92,967
  • Since beginning of last month:
    • Site-wide: 59,151

Copy number heterogeneity, large origin tandem repeats, and interspecies recombination in HHV-6A and HHV-6B reference strains

genomics more details view paper
  • Downloaded 323 times
  • Download rankings, all-time:
    • Site-wide: 92,427
    • In genomics: 5,779
  • Year to date:
    • Site-wide: 134,324
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    • Site-wide: None

Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of small-colony variant Enterobactericeae

microbiology more details view paper
  • Downloaded 303 times
  • Download rankings, all-time:
    • Site-wide: 97,012
    • In microbiology: 6,947
  • Year to date:
    • Site-wide: 96,244
  • Since beginning of last month:
    • Site-wide: 86,116

LAVA: a streamlined visualization tool for longitudinal analysis of viral alleles

bioinformatics more details view paper
  • Downloaded 285 times
  • Download rankings, all-time:
    • Site-wide: 101,038
    • In bioinformatics: 8,720
  • Year to date:
    • Site-wide: 112,272
  • Since beginning of last month:
    • Site-wide: 93,113

Sensitive detection of highly fragmented cytomegalovirus nucleic acid in human cfDNA

microbiology more details view paper
  • Downloaded 254 times
  • Download rankings, all-time:
    • Site-wide: 108,463
    • In microbiology: 7,888
  • Year to date:
    • Site-wide: 134,714
  • Since beginning of last month:
    • Site-wide: 22,126

Estimation of Full-Length TprK Diversity in Treponema pallidum subspecies pallidum

microbiology more details view paper
  • Downloaded 247 times
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    • Site-wide: 110,363
    • In microbiology: 8,051
  • Year to date:
    • Site-wide: 142,497
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    • Site-wide: None

Prospective real-time metagenomic sequencing during norovirus outbreak reveals discrete transmission clusters

genomics more details view paper
  • Downloaded 238 times
  • Download rankings, all-time:
    • Site-wide: 112,431
    • In genomics: 6,449
  • Year to date:
    • Site-wide: 150,591
  • Since beginning of last month:
    • Site-wide: 81,924

Inherited chromosomally integrated HHV-6 demonstrates tissue-specific RNA expression in vivo that correlates with increased antibody immune response.

genomics more details view paper
  • Downloaded 235 times
  • Download rankings, all-time:
    • Site-wide: 113,191
    • In genomics: 6,469
  • Year to date:
    • Site-wide: 149,500
  • Since beginning of last month:
    • Site-wide: 88,633

Phylogenetic estimates of SARS-CoV-2 introductions into Washington State

epidemiology more details view paper
  • Downloaded 232 times
  • Download rankings, all-time:
    • Site-wide: 113,966
    • In epidemiology: 4,754
  • Year to date:
    • Site-wide: 25,020
  • Since beginning of last month:
    • Site-wide: 36,230

Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19

infectious diseases more details view paper
  • Downloaded 198 times
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    • Site-wide: 122,505
    • In infectious diseases: 4,917
  • Year to date:
    • Site-wide: 30,609
  • Since beginning of last month:
    • Site-wide: 105,937

Comparative Genomics and Full-Length TprK Profiling of Treponema pallidum subsp. pallidum Reinfection

microbiology more details view paper
  • Downloaded 190 times
  • Download rankings, all-time:
    • Site-wide: 124,454
    • In microbiology: 9,337
  • Year to date:
    • Site-wide: 150,781
  • Since beginning of last month:
    • Site-wide: 42,466

Phenotypic and Genotypic Antiviral Resistance Testing of HSV-1 Causing Recurrent Cutaneous Lesions in a Patient with DOCK8 Deficiency

genomics more details view paper
  • Downloaded 174 times
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    • Site-wide: 128,232
    • In genomics: 6,934
  • Year to date:
    • Site-wide: 138,100
  • Since beginning of last month:
    • Site-wide: None

Herpes Simplex Virus Mistyping due to HSV-1 x HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B

genomics more details view paper
  • Downloaded 156 times
  • Download rankings, all-time:
    • Site-wide: 132,234
    • In genomics: 7,058
  • Year to date:
    • Site-wide: 131,088
  • Since beginning of last month:
    • Site-wide: None

A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo

microbiology more details view paper
  • Downloaded 135 times
  • Download rankings, all-time:
    • Site-wide: 136,944
    • In microbiology: 10,444
  • Year to date:
    • Site-wide: 47,431
  • Since beginning of last month:
    • Site-wide: 28,778

Estimating the false positive rate of highly automated SARS-CoV-2 nucleic acid amplification testing

infectious diseases more details view paper
  • Downloaded 131 times
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    • Site-wide: 137,687
    • In infectious diseases: 5,394
  • Year to date:
    • Site-wide: 48,746
  • Since beginning of last month:
    • Site-wide: 51,941

Trajectory of viral load in a prospective population-based cohort with incident SARS-CoV-2 G614 infection

infectious diseases more details view paper
  • Downloaded 86 times
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    • Site-wide: 146,091
    • In infectious diseases: 5,700
  • Year to date:
    • Site-wide: 71,853
  • Since beginning of last month:
    • Site-wide: 500

Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus.

microbiology more details view paper
  • Downloaded 78 times
  • Download rankings, all-time:
    • Site-wide: 147,276
    • In microbiology: 11,419
  • Year to date:
    • Site-wide: 142,383
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    • Site-wide: None

In vivo generation of BK and JC polyomavirus defective viral genomes in human urine samples associated with higher viral loads

microbiology more details view paper
  • Downloaded 73 times
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    • Site-wide: 147,880
    • In microbiology: 11,477
  • Year to date:
    • Site-wide: 82,247
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    • Site-wide: None

Longitudinal accumulation of in vivo and in vitro-grown Treponema pallidum subsp. pallidum TprK variants in the presence and absence of immune pressure

microbiology more details view paper
  • Downloaded 29 times
  • Download rankings, all-time:
    • Site-wide: 151,353
    • In microbiology: 11,850
  • Year to date:
    • Site-wide: 135,468
  • Since beginning of last month:
    • Site-wide: 54,631

Genome sequencing of 196 Treponema pallidum strains from six continents reveals additional variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar

genomics more details view paper
  • Downloaded 1 times
  • Download rankings, all-time:
    • Site-wide: 154,497
    • In genomics: 7,684
  • Year to date:
    • Site-wide: 154,383
  • Since beginning of last month:
    • Site-wide: 44,579

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