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Author: Jason A Papin

Rankings

  • All-time downloads: 15,134 (rank: 16,225 (tie) )
  • Categories:
    • bioengineering: 391 (rank: 12,329 (tie) )
    • cell biology: 457 (rank: 27,018 (tie) )
    • microbiology: 4,249 (rank: 4,182 (tie) )
    • systems biology: 10,037 (rank: 319 )

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Preprints

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

systems biology more details view paper
  • Downloaded 2,291 times
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    • Site-wide: 8,166
    • In systems biology: 130
  • Year to date:
    • Site-wide: 40,201
  • Since beginning of last month:
    • Site-wide: 108,035

Novel Co-Culture Plate Enables Growth Dynamic-Based Assessment Of Contact-Independent Microbial Interactions

microbiology more details view paper
  • Downloaded 1,286 times
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    • Site-wide: 19,489
    • In microbiology: 1,135
  • Year to date:
    • Site-wide: 68,922
  • Since beginning of last month:
    • Site-wide: 127,570

Metabolic mechanisms of interaction within a defined gut microbiota

microbiology more details view paper
  • Downloaded 1,229 times
  • Download rankings, all-time:
    • Site-wide: 20,881
    • In microbiology: 1,217
  • Year to date:
    • Site-wide: 94,489
  • Since beginning of last month:
    • Site-wide: 135,252

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

systems biology more details view paper
  • Downloaded 988 times
  • Download rankings, all-time:
    • Site-wide: 29,035
    • In systems biology: 568
  • Year to date:
    • Site-wide: 67,562
  • Since beginning of last month:
    • Site-wide: 29,910

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

systems biology more details view paper
  • Downloaded 847 times
  • Download rankings, all-time:
    • Site-wide: 36,346
    • In systems biology: 740
  • Year to date:
    • Site-wide: 137,364
  • Since beginning of last month:
    • Site-wide: 142,201

Network analysis reveals differential metabolic functionality in antibiotic-resistant Pseudomonas aeruginosa

systems biology more details view paper
  • Downloaded 826 times
  • Download rankings, all-time:
    • Site-wide: 37,771
    • In systems biology: 773
  • Year to date:
    • Site-wide: 121,270
  • Since beginning of last month:
    • Site-wide: 117,037

Community standards to facilitate development and address challenges in metabolic modeling

systems biology more details view paper
  • Downloaded 781 times
  • Download rankings, all-time:
    • Site-wide: 40,867
    • In systems biology: 865
  • Year to date:
    • Site-wide: 126,891
  • Since beginning of last month:
    • Site-wide: 127,534

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

systems biology more details view paper
  • Downloaded 729 times
  • Download rankings, all-time:
    • Site-wide: 45,097
    • In systems biology: 956
  • Year to date:
    • Site-wide: 137,892
  • Since beginning of last month:
    • Site-wide: 131,665

Medusa: software to build and analyze ensembles of genome-scale metabolic network reconstructions

systems biology more details view paper
  • Downloaded 710 times
  • Download rankings, all-time:
    • Site-wide: 46,802
    • In systems biology: 1,001
  • Year to date:
    • Site-wide: 140,033
  • Since beginning of last month:
    • Site-wide: 148,940

Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models.

systems biology more details view paper
  • Downloaded 604 times
  • Download rankings, all-time:
    • Site-wide: 58,237
    • In systems biology: 1,263
  • Year to date:
    • Site-wide: 97,688
  • Since beginning of last month:
    • Site-wide: 90,639

History of Antibiotic Adaptation Influences Microbial Evolutionary Dynamics During Subsequent Treatment

systems biology more details view paper
  • Downloaded 538 times
  • Download rankings, all-time:
    • Site-wide: 67,137
    • In systems biology: 1,490
  • Year to date:
    • Site-wide: 151,170
  • Since beginning of last month:
    • Site-wide: 158,699

Influential parameters for the analysis of intracellular parasite metabolomics

microbiology more details view paper
  • Downloaded 533 times
  • Download rankings, all-time:
    • Site-wide: 67,895
    • In microbiology: 4,365
  • Year to date:
    • Site-wide: 140,145
  • Since beginning of last month:
    • Site-wide: 126,752

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

systems biology more details view paper
  • Downloaded 474 times
  • Download rankings, all-time:
    • Site-wide: 77,589
    • In systems biology: 1,740
  • Year to date:
    • Site-wide: 94,849
  • Since beginning of last month:
    • Site-wide: 84,704

Growth-Altering Microbial Interactions Are Highly Sensitive to Environmental Context

microbiology more details view paper
  • Downloaded 465 times
  • Download rankings, all-time:
    • Site-wide: 79,144
    • In microbiology: 5,235
  • Year to date:
    • Site-wide: 156,560
  • Since beginning of last month:
    • Site-wide: 153,055

Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms

cell biology more details view paper
  • Downloaded 457 times
  • Download rankings, all-time:
    • Site-wide: 80,587
    • In cell biology: 3,675
  • Year to date:
    • Site-wide: 46,957
  • Since beginning of last month:
    • Site-wide: 56,516

Managing Uncertainty in Metabolic Network Structure and Improving Predictions Using EnsembleFBA

systems biology more details view paper
  • Downloaded 428 times
  • Download rankings, all-time:
    • Site-wide: 86,370
    • In systems biology: 1,915
  • Year to date:
    • Site-wide: 156,016
  • Since beginning of last month:
    • Site-wide: 144,579

Functional Anabolic Network Analysis of Human-associated Lactobacillus Strains

systems biology more details view paper
  • Downloaded 369 times
  • Download rankings, all-time:
    • Site-wide: 99,146
    • In systems biology: 2,184
  • Year to date:
    • Site-wide: 124,204
  • Since beginning of last month:
    • Site-wide: 121,025

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies

microbiology more details view paper
  • Downloaded 349 times
  • Download rankings, all-time:
    • Site-wide: 104,132
    • In microbiology: 7,255
  • Year to date:
    • Site-wide: 155,253
  • Since beginning of last month:
    • Site-wide: 151,726

Identifying functional metabolic shifts in heart failure with the integration of omics data and a cardiomyocyte-specific, genome-scale model

bioengineering more details view paper
  • Downloaded 328 times
  • Download rankings, all-time:
    • Site-wide: 109,170
    • In bioengineering: 2,149
  • Year to date:
    • Site-wide: 68,522
  • Since beginning of last month:
    • Site-wide: 94,366

Reconciling high-throughput gene essentiality data with metabolic network reconstructions

systems biology more details view paper
  • Downloaded 319 times
  • Download rankings, all-time:
    • Site-wide: 111,620
    • In systems biology: 2,415
  • Year to date:
    • Site-wide: 140,342
  • Since beginning of last month:
    • Site-wide: 60,745

Megasphaera in the stool microbiota is negatively associated with diarrheal cryptosporidiosis

microbiology more details view paper
  • Downloaded 239 times
  • Download rankings, all-time:
    • Site-wide: 132,611
    • In microbiology: 9,715
  • Year to date:
    • Site-wide: 80,345
  • Since beginning of last month:
    • Site-wide: 104,621

Genome-scale metabolic modeling reveals increased reliance on valine catabolism in clinical isolates of Klebsiella pneumoniae

microbiology more details view paper
  • Downloaded 148 times
  • Download rankings, all-time:
    • Site-wide: 153,237
    • In microbiology: 11,642
  • Year to date:
    • Site-wide: 81,218
  • Since beginning of last month:
    • Site-wide: 58,648

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

systems biology more details view paper
  • Downloaded 133 times
  • Download rankings, all-time:
    • Site-wide: 155,778
    • In systems biology: 3,207
  • Year to date:
    • Site-wide: 90,204
  • Since beginning of last month:
    • Site-wide: 154,843

Identifying metabolic adaptations during cardiotoxicity using paired transcriptomics andmetabolomics data integrated with a model of heart metabolism

bioengineering more details view paper
  • Downloaded 63 times
  • Download rankings, all-time:
    • Site-wide: 163,359
    • In bioengineering: 3,444
  • Year to date:
    • Site-wide: 145,974
  • Since beginning of last month:
    • Site-wide: 37,819

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