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Author: Nicola De Maio

Rankings

  • All-time downloads: 26,290 (rank: 7,304 )
  • Categories:
    • bioinformatics: 12,324 (rank: 623 )
    • epidemiology: 1,869 (rank: 6,716 (tie) )
    • evolutionary biology: 7,323 (rank: 354 )
    • genetics: 432 (rank: 29,584 (tie) )
    • genomics: 2,344 (rank: 11,019 )
    • microbiology: 1,317 (rank: 12,431 (tie) )
    • pharmacology and toxicology: 386 (rank: 4,092 (tie) )
    • plant biology: 295 (rank: 15,089 (tie) )

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Preprints

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

bioinformatics more details view paper
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    • Site-wide: 1,166
    • In bioinformatics: 66
  • Year to date:
    • Site-wide: 23,219
  • Since beginning of last month:
    • Site-wide: 3,275

A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

evolutionary biology more details view paper
  • Downloaded 2,484 times
  • Download rankings, all-time:
    • Site-wide: 6,373
    • In evolutionary biology: 140
  • Year to date:
    • Site-wide: 13,845
  • Since beginning of last month:
    • Site-wide: 34,236

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,240 times
  • Download rankings, all-time:
    • Site-wide: 7,417
    • In bioinformatics: 848
  • Year to date:
    • Site-wide: 23,978
  • Since beginning of last month:
    • Site-wide: 32,053

Genomic reconstruction of the SARS-CoV-2 epidemic in England

epidemiology more details view paper
  • Downloaded 1,605 times
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    • Site-wide: 12,101
    • In epidemiology: 867
  • Year to date:
    • Site-wide: 1,637
  • Since beginning of last month:
    • Site-wide: 7,752

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,369 times
  • Download rankings, all-time:
    • Site-wide: 15,355
    • In evolutionary biology: 525
  • Year to date:
    • Site-wide: 52,700
  • Since beginning of last month:
    • Site-wide: 88,495

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

microbiology more details view paper
  • Downloaded 1,317 times
  • Download rankings, all-time:
    • Site-wide: 16,301
    • In microbiology: 956
  • Year to date:
    • Site-wide: 68,339
  • Since beginning of last month:
    • Site-wide: None

BOSS-RUNS: a flexible and practical dynamic read sampling framework for nanopore sequencing

genomics more details view paper
  • Downloaded 1,290 times
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    • Site-wide: 16,824
    • In genomics: 1,656
  • Year to date:
    • Site-wide: 20,675
  • Since beginning of last month:
    • Site-wide: 39,193

Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic

genomics more details view paper
  • Downloaded 1,054 times
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    • Site-wide: 22,623
    • In genomics: 2,144
  • Year to date:
    • Site-wide: 6,447
  • Since beginning of last month:
    • Site-wide: None

PoMo: An Allele Frequency-based Approach for Species Tree Estimation

evolutionary biology more details view paper
  • Downloaded 1,023 times
  • Download rankings, all-time:
    • Site-wide: 23,623
    • In evolutionary biology: 984
  • Year to date:
    • Site-wide: 59,654
  • Since beginning of last month:
    • Site-wide: 4,955

Mutation rates and selection on synonymous mutations in SARS-CoV-2

evolutionary biology more details view paper
  • Downloaded 908 times
  • Download rankings, all-time:
    • Site-wide: 28,072
    • In evolutionary biology: 1,205
  • Year to date:
    • Site-wide: 3,577
  • Since beginning of last month:
    • Site-wide: 54,673

Sampling bias and model choice in continuous phylogeography: getting lost on a random walk

evolutionary biology more details view paper
  • Downloaded 518 times
  • Download rankings, all-time:
    • Site-wide: 58,709
    • In evolutionary biology: 3,031
  • Year to date:
    • Site-wide: 89,344
  • Since beginning of last month:
    • Site-wide: 79,575

Reversible Polymorphism-Aware Phylogenetic Models and their Application to Tree Inference

bioinformatics more details view paper
  • Downloaded 490 times
  • Download rankings, all-time:
    • Site-wide: 62,559
    • In bioinformatics: 6,170
  • Year to date:
    • Site-wide: 149,006
  • Since beginning of last month:
    • Site-wide: 82,564

Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes.

evolutionary biology more details view paper
  • Downloaded 477 times
  • Download rankings, all-time:
    • Site-wide: 64,285
    • In evolutionary biology: 3,355
  • Year to date:
    • Site-wide: 119,182
  • Since beginning of last month:
    • Site-wide: None

The Bacterial Sequential Markov Coalescent

evolutionary biology more details view paper
  • Downloaded 436 times
  • Download rankings, all-time:
    • Site-wide: 70,869
    • In evolutionary biology: 3,702
  • Year to date:
    • Site-wide: 145,471
  • Since beginning of last month:
    • Site-wide: None

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

genetics more details view paper
  • Downloaded 432 times
  • Download rankings, all-time:
    • Site-wide: 71,485
    • In genetics: 3,150
  • Year to date:
    • Site-wide: 144,089
  • Since beginning of last month:
    • Site-wide: None

The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs

pharmacology and toxicology more details view paper
  • Downloaded 386 times
  • Download rankings, all-time:
    • Site-wide: 79,680
    • In pharmacology and toxicology: 520
  • Year to date:
    • Site-wide: 12,442
  • Since beginning of last month:
    • Site-wide: 111,982

A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees

bioinformatics more details view paper
  • Downloaded 335 times
  • Download rankings, all-time:
    • Site-wide: 89,994
    • In bioinformatics: 8,042
  • Year to date:
    • Site-wide: 15,236
  • Since beginning of last month:
    • Site-wide: 1,890

Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences

bioinformatics more details view paper
  • Downloaded 315 times
  • Download rankings, all-time:
    • Site-wide: 94,329
    • In bioinformatics: 8,307
  • Year to date:
    • Site-wide: 60,818
  • Since beginning of last month:
    • Site-wide: 100,560

Repeated global migrations on different plant hosts by the tropical pathogen Phytophthora palmivora

plant biology more details view paper
  • Downloaded 295 times
  • Download rankings, all-time:
    • Site-wide: 98,802
    • In plant biology: 2,623
  • Year to date:
    • Site-wide: 64,838
  • Since beginning of last month:
    • Site-wide: None

phastSim: efficient simulation of sequence evolution for pandemic-scale datasets

bioinformatics more details view paper
  • Downloaded 268 times
  • Download rankings, all-time:
    • Site-wide: 105,102
    • In bioinformatics: 8,984
  • Year to date:
    • Site-wide: 20,746
  • Since beginning of last month:
    • Site-wide: 28,081

VGsim: scalable viral genealogy simulator for global pandemic

epidemiology more details view paper
  • Downloaded 264 times
  • Download rankings, all-time:
    • Site-wide: 106,149
    • In epidemiology: 4,422
  • Year to date:
    • Site-wide: 21,210
  • Since beginning of last month:
    • Site-wide: 46,631

Short-range template switching in great ape genomes explored using a pair hidden Markov model

bioinformatics more details view paper
  • Downloaded 181 times
  • Download rankings, all-time:
    • Site-wide: 126,726
    • In bioinformatics: 10,199
  • Year to date:
    • Site-wide: 92,191
  • Since beginning of last month:
    • Site-wide: 108,002

Global spread and evolutionary history of HCV subtype 3a

evolutionary biology more details view paper
  • Downloaded 100 times
  • Download rankings, all-time:
    • Site-wide: 143,882
    • In evolutionary biology: 6,968
  • Year to date:
    • Site-wide: 63,456
  • Since beginning of last month:
    • Site-wide: 112,966

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

evolutionary biology more details view paper
  • Downloaded 8 times
  • Download rankings, all-time:
    • Site-wide: 152,734
    • In evolutionary biology: 7,272
  • Year to date:
    • Site-wide: 152,567
  • Since beginning of last month:
    • Site-wide: 12,786

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