Rxivist logo

Author: Rob Knight

  • ORCiD: http://orcid.org/0000-0002-0975-9019
  • Most recently observed institution: Center for Microbiome Innovation and Departments of Pediatrics, Bioengineering, and Computer Science & Engineering, University of California San Diego, La Jolla, CA

Rankings

  • All-time downloads: 49,454 (rank: 724 out of 383,801)
  • Categories:
    • bioinformatics: 17,650 (rank: 156 out of 32,862)
    • ecology: 2,309 (rank: 627 out of 16,475)
    • genomics: 7,410 (rank: 2,187 (tie) out of 40,853)
    • immunology: 336 (rank: 12,169 (tie) out of 20,902)
    • microbiology: 12,869 (rank: 614 out of 43,354)
    • molecular biology: 8,576 (rank: 173 (tie) out of 19,938)
    • systems biology: 304 (rank: 8,526 (tie) out of 11,274)

Downloads per author, site-wide

Preprints

Genetics of human gut microbiome composition

genetics more details view paper

No bioRxiv download data for this paper yet.

Reference data based insights expand understanding of human metabolomes

systems biology more details view paper

No bioRxiv download data for this paper yet.

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

molecular biology more details view paper
  • Downloaded 8,576 times
  • Download rankings, all-time:
    • Site-wide: 307 out of 89,581
    • In molecular biology: 10 out of 3,038
  • Year to date:
    • Site-wide: 191 out of 89,581
  • Since beginning of last month:
    • Site-wide: 162 out of 89,581

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data.

bioinformatics more details view paper
  • Downloaded 5,801 times
  • Download rankings, all-time:
    • Site-wide: 576 out of 89,581
    • In bioinformatics: 91 out of 8,443
  • Year to date:
    • Site-wide: 10,300 out of 89,581
  • Since beginning of last month:
    • Site-wide: 49,702 out of 89,581

Evaluating the information content of shallow shotgun metagenomics

genomics more details view paper
  • Downloaded 3,488 times
  • Download rankings, all-time:
    • Site-wide: 1,428 out of 89,581
    • In genomics: 301 out of 5,703
  • Year to date:
    • Site-wide: 31,929 out of 89,581
  • Since beginning of last month:
    • Site-wide: 40,458 out of 89,581

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

microbiology more details view paper
  • Downloaded 3,320 times
  • Download rankings, all-time:
    • Site-wide: 1,545 out of 89,581
    • In microbiology: 138 out of 7,723
  • Year to date:
    • Site-wide: 12,794 out of 89,581
  • Since beginning of last month:
    • Site-wide: 16,979 out of 89,581

Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
  • Downloaded 3,261 times
  • Download rankings, all-time:
    • Site-wide: 1,593 out of 89,581
    • In bioinformatics: 284 out of 8,443
  • Year to date:
    • Site-wide: 718 out of 89,581
  • Since beginning of last month:
    • Site-wide: 273 out of 89,581

BugBase Predicts Organism Level Microbiome Phenotypes

bioinformatics more details view paper
  • Downloaded 3,131 times
  • Download rankings, all-time:
    • Site-wide: 1,717 out of 89,581
    • In bioinformatics: 305 out of 8,443
  • Year to date:
    • Site-wide: 3,934 out of 89,581
  • Since beginning of last month:
    • Site-wide: 6,277 out of 89,581

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 2,328 times
  • Download rankings, all-time:
    • Site-wide: 2,853 out of 89,581
    • In genomics: 544 out of 5,703
  • Year to date:
    • Site-wide: 710 out of 89,581
  • Since beginning of last month:
    • Site-wide: 2,837 out of 89,581

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

genomics more details view paper
  • Downloaded 1,495 times
  • Download rankings, all-time:
    • Site-wide: 5,932 out of 89,581
    • In genomics: 965 out of 5,703
  • Year to date:
    • Site-wide: 30,243 out of 89,581
  • Since beginning of last month:
    • Site-wide: 45,998 out of 89,581

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

microbiology more details view paper
  • Downloaded 1,288 times
  • Download rankings, all-time:
    • Site-wide: 7,595 out of 89,581
    • In microbiology: 454 out of 7,723
  • Year to date:
    • Site-wide: 11,599 out of 89,581
  • Since beginning of last month:
    • Site-wide: 33,390 out of 89,581

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

microbiology more details view paper
  • Downloaded 1,274 times
  • Download rankings, all-time:
    • Site-wide: 7,734 out of 89,581
    • In microbiology: 464 out of 7,723
  • Year to date:
    • Site-wide: 25,113 out of 89,581
  • Since beginning of last month:
    • Site-wide: 44,991 out of 89,581

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

bioinformatics more details view paper
  • Downloaded 1,169 times
  • Download rankings, all-time:
    • Site-wide: 8,938 out of 89,581
    • In bioinformatics: 1,484 out of 8,443
  • Year to date:
    • Site-wide: 1,169 out of 89,581
  • Since beginning of last month:
    • Site-wide: 2,657 out of 89,581

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

ecology more details view paper
  • Downloaded 1,116 times
  • Download rankings, all-time:
    • Site-wide: 9,638 out of 89,581
    • In ecology: 201 out of 3,927
  • Year to date:
    • Site-wide: 66,241 out of 89,581
  • Since beginning of last month:
    • Site-wide: 52,319 out of 89,581

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

microbiology more details view paper
  • Downloaded 1,115 times
  • Download rankings, all-time:
    • Site-wide: 9,660 out of 89,581
    • In microbiology: 591 out of 7,723
  • Year to date:
    • Site-wide: 7,337 out of 89,581
  • Since beginning of last month:
    • Site-wide: 33,871 out of 89,581

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

microbiology more details view paper
  • Downloaded 1,083 times
  • Download rankings, all-time:
    • Site-wide: 10,148 out of 89,581
    • In microbiology: 618 out of 7,723
  • Year to date:
    • Site-wide: 48,346 out of 89,581
  • Since beginning of last month:
    • Site-wide: 46,625 out of 89,581

Species abundance information improves sequence taxonomy classification accuracy

bioinformatics more details view paper
  • Downloaded 954 times
  • Download rankings, all-time:
    • Site-wide: 12,431 out of 89,581
    • In bioinformatics: 1,985 out of 8,443
  • Year to date:
    • Site-wide: 20,034 out of 89,581
  • Since beginning of last month:
    • Site-wide: 23,447 out of 89,581

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

bioinformatics more details view paper
  • Downloaded 944 times
  • Download rankings, all-time:
    • Site-wide: 12,624 out of 89,581
    • In bioinformatics: 2,015 out of 8,443
  • Year to date:
    • Site-wide: 1,620 out of 89,581
  • Since beginning of last month:
    • Site-wide: 8,709 out of 89,581

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

microbiology more details view paper
  • Downloaded 934 times
  • Download rankings, all-time:
    • Site-wide: 12,838 out of 89,581
    • In microbiology: 771 out of 7,723
  • Year to date:
    • Site-wide: 34,611 out of 89,581
  • Since beginning of last month:
    • Site-wide: 57,628 out of 89,581

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

microbiology more details view paper
  • Downloaded 873 times
  • Download rankings, all-time:
    • Site-wide: 14,288 out of 89,581
    • In microbiology: 861 out of 7,723
  • Year to date:
    • Site-wide: 72,197 out of 89,581
  • Since beginning of last month:
    • Site-wide: 54,046 out of 89,581

Microbial biogeography and ecology of the mouth and implications for periodontal diseases

ecology more details view paper
  • Downloaded 850 times
  • Download rankings, all-time:
    • Site-wide: 14,882 out of 89,581
    • In ecology: 359 out of 3,927
  • Year to date:
    • Site-wide: 12,352 out of 89,581
  • Since beginning of last month:
    • Site-wide: 17,163 out of 89,581

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

microbiology more details view paper
  • Downloaded 780 times
  • Download rankings, all-time:
    • Site-wide: 17,007 out of 89,581
    • In microbiology: 1,034 out of 7,723
  • Year to date:
    • Site-wide: 4,903 out of 89,581
  • Since beginning of last month:
    • Site-wide: 9,345 out of 89,581

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

bioinformatics more details view paper
  • Downloaded 751 times
  • Download rankings, all-time:
    • Site-wide: 18,040 out of 89,581
    • In bioinformatics: 2,703 out of 8,443
  • Year to date:
    • Site-wide: 6,785 out of 89,581
  • Since beginning of last month:
    • Site-wide: 7,336 out of 89,581

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

bioinformatics more details view paper
  • Downloaded 740 times
  • Download rankings, all-time:
    • Site-wide: 18,431 out of 89,581
    • In bioinformatics: 2,748 out of 8,443
  • Year to date:
    • Site-wide: 50,870 out of 89,581
  • Since beginning of last month:
    • Site-wide: 59,222 out of 89,581

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

microbiology more details view paper
  • Downloaded 497 times
  • Download rankings, all-time:
    • Site-wide: 31,709 out of 89,581
    • In microbiology: 2,083 out of 7,723
  • Year to date:
    • Site-wide: 7,654 out of 89,581
  • Since beginning of last month:
    • Site-wide: 13,803 out of 89,581

Revisiting microbe-metabolite interactions: doing better than random

bioinformatics more details view paper
  • Downloaded 478 times
  • Download rankings, all-time:
    • Site-wide: 33,277 out of 89,581
    • In bioinformatics: 4,242 out of 8,443
  • Year to date:
    • Site-wide: 14,890 out of 89,581
  • Since beginning of last month:
    • Site-wide: 22,499 out of 89,581

Visualizing 'omic feature rankings and log-ratios using Qurro

bioinformatics more details view paper
  • Downloaded 421 times
  • Download rankings, all-time:
    • Site-wide: 38,546 out of 89,581
    • In bioinformatics: 4,721 out of 8,443
  • Year to date:
    • Site-wide: 13,010 out of 89,581
  • Since beginning of last month:
    • Site-wide: 74,039 out of 89,581

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

microbiology more details view paper
  • Downloaded 352 times
  • Download rankings, all-time:
    • Site-wide: 46,263 out of 89,581
    • In microbiology: 3,324 out of 7,723
  • Year to date:
    • Site-wide: 78,035 out of 89,581
  • Since beginning of last month:
    • Site-wide: 86,370 out of 89,581

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

ecology more details view paper
  • Downloaded 343 times
  • Download rankings, all-time:
    • Site-wide: 47,536 out of 89,581
    • In ecology: 1,555 out of 3,927
  • Year to date:
    • Site-wide: 22,809 out of 89,581
  • Since beginning of last month:
    • Site-wide: 23,341 out of 89,581

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

immunology more details view paper
  • Downloaded 336 times
  • Download rankings, all-time:
    • Site-wide: 48,409 out of 89,581
    • In immunology: 1,244 out of 2,586
  • Year to date:
    • Site-wide: 74,672 out of 89,581
  • Since beginning of last month:
    • Site-wide: 61,827 out of 89,581

Early-life gut dysbiosis linked to mass mortality in ostriches

microbiology more details view paper
  • Downloaded 323 times
  • Download rankings, all-time:
    • Site-wide: 50,235 out of 89,581
    • In microbiology: 3,670 out of 7,723
  • Year to date:
    • Site-wide: 27,239 out of 89,581
  • Since beginning of last month:
    • Site-wide: 27,888 out of 89,581

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

microbiology more details view paper
  • Downloaded 317 times
  • Download rankings, all-time:
    • Site-wide: 51,003 out of 89,581
    • In microbiology: 3,737 out of 7,723
  • Year to date:
    • Site-wide: 17,739 out of 89,581
  • Since beginning of last month:
    • Site-wide: 9,234 out of 89,581

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

systems biology more details view paper
  • Downloaded 304 times
  • Download rankings, all-time:
    • Site-wide: 52,847 out of 89,581
    • In systems biology: 1,546 out of 2,312
  • Year to date:
    • Site-wide: 34,349 out of 89,581
  • Since beginning of last month:
    • Site-wide: 41,707 out of 89,581

Expanding magnetic organelle biogenesis in the domain Bacteria

microbiology more details view paper
  • Downloaded 264 times
  • Download rankings, all-time:
    • Site-wide: 58,839 out of 89,581
    • In microbiology: 4,481 out of 7,723
  • Year to date:
    • Site-wide: 11,021 out of 89,581
  • Since beginning of last month:
    • Site-wide: 12,816 out of 89,581

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

microbiology more details view paper
  • Downloaded 262 times
  • Download rankings, all-time:
    • Site-wide: 59,158 out of 89,581
    • In microbiology: 4,511 out of 7,723
  • Year to date:
    • Site-wide: 86,033 out of 89,581
  • Since beginning of last month:
    • Site-wide: 83,667 out of 89,581

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

genomics more details view paper
  • Downloaded 99 times
  • Download rankings, all-time:
    • Site-wide: 83,647 out of 89,581
    • In genomics: 5,474 out of 5,703
  • Year to date:
    • Site-wide: 40,416 out of 89,581
  • Since beginning of last month:
    • Site-wide: 10,963 out of 89,581

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

microbiology more details view paper
  • Downloaded 76 times
  • Download rankings, all-time:
    • Site-wide: 85,578 out of 89,581
    • In microbiology: 7,244 out of 7,723
  • Year to date:
    • Site-wide: 53,506 out of 89,581
  • Since beginning of last month:
    • Site-wide: 28,756 out of 89,581

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

microbiology more details view paper
  • Downloaded 58 times
  • Download rankings, all-time:
    • Site-wide: 86,757 out of 89,581
    • In microbiology: 7,398 out of 7,723
  • Year to date:
    • Site-wide: 67,030 out of 89,581
  • Since beginning of last month:
    • Site-wide: 28,580 out of 89,581

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

microbiology more details view paper
  • Downloaded 53 times
  • Download rankings, all-time:
    • Site-wide: 87,018 out of 89,581
    • In microbiology: 7,428 out of 7,723
  • Year to date:
    • Site-wide: 72,289 out of 89,581
  • Since beginning of last month:
    • Site-wide: 32,069 out of 89,581

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News