Author: Aaron E. Darling

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Preprints

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

• Downloaded 6,952 times
• Download rankings, all-time:
  • Site-wide: 1,123
  • In bioinformatics: 77
• Year to date:
  • Site-wide: 25,682
• Since beginning of last month:
  • Site-wide: 22,404

Hackflex: low cost Illumina sequencing library construction for high sample counts

• Downloaded 4,062 times
• Download rankings, all-time:
  • Site-wide: 2,331
  • In genomics: 280
• Year to date:
  • Site-wide: 1,999
• Since beginning of last month:
  • Site-wide: 3,590

Alignathon: A competitive assessment of whole genome alignment methods.

• Downloaded 3,295 times
• Download rankings, all-time:
  • Site-wide: 3,177
  • In bioinformatics: 346
• Year to date:
  • Site-wide: 26,587
• Since beginning of last month:
  • Site-wide: 76,032

CAMISIM: Simulating metagenomes and microbial communities

• Downloaded 1,741 times
• Download rankings, all-time:
  • Site-wide: 8,035
  • In bioinformatics: 1,014
• Year to date:
  • Site-wide: 22,272
• Since beginning of last month:
  • Site-wide: 69,675

bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)

• Downloaded 801 times
• Download rankings, all-time:
  • Site-wide: 25,486
  • In bioinformatics: 3,060
• Year to date:
  • Site-wide: 91,048
• Since beginning of last month:
  • Site-wide: 53,453

Effective Online Bayesian Phylogenetics Via Sequential Monte Carlo With Guided Proposals

• Downloaded 798 times
• Download rankings, all-time:
  • Site-wide: 25,627
  • In bioinformatics: 3,069
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 120,093

Metagenomics Strain Resolution on Assembly Graphs

• Downloaded 763 times
• Download rankings, all-time:
  • Site-wide: 27,279
  • In bioinformatics: 3,235
• Year to date:
  • Site-wide: 12,393
• Since beginning of last month:
  • Site-wide: 9,000

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

• Downloaded 758 times
• Download rankings, all-time:
  • Site-wide: 27,528
  • In bioinformatics: 3,256
• Year to date:
  • Site-wide: 103,604
• Since beginning of last month:
  • Site-wide: 56,397

Sim3C: Simulation Of HiC And Meta3C Proximity Ligation Sequencing Technologies

• Downloaded 662 times
• Download rankings, all-time:
  • Site-wide: 33,139
  • In bioinformatics: 3,783
• Year to date:
  • Site-wide: 85,888
• Since beginning of last month:
  • Site-wide: 74,860

A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan

• Downloaded 622 times
• Download rankings, all-time:
  • Site-wide: 35,933
  • In microbiology: 2,160
• Year to date:
  • Site-wide: 45,175
• Since beginning of last month:
  • Site-wide: 40,750

The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America

• Downloaded 562 times
• Download rankings, all-time:
  • Site-wide: 40,865
  • In evolutionary biology: 2,232
• Year to date:
  • Site-wide: 117,858
• Since beginning of last month:
  • Site-wide: 102,843

Porcine commensal Escherichia coli: A reservoir for class 1 integrons associated with IS26

• Downloaded 506 times
• Download rankings, all-time:
  • Site-wide: 46,375
  • In genomics: 3,753
• Year to date:
  • Site-wide: 53,018
• Since beginning of last month:
  • Site-wide: 103,667

Evaluation of ddRADseq for reduced representation metagenome sequencing

• Downloaded 414 times
• Download rankings, all-time:
  • Site-wide: 57,732
  • In genomics: 4,341
• Year to date:
  • Site-wide: 107,671
• Since beginning of last month:
  • Site-wide: 116,520

Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit

• Downloaded 403 times
• Download rankings, all-time:
  • Site-wide: 59,263
  • In bioinformatics: 5,968
• Year to date:
  • Site-wide: 8,814
• Since beginning of last month:
  • Site-wide: 11,816

Genomes from Bacteria Associated with the Canine Oral Cavity: a Test Case for Automated Genome-Based Taxonomic Assignment

• Downloaded 360 times
• Download rankings, all-time:
  • Site-wide: 65,979
  • In bioinformatics: 6,448
• Year to date:
  • Site-wide: 80,028
• Since beginning of last month:
  • Site-wide: 58,105

Post-weaning shifts in microbiome composition and metabolism revealed by over 25,000 pig gut metagenome assembled genomes

• Downloaded 340 times
• Download rankings, all-time:
  • Site-wide: 69,402
  • In microbiology: 4,790
• Year to date:
  • Site-wide: 9,631
• Since beginning of last month:
  • Site-wide: 34,265

Trial by phylogenetics - Evaluating the Multi-Species Coalescent for evolutionary inference on taxa with high levels of paralogy (Gonyaulacales, Dinophyceae).

• Downloaded 273 times
• Download rankings, all-time:
  • Site-wide: 81,942
  • In evolutionary biology: 4,571
• Year to date:
  • Site-wide: 57,410
• Since beginning of last month:
  • Site-wide: 118,697

Community composition and development of the post-weaning piglet gut microbiome

• Downloaded 186 times
• Download rankings, all-time:
  • Site-wide: 100,323
  • In microbiology: 7,523
• Year to date:
  • Site-wide: 57,740
• Since beginning of last month:
  • Site-wide: 67,270