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Author: Todd J Treangen

Rankings

  • All-time downloads: 91,854 (rank: 1,756 )
  • Categories:
    • bioinformatics: 33,644 (rank: 94 )
    • genetics: 481 (rank: 28,871 (tie) )
    • genomics: 50,952 (rank: 196 )
    • infectious diseases: 3,222 (rank: 13,634 (tie) )
    • microbiology: 1,218 (rank: 14,397 (tie) )
    • neurology: 179 (rank: 6,844 (tie) )
    • systems biology: 2,158 (rank: 2,115 (tie) )

Downloads per author, site-wide

Preprints

Bakdrive: Identifying the Minimum Set of Bacterial Driver Species across Multiple Microbial Communities

bioinformatics more details view paper

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Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

genomics more details view paper
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    • Site-wide: 702
    • In genomics: 40
  • Year to date:
    • Site-wide: 5,194
  • Since beginning of last month:
    • Site-wide: 7,092

Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

bioinformatics more details view paper
  • Downloaded 11,987 times
  • Download rankings, all-time:
    • Site-wide: 820
    • In bioinformatics: 32
  • Year to date:
    • Site-wide: 19,595
  • Since beginning of last month:
    • Site-wide: 20,509

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

bioinformatics more details view paper
  • Downloaded 6,944 times
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    • Site-wide: 1,620
    • In bioinformatics: 93
  • Year to date:
    • Site-wide: 24,645
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    • Site-wide: 25,295

Complete assembly of parental haplotypes with trio binning

genomics more details view paper
  • Downloaded 6,441 times
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    • Site-wide: 1,808
    • In genomics: 145
  • Year to date:
    • Site-wide: 19,325
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    • Site-wide: 15,152

A robust benchmark for germline structural variant detection

genomics more details view paper
  • Downloaded 6,313 times
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    • Site-wide: 1,859
    • In genomics: 148
  • Year to date:
    • Site-wide: 5,442
  • Since beginning of last month:
    • Site-wide: 7,239

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

genomics more details view paper
  • Downloaded 4,739 times
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    • Site-wide: 2,746
    • In genomics: 267
  • Year to date:
    • Site-wide: 11,402
  • Since beginning of last month:
    • Site-wide: 22,176

The structure, function, and evolution of a complete human chromosome 8

genomics more details view paper
  • Downloaded 3,951 times
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    • Site-wide: 3,536
    • In genomics: 358
  • Year to date:
    • Site-wide: 2,548
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    • Site-wide: 16,604

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

genomics more details view paper
  • Downloaded 3,406 times
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    • Site-wide: 4,336
    • In genomics: 434
  • Year to date:
    • Site-wide: 67,695
  • Since beginning of last month:
    • Site-wide: 81,667

Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection

infectious diseases more details view paper
  • Downloaded 3,222 times
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    • Site-wide: 4,711
    • In infectious diseases: 907
  • Year to date:
    • Site-wide: 888
  • Since beginning of last month:
    • Site-wide: 466

Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes

bioinformatics more details view paper
  • Downloaded 3,186 times
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    • Site-wide: 4,773
    • In bioinformatics: 452
  • Year to date:
    • Site-wide: 59,298
  • Since beginning of last month:
    • Site-wide: 100,206

The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection

systems biology more details view paper
  • Downloaded 2,158 times
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    • Site-wide: 8,390
    • In systems biology: 134
  • Year to date:
    • Site-wide: 1,487
  • Since beginning of last month:
    • Site-wide: 704

Long-read, whole genome shotgun sequence data for five model organisms

genomics more details view paper
  • Downloaded 2,110 times
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    • Site-wide: 8,674
    • In genomics: 872
  • Year to date:
    • Site-wide: 93,607
  • Since beginning of last month:
    • Site-wide: 121,891

Automated ensemble assembly and validation of microbial genomes

bioinformatics more details view paper
  • Downloaded 2,060 times
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    • Site-wide: 8,972
    • In bioinformatics: 994
  • Year to date:
    • Site-wide: 136,495
  • Since beginning of last month:
    • Site-wide: 133,813

De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

genomics more details view paper
  • Downloaded 2,057 times
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    • Site-wide: 8,984
    • In genomics: 906
  • Year to date:
    • Site-wide: 97,523
  • Since beginning of last month:
    • Site-wide: 130,615

A long read mapping method for highly repetitive reference sequences

bioinformatics more details view paper
  • Downloaded 1,923 times
  • Download rankings, all-time:
    • Site-wide: 9,928
    • In bioinformatics: 1,141
  • Year to date:
    • Site-wide: 3,191
  • Since beginning of last month:
    • Site-wide: 6,885

An improved pig reference genome sequence to enable pig genetics and genomics research

genomics more details view paper
  • Downloaded 1,783 times
  • Download rankings, all-time:
    • Site-wide: 11,108
    • In genomics: 1,118
  • Year to date:
    • Site-wide: 35,262
  • Since beginning of last month:
    • Site-wide: 67,921

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

genomics more details view paper
  • Downloaded 1,663 times
  • Download rankings, all-time:
    • Site-wide: 12,316
    • In genomics: 1,247
  • Year to date:
    • Site-wide: 47,617
  • Since beginning of last month:
    • Site-wide: 58,252

RefSeq database growth influences the accuracy of k-mer-based species identification

bioinformatics more details view paper
  • Downloaded 1,531 times
  • Download rankings, all-time:
    • Site-wide: 13,878
    • In bioinformatics: 1,576
  • Year to date:
    • Site-wide: 114,858
  • Since beginning of last month:
    • Site-wide: 123,187

MetaCompass: Reference-guided Assembly of Metagenomes

bioinformatics more details view paper
  • Downloaded 1,493 times
  • Download rankings, all-time:
    • Site-wide: 14,450
    • In bioinformatics: 1,640
  • Year to date:
    • Site-wide: 39,344
  • Since beginning of last month:
    • Site-wide: 20,407

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

genomics more details view paper
  • Downloaded 1,345 times
  • Download rankings, all-time:
    • Site-wide: 16,958
    • In genomics: 1,649
  • Year to date:
    • Site-wide: 32,342
  • Since beginning of last month:
    • Site-wide: 58,084

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

genomics more details view paper
  • Downloaded 1,279 times
  • Download rankings, all-time:
    • Site-wide: 18,247
    • In genomics: 1,749
  • Year to date:
    • Site-wide: 28,556
  • Since beginning of last month:
    • Site-wide: 33,775

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

microbiology more details view paper
  • Downloaded 1,218 times
  • Download rankings, all-time:
    • Site-wide: 19,644
    • In microbiology: 1,147
  • Year to date:
    • Site-wide: 140,289
  • Since beginning of last month:
    • Site-wide: 157,096

Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

genomics more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 28,789
    • In genomics: 2,555
  • Year to date:
    • Site-wide: 87,263
  • Since beginning of last month:
    • Site-wide: 66,961

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation

genomics more details view paper
  • Downloaded 892 times
  • Download rankings, all-time:
    • Site-wide: 31,039
    • In genomics: 2,693
  • Year to date:
    • Site-wide: 135,643
  • Since beginning of last month:
    • Site-wide: 101,378

HLA*PRG:LA - HLA typing from linearly projected graph alignments

bioinformatics more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 35,322
    • In bioinformatics: 3,840
  • Year to date:
    • Site-wide: 98,613
  • Since beginning of last month:
    • Site-wide: 122,959

Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads

bioinformatics more details view paper
  • Downloaded 682 times
  • Download rankings, all-time:
    • Site-wide: 45,093
    • In bioinformatics: 4,729
  • Year to date:
    • Site-wide: 7,496
  • Since beginning of last month:
    • Site-wide: 5,143

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

bioinformatics more details view paper
  • Downloaded 658 times
  • Download rankings, all-time:
    • Site-wide: 47,232
    • In bioinformatics: 4,886
  • Year to date:
    • Site-wide: 97,644
  • Since beginning of last month:
    • Site-wide: 143,357

KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities

bioinformatics more details view paper
  • Downloaded 615 times
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    • Site-wide: 51,562
    • In bioinformatics: 5,212
  • Year to date:
    • Site-wide: 39,567
  • Since beginning of last month:
    • Site-wide: 48,270

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

genomics more details view paper
  • Downloaded 567 times
  • Download rankings, all-time:
    • Site-wide: 57,072
    • In genomics: 4,235
  • Year to date:
    • Site-wide: 82,559
  • Since beginning of last month:
    • Site-wide: 98,603

Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment

bioinformatics more details view paper
  • Downloaded 530 times
  • Download rankings, all-time:
    • Site-wide: 61,835
    • In bioinformatics: 6,041
  • Year to date:
    • Site-wide: 10,921
  • Since beginning of last month:
    • Site-wide: 11,592

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

genetics more details view paper
  • Downloaded 481 times
  • Download rankings, all-time:
    • Site-wide: 69,150
    • In genetics: 2,997
  • Year to date:
    • Site-wide: 156,528
  • Since beginning of last month:
    • Site-wide: 142,502

PlasmidHawk: Alignment-based Lab-of-Origin Prediction of Synthetic Plasmids

bioinformatics more details view paper
  • Downloaded 411 times
  • Download rankings, all-time:
    • Site-wide: 81,339
    • In bioinformatics: 7,404
  • Year to date:
    • Site-wide: 70,205
  • Since beginning of last month:
    • Site-wide: 89,066

SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning

bioinformatics more details view paper
  • Downloaded 361 times
  • Download rankings, all-time:
    • Site-wide: 91,469
    • In bioinformatics: 8,073
  • Year to date:
    • Site-wide: 19,234
  • Since beginning of last month:
    • Site-wide: 28,554

Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes

bioinformatics more details view paper
  • Downloaded 248 times
  • Download rankings, all-time:
    • Site-wide: 118,964
    • In bioinformatics: 9,728
  • Year to date:
    • Site-wide: 32,433
  • Since beginning of last month:
    • Site-wide: 40,309

Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data

bioinformatics more details view paper
  • Downloaded 201 times
  • Download rankings, all-time:
    • Site-wide: 131,398
    • In bioinformatics: 10,385
  • Year to date:
    • Site-wide: 42,079
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    • Site-wide: 2,486

Alterations to the gut microbiome after sport-related concussion and subconcussive impacts in a collegiate football players cohort.

neurology more details view paper
  • Downloaded 179 times
  • Download rankings, all-time:
    • Site-wide: 136,594
    • In neurology: 653
  • Year to date:
    • Site-wide: 48,276
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    • Site-wide: 29,817

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