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Author: Benedict Paten

Rankings

  • All-time downloads: 96,577 (rank: 1,247 )
  • Categories:
    • bioinformatics: 56,910 (rank: 37 )
    • evolutionary biology: 604 (rank: 11,243 (tie) )
    • genomics: 39,063 (rank: 199 )

Downloads per author, site-wide

Preprints

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

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Genome Graphs

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    • Site-wide: 897
    • In bioinformatics: 48
  • Year to date:
    • Site-wide: 10,516
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    • Site-wide: 13,801

Nanopore native RNA sequencing of a human poly(A) transcriptome

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  • Downloaded 9,053 times
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    • Site-wide: 905
    • In genomics: 73
  • Year to date:
    • Site-wide: 12,780
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Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

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  • Downloaded 8,681 times
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    • Site-wide: 959
    • In bioinformatics: 55
  • Year to date:
    • Site-wide: 5,682
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    • Site-wide: 6,253

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

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    • Site-wide: 1,388
    • In bioinformatics: 93
  • Year to date:
    • Site-wide: 26,274
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Telomere-to-telomere assembly of a complete human X chromosome

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    • Site-wide: 1,414
    • In bioinformatics: 96
  • Year to date:
    • Site-wide: 10,758
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    • Site-wide: 9,864

Towards complete and error-free genome assemblies of all vertebrate species

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  • Downloaded 5,211 times
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    • Site-wide: 1,866
    • In genomics: 183
  • Year to date:
    • Site-wide: 982
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Computational Pan-Genomics: Status, Promises and Challenges

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  • Downloaded 4,625 times
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    • Site-wide: 2,205
    • In genomics: 237
  • Year to date:
    • Site-wide: 27,215
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Sequence variation aware genome references and read mapping with the variation graph toolkit

genomics more details view paper
  • Downloaded 3,861 times
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    • Site-wide: 2,863
    • In genomics: 325
  • Year to date:
    • Site-wide: 36,473
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    • Site-wide: 26,159

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

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    • Site-wide: 3,028
    • In genomics: 346
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    • Site-wide: 7,274
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    • Site-wide: 10,882

Alignathon: A competitive assessment of whole genome alignment methods.

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    • Site-wide: 3,564
    • In bioinformatics: 363
  • Year to date:
    • Site-wide: 65,913
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    • Site-wide: 100,897

Haplotype-aware genotyping from noisy long reads

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  • Downloaded 2,806 times
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    • Site-wide: 4,502
    • In bioinformatics: 474
  • Year to date:
    • Site-wide: 48,605
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    • Site-wide: 40,331

Linear Assembly of a Human Y Centromere

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  • Downloaded 2,746 times
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    • Site-wide: 4,647
    • In genomics: 518
  • Year to date:
    • Site-wide: 59,184
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    • Site-wide: 80,469

A fully phased accurate assembly of an individual human genome

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  • Downloaded 2,483 times
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    • Site-wide: 5,404
    • In bioinformatics: 601
  • Year to date:
    • Site-wide: 17,109
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    • Site-wide: 18,102

Cytosine Variant Calling with High-throughput Nanopore Sequencing

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  • Downloaded 2,087 times
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    • Site-wide: 6,962
    • In genomics: 771
  • Year to date:
    • Site-wide: 98,525
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    • Site-wide: 64,668

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

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  • Downloaded 1,948 times
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    • Site-wide: 7,701
    • In bioinformatics: 935
  • Year to date:
    • Site-wide: 27,742
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    • Site-wide: 31,807

Chromosome assembly of large and complex genomes using multiple references

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  • Downloaded 1,820 times
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    • Site-wide: 8,555
    • In bioinformatics: 1,039
  • Year to date:
    • Site-wide: 73,254
  • Since beginning of last month:
    • Site-wide: 74,059

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

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  • Downloaded 1,671 times
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    • Site-wide: 9,736
    • In bioinformatics: 1,174
  • Year to date:
    • Site-wide: 1,514
  • Since beginning of last month:
    • Site-wide: 1,911

Genotyping structural variants in pangenome graphs using the vg toolkit

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  • Downloaded 1,640 times
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    • Site-wide: 9,996
    • In bioinformatics: 1,210
  • Year to date:
    • Site-wide: 34,150
  • Since beginning of last month:
    • Site-wide: 33,921

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

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  • Downloaded 1,475 times
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    • Site-wide: 11,619
    • In genomics: 1,271
  • Year to date:
    • Site-wide: 68,586
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    • Site-wide: 64,144

A Graph Extension of the Positional Burrows-Wheeler Transform and its Applications

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  • Downloaded 1,455 times
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    • Site-wide: 11,881
    • In bioinformatics: 1,456
  • Year to date:
    • Site-wide: 121,868
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    • Site-wide: 130,538

Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit

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  • Downloaded 1,446 times
  • Download rankings, all-time:
    • Site-wide: 11,983
    • In bioinformatics: 1,471
  • Year to date:
    • Site-wide: 1,812
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    • Site-wide: 2,874

The UCSC Genome Browser database: 2016 update

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  • Downloaded 1,427 times
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    • Site-wide: 12,255
    • In genomics: 1,331
  • Year to date:
    • Site-wide: 42,732
  • Since beginning of last month:
    • Site-wide: 33,793

Genome Graphs and the Evolution of Genome Inference

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  • Downloaded 1,362 times
  • Download rankings, all-time:
    • Site-wide: 13,174
    • In bioinformatics: 1,599
  • Year to date:
    • Site-wide: 120,374
  • Since beginning of last month:
    • Site-wide: 98,669

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

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  • Downloaded 1,186 times
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    • Site-wide: 16,221
    • In genomics: 1,669
  • Year to date:
    • Site-wide: 64,004
  • Since beginning of last month:
    • Site-wide: 60,095

Superbubbles, Ultrabubbles and Cacti

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  • Downloaded 1,148 times
  • Download rankings, all-time:
    • Site-wide: 17,054
    • In bioinformatics: 2,057
  • Year to date:
    • Site-wide: 86,739
  • Since beginning of last month:
    • Site-wide: 93,863

The genome of C57BL/6J "Eve", the mother of the laboratory mouse genome reference strain

genomics more details view paper
  • Downloaded 1,006 times
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    • Site-wide: 20,661
    • In genomics: 2,065
  • Year to date:
    • Site-wide: 50,016
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    • Site-wide: 67,030

A Flow Procedure for the Linearization of Genome Sequence Graphs.

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  • Downloaded 1,001 times
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    • Site-wide: 20,810
    • In bioinformatics: 2,479
  • Year to date:
    • Site-wide: 125,869
  • Since beginning of last month:
    • Site-wide: 116,695

Haplotype-aware graph indexes

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  • Downloaded 804 times
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    • Site-wide: 28,411
    • In bioinformatics: 3,273
  • Year to date:
    • Site-wide: 73,124
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    • Site-wide: 64,232

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

genomics more details view paper
  • Downloaded 800 times
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    • Site-wide: 28,632
    • In genomics: 2,637
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    • Site-wide: 26,425
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    • Site-wide: 27,127

A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

genomics more details view paper
  • Downloaded 733 times
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    • Site-wide: 32,388
    • In genomics: 2,871
  • Year to date:
    • Site-wide: 31,379
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    • Site-wide: 28,276

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

genomics more details view paper
  • Downloaded 650 times
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    • Site-wide: 38,037
    • In genomics: 3,215
  • Year to date:
    • Site-wide: 116,702
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    • Site-wide: 102,923

KRAB Zinc Finger Proteins coordinate across evolutionary time scales to battle retroelements

evolutionary biology more details view paper
  • Downloaded 604 times
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    • Site-wide: 41,806
    • In evolutionary biology: 2,161
  • Year to date:
    • Site-wide: 68,226
  • Since beginning of last month:
    • Site-wide: 101,859

Succinct dynamic variation graphs

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  • Downloaded 595 times
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    • Site-wide: 42,532
    • In bioinformatics: 4,572
  • Year to date:
    • Site-wide: 65,173
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    • Site-wide: 59,486

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

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  • Downloaded 576 times
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    • Site-wide: 44,245
    • In bioinformatics: 4,705
  • Year to date:
    • Site-wide: 93,617
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    • Site-wide: 116,440

Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

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  • Downloaded 563 times
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    • Site-wide: 45,657
    • In bioinformatics: 4,816
  • Year to date:
    • Site-wide: 2,337
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    • Site-wide: 605

Modelling haplotypes with respect to reference cohort variation graphs

genomics more details view paper
  • Downloaded 493 times
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    • Site-wide: 53,358
    • In genomics: 4,111
  • Year to date:
    • Site-wide: 131,140
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    • Site-wide: 125,980

Describing the Local Structure of Sequence Graphs

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  • Downloaded 466 times
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    • Site-wide: 56,772
    • In bioinformatics: 5,725
  • Year to date:
    • Site-wide: 127,657
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    • Site-wide: 129,026

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

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  • Downloaded 397 times
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    • Site-wide: 66,953
    • In bioinformatics: 6,470
  • Year to date:
    • Site-wide: 86,395
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    • Site-wide: 114,207

Distance Indexing and Seed Clustering in Sequence Graphs

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  • Downloaded 394 times
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    • Site-wide: 67,337
    • In bioinformatics: 6,517
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    • Site-wide: 122,955
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Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

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  • Downloaded 392 times
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    • Site-wide: 67,776
    • In bioinformatics: 6,537
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