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Author: Nicola De Maio

Rankings

  • All-time downloads: 29,238 (rank: 7,230 (tie) )
  • Categories:
    • bioinformatics: 13,008 (rank: 660 )
    • epidemiology: 2,605 (rank: 5,786 )
    • evolutionary biology: 8,329 (rank: 334 )
    • genetics: 447 (rank: 31,991 (tie) )
    • genomics: 2,661 (rank: 10,357 (tie) )
    • microbiology: 1,342 (rank: 13,998 (tie) )
    • pharmacology and toxicology: 481 (rank: 4,070 (tie) )
    • plant biology: 365 (rank: 15,588 (tie) )

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Preprints

Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches

bioinformatics more details view paper

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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: 1,306
    • In bioinformatics: 69
  • Year to date:
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    • Site-wide: 19,077

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 2,559 times
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    • Site-wide: 6,935
    • In evolutionary biology: 148
  • Year to date:
    • Site-wide: 19,962
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    • Site-wide: 108,129

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

bioinformatics more details view paper
  • Downloaded 2,338 times
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    • Site-wide: 7,929
    • In bioinformatics: 867
  • Year to date:
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Genomic reconstruction of the SARS-CoV-2 epidemic in England

epidemiology more details view paper
  • Downloaded 2,256 times
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    • Site-wide: 8,359
    • In epidemiology: 683
  • Year to date:
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BOSS-RUNS: a flexible and practical dynamic read sampling framework for nanopore sequencing

genomics more details view paper
  • Downloaded 1,471 times
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    • Site-wide: 15,941
    • In genomics: 1,549
  • Year to date:
    • Site-wide: 18,875
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    • Site-wide: 16,742

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,415 times
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    • Site-wide: 16,911
    • In evolutionary biology: 554
  • Year to date:
    • Site-wide: 71,193
  • Since beginning of last month:
    • Site-wide: 133,992

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

microbiology more details view paper
  • Downloaded 1,342 times
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    • Site-wide: 18,307
    • In microbiology: 1,061
  • Year to date:
    • Site-wide: 101,068
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    • Site-wide: 155,088

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

genomics more details view paper
  • Downloaded 1,190 times
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    • Site-wide: 21,946
    • In genomics: 2,042
  • Year to date:
    • Site-wide: 8,636
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    • Site-wide: 65,924

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

evolutionary biology more details view paper
  • Downloaded 1,062 times
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    • Site-wide: 26,151
    • In evolutionary biology: 1,041
  • Year to date:
    • Site-wide: 4,924
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    • Site-wide: 24,382

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

evolutionary biology more details view paper
  • Downloaded 1,046 times
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    • Site-wide: 26,740
    • In evolutionary biology: 1,079
  • Year to date:
    • Site-wide: 91,945
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    • Site-wide: 145,905

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

evolutionary biology more details view paper
  • Downloaded 555 times
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    • Site-wide: 64,704
    • In evolutionary biology: 3,189
  • Year to date:
    • Site-wide: 13,572
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    • Site-wide: 6,233

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

evolutionary biology more details view paper
  • Downloaded 537 times
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    • Site-wide: 67,295
    • In evolutionary biology: 3,336
  • Year to date:
    • Site-wide: 127,832
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    • Site-wide: 155,503

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

bioinformatics more details view paper
  • Downloaded 530 times
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    • Site-wide: 68,328
    • In bioinformatics: 6,504
  • Year to date:
    • Site-wide: 149,588
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    • Site-wide: 113,481

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

evolutionary biology more details view paper
  • Downloaded 526 times
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    • Site-wide: 68,946
    • In evolutionary biology: 3,427
  • Year to date:
    • Site-wide: 123,124
  • Since beginning of last month:
    • Site-wide: 112,376

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 481 times
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    • Site-wide: 76,385
    • In pharmacology and toxicology: 499
  • Year to date:
    • Site-wide: 16,922
  • Since beginning of last month:
    • Site-wide: 62,933

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

bioinformatics more details view paper
  • Downloaded 453 times
  • Download rankings, all-time:
    • Site-wide: 81,614
    • In bioinformatics: 7,377
  • Year to date:
    • Site-wide: 18,585
  • Since beginning of last month:
    • Site-wide: 32,768

The Bacterial Sequential Markov Coalescent

evolutionary biology more details view paper
  • Downloaded 450 times
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    • Site-wide: 82,077
    • In evolutionary biology: 4,131
  • Year to date:
    • Site-wide: 162,382
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    • Site-wide: 160,127

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

genetics more details view paper
  • Downloaded 447 times
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    • Site-wide: 82,594
    • In genetics: 3,479
  • Year to date:
    • Site-wide: 161,504
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    • Site-wide: 160,768

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

bioinformatics more details view paper
  • Downloaded 445 times
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    • Site-wide: 83,038
    • In bioinformatics: 7,483
  • Year to date:
    • Site-wide: 19,110
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    • Site-wide: 35,221

Phylogenetic Novelty Scores: a New Approach for Weighting Genetic Sequences

bioinformatics more details view paper
  • Downloaded 368 times
  • Download rankings, all-time:
    • Site-wide: 99,490
    • In bioinformatics: 8,558
  • Year to date:
    • Site-wide: 75,842
  • Since beginning of last month:
    • Site-wide: 95,308

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

plant biology more details view paper
  • Downloaded 365 times
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    • Site-wide: 100,349
    • In plant biology: 2,667
  • Year to date:
    • Site-wide: 70,941
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    • Site-wide: 80,295

VGsim: scalable viral genealogy simulator for global pandemic

epidemiology more details view paper
  • Downloaded 349 times
  • Download rankings, all-time:
    • Site-wide: 104,155
    • In epidemiology: 4,432
  • Year to date:
    • Site-wide: 27,596
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    • Site-wide: 85,563

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

bioinformatics more details view paper
  • Downloaded 235 times
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    • Site-wide: 133,558
    • In bioinformatics: 10,536
  • Year to date:
    • Site-wide: 100,761
  • Since beginning of last month:
    • Site-wide: 93,790

Global spread and evolutionary history of HCV subtype 3a

evolutionary biology more details view paper
  • Downloaded 179 times
  • Download rankings, all-time:
    • Site-wide: 147,121
    • In evolutionary biology: 7,015
  • Year to date:
    • Site-wide: 66,139
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    • Site-wide: 49,391

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