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Author: Benedict Paten

Rankings

  • All-time downloads: 139,376 (rank: 676 )
  • Categories:
    • bioinformatics: 61,884 (rank: 27 )
    • evolutionary biology: 643 (rank: 11,752 (tie) )
    • genomics: 76,849 (rank: 117 )

Downloads per author, site-wide

Preprints

The complete sequence of a human genome

genomics more details view paper
  • Downloaded 33,007 times
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    • Site-wide: 223
    • In genomics: 10
  • Year to date:
    • Site-wide: 43
  • Since beginning of last month:
    • Site-wide: 69

Genome Graphs

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  • Downloaded 9,337 times
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    • Site-wide: 1,013
    • In bioinformatics: 51
  • Year to date:
    • Site-wide: 10,038
  • Since beginning of last month:
    • Site-wide: 30,213

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

genomics more details view paper
  • Downloaded 9,250 times
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    • Site-wide: 1,026
    • In genomics: 74
  • Year to date:
    • Site-wide: 12,669
  • Since beginning of last month:
    • Site-wide: 8,454

Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

bioinformatics more details view paper
  • Downloaded 9,007 times
  • Download rankings, all-time:
    • Site-wide: 1,066
    • In bioinformatics: 58
  • Year to date:
    • Site-wide: 5,764
  • Since beginning of last month:
    • Site-wide: 25,483

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

bioinformatics more details view paper
  • Downloaded 6,630 times
  • Download rankings, all-time:
    • Site-wide: 1,566
    • In bioinformatics: 100
  • Year to date:
    • Site-wide: 21,518
  • Since beginning of last month:
    • Site-wide: 13,583

Telomere-to-telomere assembly of a complete human X chromosome

bioinformatics more details view paper
  • Downloaded 6,568 times
  • Download rankings, all-time:
    • Site-wide: 1,591
    • In bioinformatics: 101
  • Year to date:
    • Site-wide: 11,661
  • Since beginning of last month:
    • Site-wide: 21,810

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

genomics more details view paper
  • Downloaded 5,770 times
  • Download rankings, all-time:
    • Site-wide: 1,904
    • In genomics: 164
  • Year to date:
    • Site-wide: 1,520
  • Since beginning of last month:
    • Site-wide: 6,038

Computational Pan-Genomics: Status, Promises and Challenges

genomics more details view paper
  • Downloaded 4,692 times
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    • Site-wide: 2,534
    • In genomics: 255
  • Year to date:
    • Site-wide: 38,155
  • Since beginning of last month:
    • Site-wide: 65,712

Sequence variation aware genome references and read mapping with the variation graph toolkit

genomics more details view paper
  • Downloaded 3,932 times
  • Download rankings, all-time:
    • Site-wide: 3,268
    • In genomics: 341
  • Year to date:
    • Site-wide: 43,574
  • Since beginning of last month:
    • Site-wide: 23,732

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

genomics more details view paper
  • Downloaded 3,904 times
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    • Site-wide: 3,315
    • In genomics: 353
  • Year to date:
    • Site-wide: 9,471
  • Since beginning of last month:
    • Site-wide: 25,312

Alignathon: A competitive assessment of whole genome alignment methods.

bioinformatics more details view paper
  • Downloaded 3,349 times
  • Download rankings, all-time:
    • Site-wide: 4,084
    • In bioinformatics: 397
  • Year to date:
    • Site-wide: 84,187
  • Since beginning of last month:
    • Site-wide: 119,657

Haplotype-aware genotyping from noisy long reads

bioinformatics more details view paper
  • Downloaded 2,907 times
  • Download rankings, all-time:
    • Site-wide: 4,990
    • In bioinformatics: 496
  • Year to date:
    • Site-wide: 39,888
  • Since beginning of last month:
    • Site-wide: 19,169

Linear Assembly of a Human Y Centromere

genomics more details view paper
  • Downloaded 2,764 times
  • Download rankings, all-time:
    • Site-wide: 5,367
    • In genomics: 560
  • Year to date:
    • Site-wide: 93,341
  • Since beginning of last month:
    • Site-wide: 122,312

A fully phased accurate assembly of an individual human genome

bioinformatics more details view paper
  • Downloaded 2,570 times
  • Download rankings, all-time:
    • Site-wide: 5,975
    • In bioinformatics: 638
  • Year to date:
    • Site-wide: 25,186
  • Since beginning of last month:
    • Site-wide: 68,662

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

bioinformatics more details view paper
  • Downloaded 2,266 times
  • Download rankings, all-time:
    • Site-wide: 7,190
    • In bioinformatics: 813
  • Year to date:
    • Site-wide: 1,930
  • Since beginning of last month:
    • Site-wide: 3,179

Cytosine Variant Calling with High-throughput Nanopore Sequencing

genomics more details view paper
  • Downloaded 2,115 times
  • Download rankings, all-time:
    • Site-wide: 7,945
    • In genomics: 837
  • Year to date:
    • Site-wide: 105,672
  • Since beginning of last month:
    • Site-wide: 59,498

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

bioinformatics more details view paper
  • Downloaded 2,017 times
  • Download rankings, all-time:
    • Site-wide: 8,523
    • In bioinformatics: 977
  • Year to date:
    • Site-wide: 37,778
  • Since beginning of last month:
    • Site-wide: 33,081

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

bioinformatics more details view paper
  • Downloaded 1,895 times
  • Download rankings, all-time:
    • Site-wide: 9,368
    • In bioinformatics: 1,093
  • Year to date:
    • Site-wide: 2,485
  • Since beginning of last month:
    • Site-wide: 3,891

Chromosome assembly of large and complex genomes using multiple references

bioinformatics more details view paper
  • Downloaded 1,852 times
  • Download rankings, all-time:
    • Site-wide: 9,682
    • In bioinformatics: 1,134
  • Year to date:
    • Site-wide: 88,367
  • Since beginning of last month:
    • Site-wide: 130,292

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

bioinformatics more details view paper
  • Downloaded 1,770 times
  • Download rankings, all-time:
    • Site-wide: 10,368
    • In bioinformatics: 1,203
  • Year to date:
    • Site-wide: 1,364
  • Since beginning of last month:
    • Site-wide: 820

Genotyping structural variants in pangenome graphs using the vg toolkit

bioinformatics more details view paper
  • Downloaded 1,694 times
  • Download rankings, all-time:
    • Site-wide: 11,056
    • In bioinformatics: 1,291
  • Year to date:
    • Site-wide: 47,921
  • Since beginning of last month:
    • Site-wide: 37,332

A complete reference genome improves analysis of human genetic variation

genomics more details view paper
  • Downloaded 1,685 times
  • Download rankings, all-time:
    • Site-wide: 11,127
    • In genomics: 1,154
  • Year to date:
    • Site-wide: 1,444
  • Since beginning of last month:
    • Site-wide: 102

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

genomics more details view paper
  • Downloaded 1,533 times
  • Download rankings, all-time:
    • Site-wide: 12,739
    • In genomics: 1,320
  • Year to date:
    • Site-wide: 65,772
  • Since beginning of last month:
    • Site-wide: 30,584

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

bioinformatics more details view paper
  • Downloaded 1,471 times
  • Download rankings, all-time:
    • Site-wide: 13,560
    • In bioinformatics: 1,576
  • Year to date:
    • Site-wide: 133,794
  • Since beginning of last month:
    • Site-wide: 124,803

The UCSC Genome Browser database: 2016 update

genomics more details view paper
  • Downloaded 1,460 times
  • Download rankings, all-time:
    • Site-wide: 13,749
    • In genomics: 1,406
  • Year to date:
    • Site-wide: 65,684
  • Since beginning of last month:
    • Site-wide: 84,809

Genome Graphs and the Evolution of Genome Inference

bioinformatics more details view paper
  • Downloaded 1,388 times
  • Download rankings, all-time:
    • Site-wide: 14,845
    • In bioinformatics: 1,731
  • Year to date:
    • Site-wide: 117,548
  • Since beginning of last month:
    • Site-wide: 109,187

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

genomics more details view paper
  • Downloaded 1,200 times
  • Download rankings, all-time:
    • Site-wide: 18,444
    • In genomics: 1,811
  • Year to date:
    • Site-wide: 102,356
  • Since beginning of last month:
    • Site-wide: 140,659

Superbubbles, Ultrabubbles and Cacti

bioinformatics more details view paper
  • Downloaded 1,177 times
  • Download rankings, all-time:
    • Site-wide: 18,978
    • In bioinformatics: 2,201
  • Year to date:
    • Site-wide: 98,577
  • Since beginning of last month:
    • Site-wide: 109,258

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

genomics more details view paper
  • Downloaded 1,042 times
  • Download rankings, all-time:
    • Site-wide: 22,766
    • In genomics: 2,172
  • Year to date:
    • Site-wide: 70,531
  • Since beginning of last month:
    • Site-wide: 110,958

A Flow Procedure for the Linearization of Genome Sequence Graphs.

bioinformatics more details view paper
  • Downloaded 1,014 times
  • Download rankings, all-time:
    • Site-wide: 23,633
    • In bioinformatics: 2,715
  • Year to date:
    • Site-wide: 140,031
  • Since beginning of last month:
    • Site-wide: 124,353

Complete genomic and epigenetic maps of human centromeres

genomics more details view paper
  • Downloaded 1,003 times
  • Download rankings, all-time:
    • Site-wide: 24,038
    • In genomics: 2,260
  • Year to date:
    • Site-wide: 2,941
  • Since beginning of last month:
    • Site-wide: 181

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

genomics more details view paper
  • Downloaded 866 times
  • Download rankings, all-time:
    • Site-wide: 29,614
    • In genomics: 2,645
  • Year to date:
    • Site-wide: 37,617
  • Since beginning of last month:
    • Site-wide: 53,848

Haplotype-aware graph indexes

bioinformatics more details view paper
  • Downloaded 822 times
  • Download rankings, all-time:
    • Site-wide: 31,857
    • In bioinformatics: 3,539
  • Year to date:
    • Site-wide: 104,043
  • Since beginning of last month:
    • Site-wide: 120,362

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 815 times
  • Download rankings, all-time:
    • Site-wide: 32,225
    • In genomics: 2,817
  • Year to date:
    • Site-wide: 37,135
  • Since beginning of last month:
    • Site-wide: 89,324

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

genomics more details view paper
  • Downloaded 656 times
  • Download rankings, all-time:
    • Site-wide: 43,382
    • In genomics: 3,493
  • Year to date:
    • Site-wide: 144,063
  • Since beginning of last month:
    • Site-wide: 140,267

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

genomics more details view paper
  • Downloaded 648 times
  • Download rankings, all-time:
    • Site-wide: 44,058
    • In genomics: 3,537
  • Year to date:
    • Site-wide: 5,545
  • Since beginning of last month:
    • Site-wide: 318

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

evolutionary biology more details view paper
  • Downloaded 643 times
  • Download rankings, all-time:
    • Site-wide: 44,484
    • In evolutionary biology: 2,185
  • Year to date:
    • Site-wide: 79,865
  • Since beginning of last month:
    • Site-wide: 45,182

Succinct dynamic variation graphs

bioinformatics more details view paper
  • Downloaded 636 times
  • Download rankings, all-time:
    • Site-wide: 45,090
    • In bioinformatics: 4,704
  • Year to date:
    • Site-wide: 75,835
  • Since beginning of last month:
    • Site-wide: 86,961

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

bioinformatics more details view paper
  • Downloaded 623 times
  • Download rankings, all-time:
    • Site-wide: 46,328
    • In bioinformatics: 4,838
  • Year to date:
    • Site-wide: 5,854
  • Since beginning of last month:
    • Site-wide: 32,101

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

bioinformatics more details view paper
  • Downloaded 587 times
  • Download rankings, all-time:
    • Site-wide: 49,888
    • In bioinformatics: 5,107
  • Year to date:
    • Site-wide: 126,828
  • Since beginning of last month:
    • Site-wide: 135,705

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

bioinformatics more details view paper
  • Downloaded 552 times
  • Download rankings, all-time:
    • Site-wide: 53,836
    • In bioinformatics: 5,454
  • Year to date:
    • Site-wide: 7,005
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    • Site-wide: 10,139

Modelling haplotypes with respect to reference cohort variation graphs

genomics more details view paper
  • Downloaded 507 times
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    • Site-wide: 59,454
    • In genomics: 4,373
  • Year to date:
    • Site-wide: 142,330
  • Since beginning of last month:
    • Site-wide: 140,380

Describing the Local Structure of Sequence Graphs

bioinformatics more details view paper
  • Downloaded 486 times
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    • Site-wide: 62,351
    • In bioinformatics: 6,127
  • Year to date:
    • Site-wide: 130,477
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    • Site-wide: 109,121

Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

bioinformatics more details view paper
  • Downloaded 439 times
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    • Site-wide: 69,386
    • In bioinformatics: 6,612
  • Year to date:
    • Site-wide: 29,427
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    • Site-wide: 82,071

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

bioinformatics more details view paper
  • Downloaded 421 times
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    • Site-wide: 72,541
    • In bioinformatics: 6,808
  • Year to date:
    • Site-wide: 105,479
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    • Site-wide: 119,773

Distance Indexing and Seed Clustering in Sequence Graphs

bioinformatics more details view paper
  • Downloaded 406 times
  • Download rankings, all-time:
    • Site-wide: 75,064
    • In bioinformatics: 7,017
  • Year to date:
    • Site-wide: 139,154
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    • Site-wide: 142,666

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