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Author: Rob Knight

Rankings

  • All-time downloads: 82,866 (rank: 1,537 )
  • Categories:
    • bioinformatics: 17,247 (rank: 318 )
    • ecology: 2,183 (rank: 1,026 (tie) )
    • epidemiology: 10,048 (rank: 1,184 )
    • gastroenterology: 550 (rank: 528 (tie) )
    • genetic and genomic medicine: 1,286 (rank: 1,227 (tie) )
    • genetics: 1,971 (rank: 8,913 (tie) )
    • genomics: 8,390 (rank: 2,271 )
    • immunology: 368 (rank: 18,953 (tie) )
    • infectious diseases: 10,410 (rank: 3,898 )
    • microbiology: 16,952 (rank: 730 )
    • molecular biology: 12,325 (rank: 153 (tie) )
    • systems biology: 1,136 (rank: 3,571 (tie) )

Downloads per author, site-wide

Preprints

Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

molecular biology more details view paper
  • Downloaded 12,325 times
  • Download rankings, all-time:
    • Site-wide: 555
    • In molecular biology: 8
  • Year to date:
    • Site-wide: 678
  • Since beginning of last month:
    • Site-wide: 678

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

infectious diseases more details view paper
  • Downloaded 7,920 times
  • Download rankings, all-time:
    • Site-wide: 1,002
    • In infectious diseases: 286
  • Year to date:
    • Site-wide: 47
  • Since beginning of last month:
    • Site-wide: 47

Emergence of an early SARS-CoV-2 epidemic in the United States

epidemiology more details view paper
  • Downloaded 5,176 times
  • Download rankings, all-time:
    • Site-wide: 1,766
    • In epidemiology: 207
  • Year to date:
    • Site-wide: 82
  • Since beginning of last month:
    • Site-wide: 82

Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
  • Downloaded 5,138 times
  • Download rankings, all-time:
    • Site-wide: 1,785
    • In bioinformatics: 151
  • Year to date:
    • Site-wide: 1,577
  • Since beginning of last month:
    • Site-wide: 1,577

BugBase Predicts Organism Level Microbiome Phenotypes

bioinformatics more details view paper
  • Downloaded 3,717 times
  • Download rankings, all-time:
    • Site-wide: 2,832
    • In bioinformatics: 276
  • Year to date:
    • Site-wide: 12,254
  • Since beginning of last month:
    • Site-wide: 12,254

Evaluating the information content of shallow shotgun metagenomics

genomics more details view paper
  • Downloaded 3,648 times
  • Download rankings, all-time:
    • Site-wide: 2,917
    • In genomics: 345
  • Year to date:
    • Site-wide: 21,971
  • Since beginning of last month:
    • Site-wide: 21,971

American Gut: an Open Platform for Citizen-Science Microbiome Research

microbiology more details view paper
  • Downloaded 3,630 times
  • Download rankings, all-time:
    • Site-wide: 2,937
    • In microbiology: 201
  • Year to date:
    • Site-wide: 17,680
  • Since beginning of last month:
    • Site-wide: 17,680

Taxonomic Signatures of Long-Term Mortality Risk in Human Gut Microbiota

epidemiology more details view paper
  • Downloaded 3,370 times
  • Download rankings, all-time:
    • Site-wide: 3,268
    • In epidemiology: 321
  • Year to date:
    • Site-wide: 17,542
  • Since beginning of last month:
    • Site-wide: 17,542

Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing

genomics more details view paper
  • Downloaded 2,856 times
  • Download rankings, all-time:
    • Site-wide: 4,104
    • In genomics: 477
  • Year to date:
    • Site-wide: 9,129
  • Since beginning of last month:
    • Site-wide: 9,129

Large-scale association analyses identify host factors influencing human gut microbiome composition

genetics more details view paper
  • Downloaded 1,971 times
  • Download rankings, all-time:
    • Site-wide: 7,080
    • In genetics: 345
  • Year to date:
    • Site-wide: 2,455
  • Since beginning of last month:
    • Site-wide: 2,455

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

microbiology more details view paper
  • Downloaded 1,813 times
  • Download rankings, all-time:
    • Site-wide: 8,034
    • In microbiology: 444
  • Year to date:
    • Site-wide: 5,474
  • Since beginning of last month:
    • Site-wide: 5,474

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

bioinformatics more details view paper
  • Downloaded 1,703 times
  • Download rankings, all-time:
    • Site-wide: 8,856
    • In bioinformatics: 1,086
  • Year to date:
    • Site-wide: 12,855
  • Since beginning of last month:
    • Site-wide: 12,855

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS.

bioinformatics more details view paper
  • Downloaded 1,632 times
  • Download rankings, all-time:
    • Site-wide: 9,466
    • In bioinformatics: 1,161
  • Year to date:
    • Site-wide: 8,681
  • Since beginning of last month:
    • Site-wide: 8,681

Quantifying and understanding well-to-well contamination in microbiome research

genomics more details view paper
  • Downloaded 1,574 times
  • Download rankings, all-time:
    • Site-wide: 9,976
    • In genomics: 1,107
  • Year to date:
    • Site-wide: 53,391
  • Since beginning of last month:
    • Site-wide: 53,391

Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids

microbiology more details view paper
  • Downloaded 1,373 times
  • Download rankings, all-time:
    • Site-wide: 12,190
    • In microbiology: 679
  • Year to date:
    • Site-wide: 94,085
  • Since beginning of last month:
    • Site-wide: 94,085

Links between environment, diet, and the hunter-gatherer microbiome

microbiology more details view paper
  • Downloaded 1,365 times
  • Download rankings, all-time:
    • Site-wide: 12,301
    • In microbiology: 685
  • Year to date:
    • Site-wide: 54,620
  • Since beginning of last month:
    • Site-wide: 54,620

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

microbiology more details view paper
  • Downloaded 1,304 times
  • Download rankings, all-time:
    • Site-wide: 13,166
    • In microbiology: 740
  • Year to date:
    • Site-wide: 18,173
  • Since beginning of last month:
    • Site-wide: 18,173

The development of gut microbiota in ostriches and its association with juvenile growth

microbiology more details view paper
  • Downloaded 1,288 times
  • Download rankings, all-time:
    • Site-wide: 13,418
    • In microbiology: 763
  • Year to date:
    • Site-wide: 34,409
  • Since beginning of last month:
    • Site-wide: 34,409

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

microbiology more details view paper
  • Downloaded 1,213 times
  • Download rankings, all-time:
    • Site-wide: 14,690
    • In microbiology: 826
  • Year to date:
    • Site-wide: 37,431
  • Since beginning of last month:
    • Site-wide: 37,431

Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

ecology more details view paper
  • Downloaded 1,200 times
  • Download rankings, all-time:
    • Site-wide: 14,932
    • In ecology: 253
  • Year to date:
    • Site-wide: 68,592
  • Since beginning of last month:
    • Site-wide: 68,592

Species abundance information improves sequence taxonomy classification accuracy

bioinformatics more details view paper
  • Downloaded 1,033 times
  • Download rankings, all-time:
    • Site-wide: 18,766
    • In bioinformatics: 2,263
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

Age and sex-dependent patterns of gut microbial diversity in human adults

microbiology more details view paper
  • Downloaded 1,012 times
  • Download rankings, all-time:
    • Site-wide: 19,319
    • In microbiology: 1,082
  • Year to date:
    • Site-wide: 109,371
  • Since beginning of last month:
    • Site-wide: 109,371

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data

bioinformatics more details view paper
  • Downloaded 983 times
  • Download rankings, all-time:
    • Site-wide: 20,100
    • In bioinformatics: 2,424
  • Year to date:
    • Site-wide: 52,784
  • Since beginning of last month:
    • Site-wide: 52,784

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

microbiology more details view paper
  • Downloaded 979 times
  • Download rankings, all-time:
    • Site-wide: 20,237
    • In microbiology: 1,136
  • Year to date:
    • Site-wide: 47,334
  • Since beginning of last month:
    • Site-wide: 47,334

A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV2

infectious diseases more details view paper
  • Downloaded 941 times
  • Download rankings, all-time:
    • Site-wide: 21,414
    • In infectious diseases: 1,628
  • Year to date:
    • Site-wide: 6,333
  • Since beginning of last month:
    • Site-wide: 6,333

SARS-CoV-2 Infection Among Symptom-Free Healthcare Workers

epidemiology more details view paper
  • Downloaded 928 times
  • Download rankings, all-time:
    • Site-wide: 21,842
    • In epidemiology: 1,223
  • Year to date:
    • Site-wide: 18,856
  • Since beginning of last month:
    • Site-wide: 18,856

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

bioinformatics more details view paper
  • Downloaded 834 times
  • Download rankings, all-time:
    • Site-wide: 25,438
    • In bioinformatics: 3,012
  • Year to date:
    • Site-wide: 70,249
  • Since beginning of last month:
    • Site-wide: 70,249

Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs

infectious diseases more details view paper
  • Downloaded 831 times
  • Download rankings, all-time:
    • Site-wide: 25,555
    • In infectious diseases: 1,789
  • Year to date:
    • Site-wide: 23,884
  • Since beginning of last month:
    • Site-wide: 23,884

Reference data based insights expand understanding of human metabolomes

systems biology more details view paper
  • Downloaded 791 times
  • Download rankings, all-time:
    • Site-wide: 27,341
    • In systems biology: 597
  • Year to date:
    • Site-wide: 40,249
  • Since beginning of last month:
    • Site-wide: 40,249

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

genetic and genomic medicine more details view paper
  • Downloaded 786 times
  • Download rankings, all-time:
    • Site-wide: 27,627
    • In genetic and genomic medicine: 81
  • Year to date:
    • Site-wide: 14,407
  • Since beginning of last month:
    • Site-wide: 14,407

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

infectious diseases more details view paper
  • Downloaded 718 times
  • Download rankings, all-time:
    • Site-wide: 31,343
    • In infectious diseases: 1,995
  • Year to date:
    • Site-wide: 4,432
  • Since beginning of last month:
    • Site-wide: 4,432

Challenges in Benchmarking Metagenomic Profilers

bioinformatics more details view paper
  • Downloaded 654 times
  • Download rankings, all-time:
    • Site-wide: 35,492
    • In bioinformatics: 3,965
  • Year to date:
    • Site-wide: 10,547
  • Since beginning of last month:
    • Site-wide: 10,547

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

microbiology more details view paper
  • Downloaded 641 times
  • Download rankings, all-time:
    • Site-wide: 36,501
    • In microbiology: 2,175
  • Year to date:
    • Site-wide: 46,698
  • Since beginning of last month:
    • Site-wide: 46,698

Revisiting microbe-metabolite interactions: doing better than random

bioinformatics more details view paper
  • Downloaded 597 times
  • Download rankings, all-time:
    • Site-wide: 39,945
    • In bioinformatics: 4,366
  • Year to date:
    • Site-wide: 41,596
  • Since beginning of last month:
    • Site-wide: 41,596

High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county

epidemiology more details view paper
  • Downloaded 574 times
  • Download rankings, all-time:
    • Site-wide: 41,904
    • In epidemiology: 1,957
  • Year to date:
    • Site-wide: 2,804
  • Since beginning of last month:
    • Site-wide: 2,804

Microbe-metabolite associations linked to the rebounding murine gut microbiome post-colonization with vancomycin resistant Enterococcus faecium

microbiology more details view paper
  • Downloaded 557 times
  • Download rankings, all-time:
    • Site-wide: 43,517
    • In microbiology: 2,696
  • Year to date:
    • Site-wide: 40,253
  • Since beginning of last month:
    • Site-wide: 40,253

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

ecology more details view paper
  • Downloaded 551 times
  • Download rankings, all-time:
    • Site-wide: 44,123
    • In ecology: 1,113
  • Year to date:
    • Site-wide: 9,901
  • Since beginning of last month:
    • Site-wide: 9,901

Links between gut microbiome composition and fatty liver disease in a large population sample

gastroenterology more details view paper
  • Downloaded 550 times
  • Download rankings, all-time:
    • Site-wide: 44,260
    • In gastroenterology: 35
  • Year to date:
    • Site-wide: 9,878
  • Since beginning of last month:
    • Site-wide: 9,878

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting

genetic and genomic medicine more details view paper
  • Downloaded 500 times
  • Download rankings, all-time:
    • Site-wide: 49,511
    • In genetic and genomic medicine: 139
  • Year to date:
    • Site-wide: 29,666
  • Since beginning of last month:
    • Site-wide: 29,666

Visualizing 'omic feature rankings and log-ratios using Qurro

bioinformatics more details view paper
  • Downloaded 491 times
  • Download rankings, all-time:
    • Site-wide: 50,550
    • In bioinformatics: 5,255
  • Year to date:
    • Site-wide: 74,973
  • Since beginning of last month:
    • Site-wide: 74,973

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

bioinformatics more details view paper
  • Downloaded 465 times
  • Download rankings, all-time:
    • Site-wide: 53,745
    • In bioinformatics: 5,523
  • Year to date:
    • Site-wide: 10,546
  • Since beginning of last month:
    • Site-wide: 10,546

Expanding magnetic organelle biogenesis in the domain Bacteria

microbiology more details view paper
  • Downloaded 452 times
  • Download rankings, all-time:
    • Site-wide: 55,409
    • In microbiology: 3,601
  • Year to date:
    • Site-wide: 41,580
  • Since beginning of last month:
    • Site-wide: 41,580

Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus

ecology more details view paper
  • Downloaded 432 times
  • Download rankings, all-time:
    • Site-wide: 58,131
    • In ecology: 1,606
  • Year to date:
    • Site-wide: 53,008
  • Since beginning of last month:
    • Site-wide: 53,008

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

microbiology more details view paper
  • Downloaded 397 times
  • Download rankings, all-time:
    • Site-wide: 63,263
    • In microbiology: 4,229
  • Year to date:
    • Site-wide: 106,936
  • Since beginning of last month:
    • Site-wide: 106,936

Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria

immunology more details view paper
  • Downloaded 368 times
  • Download rankings, all-time:
    • Site-wide: 68,019
    • In immunology: 1,839
  • Year to date:
    • Site-wide: 104,423
  • Since beginning of last month:
    • Site-wide: 104,423

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs

systems biology more details view paper
  • Downloaded 345 times
  • Download rankings, all-time:
    • Site-wide: 71,848
    • In systems biology: 1,753
  • Year to date:
    • Site-wide: 120,819
  • Since beginning of last month:
    • Site-wide: 120,819

The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment

genomics more details view paper
  • Downloaded 312 times
  • Download rankings, all-time:
    • Site-wide: 77,927
    • In genomics: 5,194
  • Year to date:
    • Site-wide: 84,123
  • Since beginning of last month:
    • Site-wide: 84,123

Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes

microbiology more details view paper
  • Downloaded 295 times
  • Download rankings, all-time:
    • Site-wide: 81,243
    • In microbiology: 5,716
  • Year to date:
    • Site-wide: 122,187
  • Since beginning of last month:
    • Site-wide: 122,187

Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

microbiology more details view paper
  • Downloaded 216 times
  • Download rankings, all-time:
    • Site-wide: 98,126
    • In microbiology: 7,198
  • Year to date:
    • Site-wide: 37,978
  • Since beginning of last month:
    • Site-wide: 37,978

Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

microbiology more details view paper
  • Downloaded 202 times
  • Download rankings, all-time:
    • Site-wide: 101,170
    • In microbiology: 7,495
  • Year to date:
    • Site-wide: 12,484
  • Since beginning of last month:
    • Site-wide: 12,484

Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

microbiology more details view paper
  • Downloaded 110 times
  • Download rankings, all-time:
    • Site-wide: 119,264
    • In microbiology: 9,129
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

A scale-free, fully connected global transition network underlies known microbiome diversity

microbiology more details view paper
  • Downloaded 105 times
  • Download rankings, all-time:
    • Site-wide: 120,076
    • In microbiology: 9,222
  • Year to date:
    • Site-wide: 67,373
  • Since beginning of last month:
    • Site-wide: 67,373

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