Rxivist logo

Author: Benedict Paten

Rankings

  • All-time downloads: 80,025 (rank: 443 out of 383,780)
  • Categories:
    • bioinformatics: 47,040 (rank: 56 out of 32,829)
    • evolutionary biology: 492 (rank: 10,194 (tie) out of 19,667)
    • genomics: 32,493 (rank: 231 out of 40,849)

Downloads per author, site-wide

Preprints

Genome Graphs

bioinformatics more details view paper
  • Downloaded 8,518 times
  • Download rankings, all-time:
    • Site-wide: 313 out of 89,568
    • In bioinformatics: 37 out of 8,443
  • Year to date:
    • Site-wide: 2,650 out of 89,568
  • Since beginning of last month:
    • Site-wide: 2,568 out of 89,568

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

genomics more details view paper
  • Downloaded 8,315 times
  • Download rankings, all-time:
    • Site-wide: 330 out of 89,568
    • In genomics: 64 out of 5,703
  • Year to date:
    • Site-wide: 1,764 out of 89,568
  • Since beginning of last month:
    • Site-wide: 2,640 out of 89,568

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

bioinformatics more details view paper
  • Downloaded 7,693 times
  • Download rankings, all-time:
    • Site-wide: 371 out of 89,568
    • In bioinformatics: 48 out of 8,443
  • Year to date:
    • Site-wide: 466 out of 89,568
  • Since beginning of last month:
    • Site-wide: 1,886 out of 89,568

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

bioinformatics more details view paper
  • Downloaded 6,163 times
  • Download rankings, all-time:
    • Site-wide: 530 out of 89,568
    • In bioinformatics: 82 out of 8,443
  • Year to date:
    • Site-wide: 11,880 out of 89,568
  • Since beginning of last month:
    • Site-wide: 12,849 out of 89,568

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

bioinformatics more details view paper
  • Downloaded 4,694 times
  • Download rankings, all-time:
    • Site-wide: 853 out of 89,568
    • In bioinformatics: 144 out of 8,443
  • Year to date:
    • Site-wide: 1,100 out of 89,568
  • Since beginning of last month:
    • Site-wide: 1,403 out of 89,568

Computational Pan-Genomics: Status, Promises and Challenges

genomics more details view paper
  • Downloaded 4,341 times
  • Download rankings, all-time:
    • Site-wide: 965 out of 89,568
    • In genomics: 204 out of 5,703
  • Year to date:
    • Site-wide: 15,578 out of 89,568
  • Since beginning of last month:
    • Site-wide: 8,369 out of 89,568

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

genomics more details view paper
  • Downloaded 3,669 times
  • Download rankings, all-time:
    • Site-wide: 1,305 out of 89,568
    • In genomics: 279 out of 5,703
  • Year to date:
    • Site-wide: 19,626 out of 89,568
  • Since beginning of last month:
    • Site-wide: 22,986 out of 89,568

Alignathon: A competitive assessment of whole genome alignment methods.

bioinformatics more details view paper
  • Downloaded 3,231 times
  • Download rankings, all-time:
    • Site-wide: 1,615 out of 89,568
    • In bioinformatics: 292 out of 8,443
  • Year to date:
    • Site-wide: 43,747 out of 89,568
  • Since beginning of last month:
    • Site-wide: 52,491 out of 89,568

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

genomics more details view paper
  • Downloaded 2,727 times
  • Download rankings, all-time:
    • Site-wide: 2,186 out of 89,568
    • In genomics: 424 out of 5,703
  • Year to date:
    • Site-wide: 1,097 out of 89,568
  • Since beginning of last month:
    • Site-wide: 1,320 out of 89,568

Haplotype-aware genotyping from noisy long reads

bioinformatics more details view paper
  • Downloaded 2,662 times
  • Download rankings, all-time:
    • Site-wide: 2,268 out of 89,568
    • In bioinformatics: 407 out of 8,443
  • Year to date:
    • Site-wide: 23,222 out of 89,568
  • Since beginning of last month:
    • Site-wide: 15,858 out of 89,568

Linear Assembly of a Human Y Centromere

genomics more details view paper
  • Downloaded 2,636 times
  • Download rankings, all-time:
    • Site-wide: 2,302 out of 89,568
    • In genomics: 441 out of 5,703
  • Year to date:
    • Site-wide: 56,669 out of 89,568
  • Since beginning of last month:
    • Site-wide: 44,627 out of 89,568

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

genomics more details view paper
  • Downloaded 2,398 times
  • Download rankings, all-time:
    • Site-wide: 2,714 out of 89,568
    • In genomics: 515 out of 5,703
  • Year to date:
    • Site-wide: 452 out of 89,568
  • Since beginning of last month:
    • Site-wide: 294 out of 89,568

Cytosine Variant Calling with High-throughput Nanopore Sequencing

genomics more details view paper
  • Downloaded 2,031 times
  • Download rankings, all-time:
    • Site-wide: 3,563 out of 89,568
    • In genomics: 646 out of 5,703
  • Year to date:
    • Site-wide: 71,430 out of 89,568
  • Since beginning of last month:
    • Site-wide: 54,924 out of 89,568

A fully phased accurate assembly of an individual human genome

bioinformatics more details view paper
  • Downloaded 1,772 times
  • Download rankings, all-time:
    • Site-wide: 4,489 out of 89,568
    • In bioinformatics: 830 out of 8,443
  • Year to date:
    • Site-wide: 2,014 out of 89,568
  • Since beginning of last month:
    • Site-wide: 2,625 out of 89,568

Chromosome assembly of large and complex genomes using multiple references

bioinformatics more details view paper
  • Downloaded 1,721 times
  • Download rankings, all-time:
    • Site-wide: 4,696 out of 89,568
    • In bioinformatics: 864 out of 8,443
  • Year to date:
    • Site-wide: 49,390 out of 89,568
  • Since beginning of last month:
    • Site-wide: 49,029 out of 89,568

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

bioinformatics more details view paper
  • Downloaded 1,688 times
  • Download rankings, all-time:
    • Site-wide: 4,839 out of 89,568
    • In bioinformatics: 892 out of 8,443
  • Year to date:
    • Site-wide: 25,285 out of 89,568
  • Since beginning of last month:
    • Site-wide: 22,434 out of 89,568

Genotyping structural variants in pangenome graphs using the vg toolkit

bioinformatics more details view paper
  • Downloaded 1,462 times
  • Download rankings, all-time:
    • Site-wide: 6,139 out of 89,568
    • In bioinformatics: 1,087 out of 8,443
  • Year to date:
    • Site-wide: 11,568 out of 89,568
  • Since beginning of last month:
    • Site-wide: 27,781 out of 89,568

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

bioinformatics more details view paper
  • Downloaded 1,410 times
  • Download rankings, all-time:
    • Site-wide: 6,523 out of 89,568
    • In bioinformatics: 1,148 out of 8,443
  • Year to date:
    • Site-wide: 75,522 out of 89,568
  • Since beginning of last month:
    • Site-wide: 51,673 out of 89,568

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

genomics more details view paper
  • Downloaded 1,355 times
  • Download rankings, all-time:
    • Site-wide: 6,976 out of 89,568
    • In genomics: 1,090 out of 5,703
  • Year to date:
    • Site-wide: 24,733 out of 89,568
  • Since beginning of last month:
    • Site-wide: 58,945 out of 89,568

Genome Graphs and the Evolution of Genome Inference

bioinformatics more details view paper
  • Downloaded 1,320 times
  • Download rankings, all-time:
    • Site-wide: 7,277 out of 89,568
    • In bioinformatics: 1,278 out of 8,443
  • Year to date:
    • Site-wide: 69,562 out of 89,568
  • Since beginning of last month:
    • Site-wide: 38,123 out of 89,568

The UCSC Genome Browser database: 2016 update

genomics more details view paper
  • Downloaded 1,318 times
  • Download rankings, all-time:
    • Site-wide: 7,307 out of 89,568
    • In genomics: 1,127 out of 5,703
  • Year to date:
    • Site-wide: 65,917 out of 89,568
  • Since beginning of last month:
    • Site-wide: 43,656 out of 89,568

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

genomics more details view paper
  • Downloaded 1,109 times
  • Download rankings, all-time:
    • Site-wide: 9,737 out of 89,568
    • In genomics: 1,427 out of 5,703
  • Year to date:
    • Site-wide: 61,441 out of 89,568
  • Since beginning of last month:
    • Site-wide: 54,350 out of 89,568

Superbubbles, Ultrabubbles and Cacti

bioinformatics more details view paper
  • Downloaded 1,083 times
  • Download rankings, all-time:
    • Site-wide: 10,132 out of 89,568
    • In bioinformatics: 1,675 out of 8,443
  • Year to date:
    • Site-wide: 50,327 out of 89,568
  • Since beginning of last month:
    • Site-wide: 47,217 out of 89,568

A Flow Procedure for the Linearization of Genome Sequence Graphs.

bioinformatics more details view paper
  • Downloaded 955 times
  • Download rankings, all-time:
    • Site-wide: 12,380 out of 89,568
    • In bioinformatics: 1,979 out of 8,443
  • Year to date:
    • Site-wide: 74,357 out of 89,568
  • Since beginning of last month:
    • Site-wide: 60,059 out of 89,568

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

genomics more details view paper
  • Downloaded 841 times
  • Download rankings, all-time:
    • Site-wide: 15,105 out of 89,568
    • In genomics: 1,951 out of 5,703
  • Year to date:
    • Site-wide: 27,695 out of 89,568
  • Since beginning of last month:
    • Site-wide: 24,580 out of 89,568

Haplotype-aware graph indexes

bioinformatics more details view paper
  • Downloaded 678 times
  • Download rankings, all-time:
    • Site-wide: 20,951 out of 89,568
    • In bioinformatics: 3,029 out of 8,443
  • Year to date:
    • Site-wide: 42,294 out of 89,568
  • Since beginning of last month:
    • Site-wide: 25,968 out of 89,568

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

genomics more details view paper
  • Downloaded 607 times
  • Download rankings, all-time:
    • Site-wide: 24,542 out of 89,568
    • In genomics: 2,686 out of 5,703
  • Year to date:
    • Site-wide: 85,147 out of 89,568
  • Since beginning of last month:
    • Site-wide: 84,309 out of 89,568

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

evolutionary biology more details view paper
  • Downloaded 492 times
  • Download rankings, all-time:
    • Site-wide: 32,074 out of 89,568
    • In evolutionary biology: 2,175 out of 5,474
  • Year to date:
    • Site-wide: 29,791 out of 89,568
  • Since beginning of last month:
    • Site-wide: 38,115 out of 89,568

Modelling haplotypes with respect to reference cohort variation graphs

genomics more details view paper
  • Downloaded 466 times
  • Download rankings, all-time:
    • Site-wide: 34,305 out of 89,568
    • In genomics: 3,337 out of 5,703
  • Year to date:
    • Site-wide: 76,132 out of 89,568
  • Since beginning of last month:
    • Site-wide: 75,499 out of 89,568

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

bioinformatics more details view paper
  • Downloaded 464 times
  • Download rankings, all-time:
    • Site-wide: 34,479 out of 89,568
    • In bioinformatics: 4,334 out of 8,443
  • Year to date:
    • Site-wide: 38,474 out of 89,568
  • Since beginning of last month:
    • Site-wide: 54,100 out of 89,568

Describing the Local Structure of Sequence Graphs

bioinformatics more details view paper
  • Downloaded 433 times
  • Download rankings, all-time:
    • Site-wide: 37,400 out of 89,568
    • In bioinformatics: 4,597 out of 8,443
  • Year to date:
    • Site-wide: 82,406 out of 89,568
  • Since beginning of last month:
    • Site-wide: 80,837 out of 89,568

Succinct dynamic variation graphs

bioinformatics more details view paper
  • Downloaded 423 times
  • Download rankings, all-time:
    • Site-wide: 38,364 out of 89,568
    • In bioinformatics: 4,691 out of 8,443
  • Year to date:
    • Site-wide: 5,279 out of 89,568
  • Since beginning of last month:
    • Site-wide: 22,319 out of 89,568

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

genomics more details view paper
  • Downloaded 400 times
  • Download rankings, all-time:
    • Site-wide: 40,778 out of 89,568
    • In genomics: 3,731 out of 5,703
  • Year to date:
    • Site-wide: 5,783 out of 89,568
  • Since beginning of last month:
    • Site-wide: 793 out of 89,568

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

bioinformatics more details view paper
  • Downloaded 344 times
  • Download rankings, all-time:
    • Site-wide: 47,352 out of 89,568
    • In bioinformatics: 5,458 out of 8,443
  • Year to date:
    • Site-wide: 44,449 out of 89,568
  • Since beginning of last month:
    • Site-wide: 42,661 out of 89,568

Distance Indexing and Seed Clustering in Sequence Graphs

bioinformatics more details view paper
  • Downloaded 326 times
  • Download rankings, all-time:
    • Site-wide: 49,712 out of 89,568
    • In bioinformatics: 5,666 out of 8,443
  • Year to date:
    • Site-wide: 15,007 out of 89,568
  • Since beginning of last month:
    • Site-wide: 21,586 out of 89,568

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 280 times
  • Download rankings, all-time:
    • Site-wide: 56,325 out of 89,568
    • In genomics: 4,501 out of 5,703
  • Year to date:
    • Site-wide: 10,021 out of 89,568
  • Since beginning of last month:
    • Site-wide: 7,767 out of 89,568

PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News