Author: Rob Knight

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Preprints

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

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  • Site-wide: 555
  • In molecular biology: 8
• Year to date:
  • Site-wide: 678
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  • Site-wide: 678

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

• Downloaded 7,920 times
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  • 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

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  • Site-wide: 1,766
  • In epidemiology: 207
• Year to date:
  • Site-wide: 82
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  • Site-wide: 82

Structure-Based Function Prediction using Graph Convolutional Networks

• Downloaded 5,138 times
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  • Site-wide: 1,785
  • In bioinformatics: 151
• Year to date:
  • Site-wide: 1,577
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  • Site-wide: 1,577

BugBase Predicts Organism Level Microbiome Phenotypes

• Downloaded 3,717 times
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  • Site-wide: 2,832
  • In bioinformatics: 276
• Year to date:
  • Site-wide: 12,254
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  • Site-wide: 12,254

Evaluating the information content of shallow shotgun metagenomics

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  • Site-wide: 2,917
  • In genomics: 345
• Year to date:
  • Site-wide: 21,971
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  • Site-wide: 21,971

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

• Downloaded 3,630 times
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  • Site-wide: 2,937
  • In microbiology: 201
• Year to date:
  • Site-wide: 17,680
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  • Site-wide: 17,680

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

• Downloaded 3,370 times
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  • Site-wide: 3,268
  • In epidemiology: 321
• Year to date:
  • Site-wide: 17,542
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  • 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

• Downloaded 2,856 times
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  • Site-wide: 4,104
  • In genomics: 477
• Year to date:
  • Site-wide: 9,129
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  • Site-wide: 9,129

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

• Downloaded 1,971 times
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  • Site-wide: 7,080
  • In genetics: 345
• Year to date:
  • Site-wide: 2,455
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  • Site-wide: 2,455

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

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  • Site-wide: 8,034
  • In microbiology: 444
• Year to date:
  • Site-wide: 5,474
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  • Site-wide: 5,474

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

• Downloaded 1,703 times
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  • Site-wide: 8,856
  • In bioinformatics: 1,086
• Year to date:
  • Site-wide: 12,855
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  • Site-wide: 12,855

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

• Downloaded 1,632 times
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  • Site-wide: 9,466
  • In bioinformatics: 1,161
• Year to date:
  • Site-wide: 8,681
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  • Site-wide: 8,681

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

• Downloaded 1,574 times
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  • Site-wide: 9,976
  • In genomics: 1,107
• Year to date:
  • Site-wide: 53,391
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  • Site-wide: 53,391

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

• Downloaded 1,373 times
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  • Site-wide: 12,190
  • In microbiology: 679
• Year to date:
  • Site-wide: 94,085
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  • Site-wide: 94,085

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

• Downloaded 1,365 times
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  • Site-wide: 12,301
  • In microbiology: 685
• Year to date:
  • Site-wide: 54,620
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  • Site-wide: 54,620

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

• Downloaded 1,304 times
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  • Site-wide: 13,166
  • In microbiology: 740
• Year to date:
  • Site-wide: 18,173
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  • Site-wide: 18,173

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

• Downloaded 1,288 times
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  • 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

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  • Site-wide: 14,690
  • In microbiology: 826
• Year to date:
  • Site-wide: 37,431
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  • Site-wide: 37,431

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

• Downloaded 1,200 times
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  • Site-wide: 14,932
  • In ecology: 253
• Year to date:
  • Site-wide: 68,592
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  • Site-wide: 68,592

Species abundance information improves sequence taxonomy classification accuracy

• 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

• Downloaded 1,012 times
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  • Site-wide: 19,319
  • In microbiology: 1,082
• Year to date:
  • Site-wide: 109,371
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  • Site-wide: 109,371

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

• Downloaded 983 times
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  • Site-wide: 20,100
  • In bioinformatics: 2,424
• Year to date:
  • Site-wide: 52,784
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  • Site-wide: 52,784

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

• Downloaded 979 times
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  • Site-wide: 20,237
  • In microbiology: 1,136
• Year to date:
  • Site-wide: 47,334
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  • Site-wide: 47,334

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

• 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

• Downloaded 928 times
• Download rankings, all-time:
  • Site-wide: 21,842
  • In epidemiology: 1,223
• Year to date:
  • Site-wide: 18,856
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  • Site-wide: 18,856

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

• 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

• 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

• 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

• 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

• Downloaded 718 times
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  • Site-wide: 31,343
  • In infectious diseases: 1,995
• Year to date:
  • Site-wide: 4,432
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  • Site-wide: 4,432

Challenges in Benchmarking Metagenomic Profilers

• Downloaded 654 times
• Download rankings, all-time:
  • Site-wide: 35,492
  • In bioinformatics: 3,965
• Year to date:
  • Site-wide: 10,547
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  • Site-wide: 10,547

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

• Downloaded 641 times
• Download rankings, all-time:
  • Site-wide: 36,501
  • In microbiology: 2,175
• Year to date:
  • Site-wide: 46,698
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  • Site-wide: 46,698

Revisiting microbe-metabolite interactions: doing better than random

• Downloaded 597 times
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  • Site-wide: 39,945
  • In bioinformatics: 4,366
• Year to date:
  • Site-wide: 41,596
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  • Site-wide: 41,596

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

• 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

• 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

• 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

• 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

• 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

• 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

• Downloaded 465 times
• Download rankings, all-time:
  • Site-wide: 53,745
  • In bioinformatics: 5,523
• Year to date:
  • Site-wide: 10,546
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  • Site-wide: 10,546

Expanding magnetic organelle biogenesis in the domain Bacteria

• 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

• Downloaded 432 times
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  • Site-wide: 58,131
  • In ecology: 1,606
• Year to date:
  • Site-wide: 53,008
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  • Site-wide: 53,008

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

• Downloaded 397 times
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  • Site-wide: 63,263
  • In microbiology: 4,229
• Year to date:
  • Site-wide: 106,936
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  • Site-wide: 106,936

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

• Downloaded 368 times
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  • Site-wide: 68,019
  • In immunology: 1,839
• Year to date:
  • Site-wide: 104,423
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  • Site-wide: 104,423

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

• Downloaded 345 times
• Download rankings, all-time:
  • Site-wide: 71,848
  • In systems biology: 1,753
• Year to date:
  • Site-wide: 120,819
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  • Site-wide: 120,819

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

• Downloaded 312 times
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  • Site-wide: 77,927
  • In genomics: 5,194
• Year to date:
  • Site-wide: 84,123
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  • Site-wide: 84,123

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

• Downloaded 295 times
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  • Site-wide: 81,243
  • In microbiology: 5,716
• Year to date:
  • Site-wide: 122,187
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  • Site-wide: 122,187

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

• Downloaded 216 times
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  • Site-wide: 98,126
  • In microbiology: 7,198
• Year to date:
  • Site-wide: 37,978
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  • Site-wide: 37,978

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

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  • Site-wide: 101,170
  • In microbiology: 7,495
• Year to date:
  • Site-wide: 12,484
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  • Site-wide: 12,484

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

• Downloaded 110 times
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  • Site-wide: 119,264
  • In microbiology: 9,129
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  • Site-wide: None
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  • Site-wide: None

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

• Downloaded 105 times
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  • Site-wide: 120,076
  • In microbiology: 9,222
• Year to date:
  • Site-wide: 67,373
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  • Site-wide: 67,373