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Author: Adam P Arkin

Rankings

  • All-time downloads: 38,616 (rank: 3,940 )
  • Categories:
    • bioengineering: 1,369 (rank: 2,261 )
    • bioinformatics: 4,430 (rank: 2,777 (tie) )
    • clinical trials: 2,432 (rank: 128 (tie) )
    • ecology: 638 (rank: 6,716 (tie) )
    • evolutionary biology: 773 (rank: 9,017 (tie) )
    • genetics: 1,064 (rank: 14,931 (tie) )
    • genomics: 1,214 (rank: 19,003 (tie) )
    • microbiology: 13,227 (rank: 1,062 )
    • synthetic biology: 8,133 (rank: 69 )
    • systems biology: 5,336 (rank: 630 )

Downloads per author, site-wide

Preprints

High-throughput mapping of the phage resistance landscape in E. coli

microbiology more details view paper
  • Downloaded 2,660 times
  • Download rankings, all-time:
    • Site-wide: 5,058
    • In microbiology: 311
  • Year to date:
    • Site-wide: 8,260
  • Since beginning of last month:
    • Site-wide: 8,831

Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides

synthetic biology more details view paper
  • Downloaded 2,562 times
  • Download rankings, all-time:
    • Site-wide: 5,332
    • In synthetic biology: 58
  • Year to date:
    • Site-wide: 98,755
  • Since beginning of last month:
    • Site-wide: 69,249

Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

microbiology more details view paper
  • Downloaded 2,490 times
  • Download rankings, all-time:
    • Site-wide: 5,602
    • In microbiology: 330
  • Year to date:
    • Site-wide: 30,447
  • Since beginning of last month:
    • Site-wide: 18,311

An interventional Soylent diet increases the Bacteroidetes to Firmicutes ratio in human gut microbiome communities: a randomized controlled trial

clinical trials more details view paper
  • Downloaded 2,432 times
  • Download rankings, all-time:
    • Site-wide: 5,801
    • In clinical trials: 10
  • Year to date:
    • Site-wide: 36,236
  • Since beginning of last month:
    • Site-wide: 38,166

Selection of chromosomal DNA libraries using a multiplex CRISPR system in Saccharomyces cerevisiae

synthetic biology more details view paper
  • Downloaded 2,371 times
  • Download rankings, all-time:
    • Site-wide: 6,029
    • In synthetic biology: 64
  • Year to date:
    • Site-wide: 76,219
  • Since beginning of last month:
    • Site-wide: 117,958

The DOE Systems Biology Knowledgebase (KBase)

bioinformatics more details view paper
  • Downloaded 1,703 times
  • Download rankings, all-time:
    • Site-wide: 9,829
    • In bioinformatics: 1,177
  • Year to date:
    • Site-wide: 56,858
  • Since beginning of last month:
    • Site-wide: 67,819

Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron

microbiology more details view paper
  • Downloaded 1,639 times
  • Download rankings, all-time:
    • Site-wide: 10,366
    • In microbiology: 588
  • Year to date:
    • Site-wide: 15,811
  • Since beginning of last month:
    • Site-wide: 19,284

A Comparison of the Costs and Benefits of Bacterial Gene Expression

systems biology more details view paper
  • Downloaded 1,562 times
  • Download rankings, all-time:
    • Site-wide: 11,132
    • In systems biology: 209
  • Year to date:
    • Site-wide: 107,325
  • Since beginning of last month:
    • Site-wide: 84,985

Deciphering microbial interactions in synthetic human gut microbiome communities

systems biology more details view paper
  • Downloaded 1,329 times
  • Download rankings, all-time:
    • Site-wide: 14,196
    • In systems biology: 275
  • Year to date:
    • Site-wide: 94,255
  • Since beginning of last month:
    • Site-wide: 134,964

A method for achieving complete microbial genomes and improving bins from metagenomics data

bioinformatics more details view paper
  • Downloaded 1,236 times
  • Download rankings, all-time:
    • Site-wide: 15,838
    • In bioinformatics: 1,900
  • Year to date:
    • Site-wide: 14,994
  • Since beginning of last month:
    • Site-wide: 15,860

The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella

microbiology more details view paper
  • Downloaded 1,155 times
  • Download rankings, all-time:
    • Site-wide: 17,501
    • In microbiology: 997
  • Year to date:
    • Site-wide: 7,051
  • Since beginning of last month:
    • Site-wide: 10,192

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

systems biology more details view paper
  • Downloaded 1,142 times
  • Download rankings, all-time:
    • Site-wide: 17,767
    • In systems biology: 357
  • Year to date:
    • Site-wide: 61,331
  • Since beginning of last month:
    • Site-wide: 53,121

The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

genetics more details view paper
  • Downloaded 1,064 times
  • Download rankings, all-time:
    • Site-wide: 19,733
    • In genetics: 941
  • Year to date:
    • Site-wide: 87,641
  • Since beginning of last month:
    • Site-wide: None

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

microbiology more details view paper
  • Downloaded 915 times
  • Download rankings, all-time:
    • Site-wide: 24,665
    • In microbiology: 1,427
  • Year to date:
    • Site-wide: 82,106
  • Since beginning of last month:
    • Site-wide: 88,653

Genetic dissection of an ancient divergence in yeast thermotolerance

evolutionary biology more details view paper
  • Downloaded 773 times
  • Download rankings, all-time:
    • Site-wide: 31,202
    • In evolutionary biology: 1,499
  • Year to date:
    • Site-wide: 125,168
  • Since beginning of last month:
    • Site-wide: 117,398

A versatile platform strain for high-fidelity multiplex genome editing

synthetic biology more details view paper
  • Downloaded 737 times
  • Download rankings, all-time:
    • Site-wide: 33,319
    • In synthetic biology: 423
  • Year to date:
    • Site-wide: 114,733
  • Since beginning of last month:
    • Site-wide: 87,144

Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits

microbiology more details view paper
  • Downloaded 723 times
  • Download rankings, all-time:
    • Site-wide: 34,127
    • In microbiology: 2,036
  • Year to date:
    • Site-wide: 105,590
  • Since beginning of last month:
    • Site-wide: 115,243

Programming mRNA decay to modulate synthetic circuit resource allocation

synthetic biology more details view paper
  • Downloaded 711 times
  • Download rankings, all-time:
    • Site-wide: 34,941
    • In synthetic biology: 444
  • Year to date:
    • Site-wide: 128,285
  • Since beginning of last month:
    • Site-wide: 135,051

Massive Factorial Design Untangles Coding Sequences Determinants Of Translation Efficacy

synthetic biology more details view paper
  • Downloaded 695 times
  • Download rankings, all-time:
    • Site-wide: 36,087
    • In synthetic biology: 462
  • Year to date:
    • Site-wide: 96,686
  • Since beginning of last month:
    • Site-wide: 74,215

The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes

systems biology more details view paper
  • Downloaded 690 times
  • Download rankings, all-time:
    • Site-wide: 36,417
    • In systems biology: 815
  • Year to date:
    • Site-wide: 37,317
  • Since beginning of last month:
    • Site-wide: 43,573

Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi

microbiology more details view paper
  • Downloaded 653 times
  • Download rankings, all-time:
    • Site-wide: 39,134
    • In microbiology: 2,341
  • Year to date:
    • Site-wide: 31,188
  • Since beginning of last month:
    • Site-wide: 29,827

Magic pools: parallel assessment of transposon delivery vectors in bacteria

genomics more details view paper
  • Downloaded 641 times
  • Download rankings, all-time:
    • Site-wide: 40,116
    • In genomics: 3,330
  • Year to date:
    • Site-wide: 105,645
  • Since beginning of last month:
    • Site-wide: 65,917

A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming

ecology more details view paper
  • Downloaded 638 times
  • Download rankings, all-time:
    • Site-wide: 40,339
    • In ecology: 962
  • Year to date:
    • Site-wide: 77,093
  • Since beginning of last month:
    • Site-wide: 57,411

Rhodosporidium toruloides: A new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

bioengineering more details view paper
  • Downloaded 596 times
  • Download rankings, all-time:
    • Site-wide: 43,973
    • In bioengineering: 798
  • Year to date:
    • Site-wide: 96,666
  • Since beginning of last month:
    • Site-wide: 87,739

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species dependent essential genes

genomics more details view paper
  • Downloaded 573 times
  • Download rankings, all-time:
    • Site-wide: 46,156
    • In genomics: 3,672
  • Year to date:
    • Site-wide: 100,489
  • Since beginning of last month:
    • Site-wide: 97,641

PaperBLAST: Text-mining papers for information about homologs

bioinformatics more details view paper
  • Downloaded 548 times
  • Download rankings, all-time:
    • Site-wide: 48,818
    • In bioinformatics: 5,062
  • Year to date:
    • Site-wide: 118,826
  • Since beginning of last month:
    • Site-wide: 112,172

QTL-guided metabolic engineering of a complex trait

bioengineering more details view paper
  • Downloaded 547 times
  • Download rankings, all-time:
    • Site-wide: 48,856
    • In bioengineering: 902
  • Year to date:
    • Site-wide: 94,488
  • Since beginning of last month:
    • Site-wide: 112,219

Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins

microbiology more details view paper
  • Downloaded 537 times
  • Download rankings, all-time:
    • Site-wide: 49,965
    • In microbiology: 3,138
  • Year to date:
    • Site-wide: 35,492
  • Since beginning of last month:
    • Site-wide: 81,256

GapMind: Automated annotation of amino acid biosynthesis

bioinformatics more details view paper
  • Downloaded 534 times
  • Download rankings, all-time:
    • Site-wide: 50,198
    • In bioinformatics: 5,181
  • Year to date:
    • Site-wide: 43,859
  • Since beginning of last month:
    • Site-wide: 37,785

Massive Phenotypic Measurements Reveal Complex Physiological Consequences Of Differential Translation Efficacies

synthetic biology more details view paper
  • Downloaded 532 times
  • Download rankings, all-time:
    • Site-wide: 50,461
    • In synthetic biology: 615
  • Year to date:
    • Site-wide: 137,652
  • Since beginning of last month:
    • Site-wide: 135,071

Kluyveromyces marxianus as a robust synthetic biology platform host

synthetic biology more details view paper
  • Downloaded 525 times
  • Download rankings, all-time:
    • Site-wide: 51,258
    • In synthetic biology: 627
  • Year to date:
    • Site-wide: 126,575
  • Since beginning of last month:
    • Site-wide: 117,926

Oxidative pathways of deoxyribose and deoxyribonate catabolism

microbiology more details view paper
  • Downloaded 504 times
  • Download rankings, all-time:
    • Site-wide: 53,799
    • In microbiology: 3,426
  • Year to date:
    • Site-wide: 93,384
  • Since beginning of last month:
    • Site-wide: 85,756

Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics

microbiology more details view paper
  • Downloaded 431 times
  • Download rankings, all-time:
    • Site-wide: 63,647
    • In microbiology: 4,203
  • Year to date:
    • Site-wide: 133,480
  • Since beginning of last month:
    • Site-wide: 133,906

Curated BLAST for Genomes

bioinformatics more details view paper
  • Downloaded 409 times
  • Download rankings, all-time:
    • Site-wide: 67,026
    • In bioinformatics: 6,476
  • Year to date:
    • Site-wide: 103,444
  • Since beginning of last month:
    • Site-wide: 76,805

Genome-wide and enzymatic analysis reveals efficient D-galacturonic acid metabolism in the basidiomycete yeast Rhodosporidium toruloides

systems biology more details view paper
  • Downloaded 376 times
  • Download rankings, all-time:
    • Site-wide: 72,615
    • In systems biology: 1,731
  • Year to date:
    • Site-wide: 121,327
  • Since beginning of last month:
    • Site-wide: 120,419

Selective carbon sources influence the end-products of microbial nitrate respiration

microbiology more details view paper
  • Downloaded 353 times
  • Download rankings, all-time:
    • Site-wide: 76,812
    • In microbiology: 5,252
  • Year to date:
    • Site-wide: 95,952
  • Since beginning of last month:
    • Site-wide: 123,040

Defining the toxicity limits on microbial range in a metal-contaminated aquifer

microbiology more details view paper
  • Downloaded 269 times
  • Download rankings, all-time:
    • Site-wide: 94,334
    • In microbiology: 6,769
  • Year to date:
    • Site-wide: 110,972
  • Since beginning of last month:
    • Site-wide: 127,359

Four Families of Folate-independent Methionine Synthases

microbiology more details view paper
  • Downloaded 263 times
  • Download rankings, all-time:
    • Site-wide: 95,568
    • In microbiology: 6,885
  • Year to date:
    • Site-wide: 56,679
  • Since beginning of last month:
    • Site-wide: 77,972

Integrated characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

systems biology more details view paper
  • Downloaded 237 times
  • Download rankings, all-time:
    • Site-wide: 101,361
    • In systems biology: 2,336
  • Year to date:
    • Site-wide: 113,352
  • Since beginning of last month:
    • Site-wide: 98,680

Systems-informed genome mining for electroautotrophic microbial production

bioengineering more details view paper
  • Downloaded 226 times
  • Download rankings, all-time:
    • Site-wide: 103,964
    • In bioengineering: 2,007
  • Year to date:
    • Site-wide: 23,830
  • Since beginning of last month:
    • Site-wide: 48,282

Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

microbiology more details view paper
  • Downloaded 206 times
  • Download rankings, all-time:
    • Site-wide: 108,451
    • In microbiology: 7,994
  • Year to date:
    • Site-wide: 81,415
  • Since beginning of last month:
    • Site-wide: 102,514

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations.

microbiology more details view paper
  • Downloaded 167 times
  • Download rankings, all-time:
    • Site-wide: 117,102
    • In microbiology: 8,804
  • Year to date:
    • Site-wide: 132,911
  • Since beginning of last month:
    • Site-wide: 131,975

Large-scale Genetic Characterization of a Model Sulfate Reducing Bacterium

microbiology more details view paper
  • Downloaded 153 times
  • Download rankings, all-time:
    • Site-wide: 120,092
    • In microbiology: 9,061
  • Year to date:
    • Site-wide: 20,460
  • Since beginning of last month:
    • Site-wide: 65,245

A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis

microbiology more details view paper
  • Downloaded 109 times
  • Download rankings, all-time:
    • Site-wide: 128,877
    • In microbiology: 9,857
  • Year to date:
    • Site-wide: 30,124
  • Since beginning of last month:
    • Site-wide: 23,044

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