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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 70,616 bioRxiv papers from 308,268 authors.

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: 33,787 (rank: 559 out of 308,293)
  • Categories:
    • bioinformatics: 12,333 (rank: 237 out of 26,826)
    • ecology: 1,889 (rank: 659 out of 12,447)
    • genomics: 4,789 (rank: 2,962 out of 34,853)
    • immunology: 290 (rank: 8,275 (tie) out of 14,770)
    • microbiology: 9,980 (rank: 57 out of 31,942)
    • molecular biology: 4,309 (rank: 201 (tie) out of 15,050)
    • systems biology: 197 (rank: 7,915 (tie) out of 9,258)

Downloads per author, site-wide

Preprints

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

bioinformatics more details view paper

No bioRxiv download data for this paper yet.

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

bioinformatics more details view paper
  • Downloaded 5,561 times
  • Download rankings, all-time:
    • Site-wide: 381 out of 70,616
    • In bioinformatics: 73 out of 6,917
  • Year to date:
    • Site-wide: 3,591 out of 70,616
  • Since beginning of last month:
    • Site-wide: 2,005 out of 70,616

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

molecular biology more details view paper
  • Downloaded 4,309 times
  • Download rankings, all-time:
    • Site-wide: 622 out of 70,616
    • In molecular biology: 14 out of 2,266
  • Year to date:
    • Site-wide: 18 out of 70,616
  • Since beginning of last month:
    • Site-wide: 260 out of 70,616

Evaluating the information content of shallow shotgun metagenomics

genomics more details view paper
  • Downloaded 3,373 times
  • Download rankings, all-time:
    • Site-wide: 991 out of 70,616
    • In genomics: 246 out of 4,714
  • Year to date:
    • Site-wide: 32,906 out of 70,616
  • Since beginning of last month:
    • Site-wide: 24,656 out of 70,616

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

microbiology more details view paper
  • Downloaded 3,102 times
  • Download rankings, all-time:
    • Site-wide: 1,182 out of 70,616
    • In microbiology: 23 out of 5,733
  • Year to date:
    • Site-wide: 7,751 out of 70,616
  • Since beginning of last month:
    • Site-wide: 5,539 out of 70,616

BugBase Predicts Organism Level Microbiome Phenotypes

bioinformatics more details view paper
  • Downloaded 2,659 times
  • Download rankings, all-time:
    • Site-wide: 1,536 out of 70,616
    • In bioinformatics: 304 out of 6,917
  • Year to date:
    • Site-wide: 2,993 out of 70,616
  • Since beginning of last month:
    • Site-wide: 4,941 out of 70,616

Structure-Based Function Prediction using Graph Convolutional Networks

bioinformatics more details view paper
  • Downloaded 1,683 times
  • Download rankings, all-time:
    • Site-wide: 3,454 out of 70,616
    • In bioinformatics: 688 out of 6,917
  • Year to date:
    • Site-wide: 2,449 out of 70,616
  • Since beginning of last month:
    • Site-wide: 789 out of 70,616

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

genomics more details view paper
  • Downloaded 1,416 times
  • Download rankings, all-time:
    • Site-wide: 4,653 out of 70,616
    • In genomics: 828 out of 4,714
  • Year to date:
    • Site-wide: 2,498 out of 70,616
  • Since beginning of last month:
    • Site-wide: 3,571 out of 70,616

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

microbiology more details view paper
  • Downloaded 1,144 times
  • Download rankings, all-time:
    • Site-wide: 6,627 out of 70,616
    • In microbiology: 262 out of 5,733
  • Year to date:
    • Site-wide: 10,867 out of 70,616
  • Since beginning of last month:
    • Site-wide: 6,420 out of 70,616

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

microbiology more details view paper
  • Downloaded 1,080 times
  • Download rankings, all-time:
    • Site-wide: 7,311 out of 70,616
    • In microbiology: 298 out of 5,733
  • Year to date:
    • Site-wide: 2,604 out of 70,616
  • Since beginning of last month:
    • Site-wide: 9,516 out of 70,616

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

ecology more details view paper
  • Downloaded 1,064 times
  • Download rankings, all-time:
    • Site-wide: 7,471 out of 70,616
    • In ecology: 160 out of 3,035
  • Year to date:
    • Site-wide: 36,690 out of 70,616
  • Since beginning of last month:
    • Site-wide: 20,091 out of 70,616

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

microbiology more details view paper
  • Downloaded 1,015 times
  • Download rankings, all-time:
    • Site-wide: 8,047 out of 70,616
    • In microbiology: 339 out of 5,733
  • Year to date:
    • Site-wide: 11,424 out of 70,616
  • Since beginning of last month:
    • Site-wide: 18,016 out of 70,616

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

microbiology more details view paper
  • Downloaded 826 times
  • Download rankings, all-time:
    • Site-wide: 11,245 out of 70,616
    • In microbiology: 501 out of 5,733
  • Year to date:
    • Site-wide: 43,046 out of 70,616
  • Since beginning of last month:
    • Site-wide: 39,183 out of 70,616

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

microbiology more details view paper
  • Downloaded 824 times
  • Download rankings, all-time:
    • Site-wide: 11,279 out of 70,616
    • In microbiology: 504 out of 5,733
  • Year to date:
    • Site-wide: 58,014 out of 70,616
  • Since beginning of last month:
    • Site-wide: 54,721 out of 70,616

Species abundance information improves sequence taxonomy classification accuracy

bioinformatics more details view paper
  • Downloaded 801 times
  • Download rankings, all-time:
    • Site-wide: 11,744 out of 70,616
    • In bioinformatics: 1,959 out of 6,917
  • Year to date:
    • Site-wide: 7,248 out of 70,616
  • Since beginning of last month:
    • Site-wide: 24,275 out of 70,616

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

microbiology more details view paper
  • Downloaded 780 times
  • Download rankings, all-time:
    • Site-wide: 12,212 out of 70,616
    • In microbiology: 564 out of 5,733
  • Year to date:
    • Site-wide: 30,121 out of 70,616
  • Since beginning of last month:
    • Site-wide: 25,013 out of 70,616

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

bioinformatics more details view paper
  • Downloaded 666 times
  • Download rankings, all-time:
    • Site-wide: 15,361 out of 70,616
    • In bioinformatics: 2,399 out of 6,917
  • Year to date:
    • Site-wide: 43,077 out of 70,616
  • Since beginning of last month:
    • Site-wide: 42,437 out of 70,616

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

ecology more details view paper
  • Downloaded 635 times
  • Download rankings, all-time:
    • Site-wide: 16,470 out of 70,616
    • In ecology: 457 out of 3,035
  • Year to date:
    • Site-wide: 5,000 out of 70,616
  • Since beginning of last month:
    • Site-wide: 9,043 out of 70,616

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

bioinformatics more details view paper
  • Downloaded 423 times
  • Download rankings, all-time:
    • Site-wide: 27,610 out of 70,616
    • In bioinformatics: 3,698 out of 6,917
  • Year to date:
    • Site-wide: 4,190 out of 70,616
  • Since beginning of last month:
    • Site-wide: 7,173 out of 70,616

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

microbiology more details view paper
  • Downloaded 359 times
  • Download rankings, all-time:
    • Site-wide: 32,902 out of 70,616
    • In microbiology: 2,040 out of 5,733
  • Year to date:
    • Site-wide: 6,422 out of 70,616
  • Since beginning of last month:
    • Site-wide: 7,665 out of 70,616

The Molecular and Microbial Microenvironments in Chronically Diseased Lungs

microbiology more details view paper
  • Downloaded 308 times
  • Download rankings, all-time:
    • Site-wide: 37,984 out of 70,616
    • In microbiology: 2,448 out of 5,733
  • Year to date:
    • Site-wide: 64,954 out of 70,616
  • Since beginning of last month:
    • Site-wide: 63,580 out of 70,616

Revisiting microbe-metabolite interactions: doing better than random

bioinformatics more details view paper
  • Downloaded 294 times
  • Download rankings, all-time:
    • Site-wide: 39,562 out of 70,616
    • In bioinformatics: 4,754 out of 6,917
  • Year to date:
    • Site-wide: 4,439 out of 70,616
  • Since beginning of last month:
    • Site-wide: 422 out of 70,616

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

immunology more details view paper
  • Downloaded 290 times
  • Download rankings, all-time:
    • Site-wide: 40,018 out of 70,616
    • In immunology: 865 out of 1,820
  • Year to date:
    • Site-wide: 54,463 out of 70,616
  • Since beginning of last month:
    • Site-wide: 56,096 out of 70,616

Visualizing 'omic feature rankings and log-ratios using Qurro

bioinformatics more details view paper
  • Downloaded 246 times
  • Download rankings, all-time:
    • Site-wide: 45,431 out of 70,616
    • In bioinformatics: 5,216 out of 6,917
  • Year to date:
    • Site-wide: 1,804 out of 70,616
  • Since beginning of last month:
    • Site-wide: 810 out of 70,616

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

microbiology more details view paper
  • Downloaded 228 times
  • Download rankings, all-time:
    • Site-wide: 47,868 out of 70,616
    • In microbiology: 3,306 out of 5,733
  • Year to date:
    • Site-wide: 67,002 out of 70,616
  • Since beginning of last month:
    • Site-wide: 61,232 out of 70,616

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

systems biology more details view paper
  • Downloaded 197 times
  • Download rankings, all-time:
    • Site-wide: 52,103 out of 70,616
    • In systems biology: 1,568 out of 1,945
  • Year to date:
    • Site-wide: 28,360 out of 70,616
  • Since beginning of last month:
    • Site-wide: 10,842 out of 70,616

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

ecology more details view paper
  • Downloaded 190 times
  • Download rankings, all-time:
    • Site-wide: 53,260 out of 70,616
    • In ecology: 1,921 out of 3,035
  • Year to date:
    • Site-wide: 42,090 out of 70,616
  • Since beginning of last month:
    • Site-wide: 23,801 out of 70,616

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

microbiology more details view paper
  • Downloaded 172 times
  • Download rankings, all-time:
    • Site-wide: 55,998 out of 70,616
    • In microbiology: 4,086 out of 5,733
  • Year to date:
    • Site-wide: 23,618 out of 70,616
  • Since beginning of last month:
    • Site-wide: 7,397 out of 70,616

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

microbiology more details view paper
  • Downloaded 142 times
  • Download rankings, all-time:
    • Site-wide: 60,408 out of 70,616
    • In microbiology: 4,531 out of 5,733
  • Year to date:
    • Site-wide: 12,470 out of 70,616
  • Since beginning of last month:
    • Site-wide: 11,320 out of 70,616

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