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Author: Benedict Paten

  • ORCiD: http://orcid.org/0000-0001-8863-3539
  • Most recently observed institution: UC Santa Cruz Genomics Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA, USA

Rankings

  • All-time downloads: 92,652 (rank: 1,254 )
  • Categories:
    • bioinformatics: 54,114 (rank: 54 )
    • evolutionary biology: 598 (rank: 10,874 (tie) )
    • genomics: 37,940 (rank: 211 )

Downloads per author, site-wide

Preprints

Genome Graphs

bioinformatics more details view paper
  • Downloaded 8,998 times
  • Download rankings, all-time:
    • Site-wide: 853
    • In bioinformatics: 45
  • Year to date:
    • Site-wide: 10,602
  • Since beginning of last month:
    • Site-wide: 10,602

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

genomics more details view paper
  • Downloaded 8,992 times
  • Download rankings, all-time:
    • Site-wide: 856
    • In genomics: 73
  • Year to date:
    • Site-wide: 8,942
  • Since beginning of last month:
    • Site-wide: 8,942

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

bioinformatics more details view paper
  • Downloaded 8,533 times
  • Download rankings, all-time:
    • Site-wide: 918
    • In bioinformatics: 53
  • Year to date:
    • Site-wide: 5,532
  • Since beginning of last month:
    • Site-wide: 5,532

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

bioinformatics more details view paper
  • Downloaded 6,420 times
  • Download rankings, all-time:
    • Site-wide: 1,303
    • In bioinformatics: 90
  • Year to date:
    • Site-wide: 27,695
  • Since beginning of last month:
    • Site-wide: 27,695

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

bioinformatics more details view paper
  • Downloaded 6,243 times
  • Download rankings, all-time:
    • Site-wide: 1,354
    • In bioinformatics: 94
  • Year to date:
    • Site-wide: 17,211
  • Since beginning of last month:
    • Site-wide: 17,211

Computational Pan-Genomics: Status, Promises and Challenges

genomics more details view paper
  • Downloaded 4,599 times
  • Download rankings, all-time:
    • Site-wide: 2,083
    • In genomics: 225
  • Year to date:
    • Site-wide: 16,823
  • Since beginning of last month:
    • Site-wide: 16,823

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

genomics more details view paper
  • Downloaded 4,511 times
  • Download rankings, all-time:
    • Site-wide: 2,131
    • In genomics: 233
  • Year to date:
    • Site-wide: 1,723
  • Since beginning of last month:
    • Site-wide: 1,723

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

genomics more details view paper
  • Downloaded 3,828 times
  • Download rankings, all-time:
    • Site-wide: 2,697
    • In genomics: 318
  • Year to date:
    • Site-wide: 31,216
  • Since beginning of last month:
    • Site-wide: 31,216

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

genomics more details view paper
  • Downloaded 3,622 times
  • Download rankings, all-time:
    • Site-wide: 2,936
    • In genomics: 346
  • Year to date:
    • Site-wide: 5,041
  • Since beginning of last month:
    • Site-wide: 5,041

Alignathon: A competitive assessment of whole genome alignment methods.

bioinformatics more details view paper
  • Downloaded 3,303 times
  • Download rankings, all-time:
    • Site-wide: 3,342
    • In bioinformatics: 350
  • Year to date:
    • Site-wide: 52,288
  • Since beginning of last month:
    • Site-wide: 52,288

Haplotype-aware genotyping from noisy long reads

bioinformatics more details view paper
  • Downloaded 2,778 times
  • Download rankings, all-time:
    • Site-wide: 4,244
    • In bioinformatics: 459
  • Year to date:
    • Site-wide: 50,421
  • Since beginning of last month:
    • Site-wide: 50,421

Linear Assembly of a Human Y Centromere

genomics more details view paper
  • Downloaded 2,727 times
  • Download rankings, all-time:
    • Site-wide: 4,365
    • In genomics: 505
  • Year to date:
    • Site-wide: 52,152
  • Since beginning of last month:
    • Site-wide: 52,152

A fully phased accurate assembly of an individual human genome

bioinformatics more details view paper
  • Downloaded 2,430 times
  • Download rankings, all-time:
    • Site-wide: 5,208
    • In bioinformatics: 594
  • Year to date:
    • Site-wide: 12,358
  • Since beginning of last month:
    • Site-wide: 12,358

Cytosine Variant Calling with High-throughput Nanopore Sequencing

genomics more details view paper
  • Downloaded 2,075 times
  • Download rankings, all-time:
    • Site-wide: 6,536
    • In genomics: 748
  • Year to date:
    • Site-wide: 100,299
  • Since beginning of last month:
    • Site-wide: 100,299

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

bioinformatics more details view paper
  • Downloaded 1,903 times
  • Download rankings, all-time:
    • Site-wide: 7,414
    • In bioinformatics: 918
  • Year to date:
    • Site-wide: 24,856
  • Since beginning of last month:
    • Site-wide: 24,856

Chromosome assembly of large and complex genomes using multiple references

bioinformatics more details view paper
  • Downloaded 1,809 times
  • Download rankings, all-time:
    • Site-wide: 7,993
    • In bioinformatics: 986
  • Year to date:
    • Site-wide: 53,837
  • Since beginning of last month:
    • Site-wide: 53,837

Genotyping structural variants in pangenome graphs using the vg toolkit

bioinformatics more details view paper
  • Downloaded 1,567 times
  • Download rankings, all-time:
    • Site-wide: 9,964
    • In bioinformatics: 1,235
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

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

genomics more details view paper
  • Downloaded 1,461 times
  • Download rankings, all-time:
    • Site-wide: 11,014
    • In genomics: 1,232
  • Year to date:
    • Site-wide: 57,057
  • Since beginning of last month:
    • Site-wide: 57,057

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

bioinformatics more details view paper
  • Downloaded 1,450 times
  • Download rankings, all-time:
    • Site-wide: 11,143
    • In bioinformatics: 1,384
  • Year to date:
    • Site-wide: 108,182
  • Since beginning of last month:
    • Site-wide: 108,182

The UCSC Genome Browser database: 2016 update

genomics more details view paper
  • Downloaded 1,388 times
  • Download rankings, all-time:
    • Site-wide: 11,922
    • In genomics: 1,320
  • Year to date:
    • Site-wide: 57,156
  • Since beginning of last month:
    • Site-wide: 57,156

Genome Graphs and the Evolution of Genome Inference

bioinformatics more details view paper
  • Downloaded 1,349 times
  • Download rankings, all-time:
    • Site-wide: 12,419
    • In bioinformatics: 1,532
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

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

genomics more details view paper
  • Downloaded 1,169 times
  • Download rankings, all-time:
    • Site-wide: 15,418
    • In genomics: 1,633
  • Year to date:
    • Site-wide: 57,075
  • Since beginning of last month:
    • Site-wide: 57,075

Superbubbles, Ultrabubbles and Cacti

bioinformatics more details view paper
  • Downloaded 1,138 times
  • Download rankings, all-time:
    • Site-wide: 16,062
    • In bioinformatics: 1,976
  • Year to date:
    • Site-wide: 71,464
  • Since beginning of last month:
    • Site-wide: 71,464

A Flow Procedure for the Linearization of Genome Sequence Graphs.

bioinformatics more details view paper
  • Downloaded 998 times
  • Download rankings, all-time:
    • Site-wide: 19,577
    • In bioinformatics: 2,369
  • Year to date:
    • Site-wide: 98,945
  • Since beginning of last month:
    • Site-wide: 98,945

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

genomics more details view paper
  • Downloaded 987 times
  • Download rankings, all-time:
    • Site-wide: 19,858
    • In genomics: 2,020
  • Year to date:
    • Site-wide: 37,564
  • Since beginning of last month:
    • Site-wide: 37,564

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

bioinformatics more details view paper
  • Downloaded 911 times
  • Download rankings, all-time:
    • Site-wide: 22,242
    • In bioinformatics: 2,664
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

Haplotype-aware graph indexes

bioinformatics more details view paper
  • Downloaded 773 times
  • Download rankings, all-time:
    • Site-wide: 28,031
    • In bioinformatics: 3,246
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

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

bioinformatics more details view paper
  • Downloaded 771 times
  • Download rankings, all-time:
    • Site-wide: 28,198
    • In bioinformatics: 3,262
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

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

genomics more details view paper
  • Downloaded 755 times
  • Download rankings, all-time:
    • Site-wide: 28,987
    • In genomics: 2,670
  • Year to date:
    • Site-wide: 22,741
  • Since beginning of last month:
    • Site-wide: 22,741

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 690 times
  • Download rankings, all-time:
    • Site-wide: 32,815
    • In genomics: 2,920
  • Year to date:
    • Site-wide: 30,717
  • Since beginning of last month:
    • Site-wide: 30,717

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

genomics more details view paper
  • Downloaded 646 times
  • Download rankings, all-time:
    • Site-wide: 35,899
    • In genomics: 3,112
  • Year to date:
    • Site-wide: 91,552
  • Since beginning of last month:
    • Site-wide: 91,552

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

evolutionary biology more details view paper
  • Downloaded 598 times
  • Download rankings, all-time:
    • Site-wide: 39,566
    • In evolutionary biology: 2,094
  • Year to date:
    • Site-wide: 40,865
  • Since beginning of last month:
    • Site-wide: 40,865

Succinct dynamic variation graphs

bioinformatics more details view paper
  • Downloaded 580 times
  • Download rankings, all-time:
    • Site-wide: 41,164
    • In bioinformatics: 4,468
  • Year to date:
    • Site-wide: 54,156
  • Since beginning of last month:
    • Site-wide: 54,156

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

bioinformatics more details view paper
  • Downloaded 570 times
  • Download rankings, all-time:
    • Site-wide: 41,975
    • In bioinformatics: 4,539
  • Year to date:
    • Site-wide: 67,059
  • Since beginning of last month:
    • Site-wide: 67,059

Modelling haplotypes with respect to reference cohort variation graphs

genomics more details view paper
  • Downloaded 490 times
  • Download rankings, all-time:
    • Site-wide: 50,466
    • In genomics: 3,970
  • Year to date:
    • Site-wide: 114,677
  • Since beginning of last month:
    • Site-wide: 114,677

Describing the Local Structure of Sequence Graphs

bioinformatics more details view paper
  • Downloaded 460 times
  • Download rankings, all-time:
    • Site-wide: 54,096
    • In bioinformatics: 5,552
  • Year to date:
    • Site-wide: 119,175
  • Since beginning of last month:
    • Site-wide: 119,175

Distance Indexing and Seed Clustering in Sequence Graphs

bioinformatics more details view paper
  • Downloaded 390 times
  • Download rankings, all-time:
    • Site-wide: 64,086
    • In bioinformatics: 6,254
  • Year to date:
    • Site-wide: 102,552
  • Since beginning of last month:
    • Site-wide: 102,552

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

bioinformatics more details view paper
  • Downloaded 373 times
  • Download rankings, all-time:
    • Site-wide: 66,832
    • In bioinformatics: 6,465
  • Year to date:
    • Site-wide: None
  • Since beginning of last month:
    • Site-wide: None

Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

bioinformatics more details view paper
  • Downloaded 367 times
  • Download rankings, all-time:
    • Site-wide: 67,734
    • In bioinformatics: 6,514
  • Year to date:
    • Site-wide: 7,542
  • Since beginning of last month:
    • Site-wide: 7,542

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