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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,553 bioRxiv papers from 264,961 authors.

Author: Benedict Paten

Rankings

  • All-time downloads: 66,618 (rank: 163 out of 264,961)
  • Categories:
    • bioinformatics: 30,836 (rank: 52 out of 23,134)
    • evolutionary biology: 278 (rank: 10,133 (tie) out of 14,397)
    • genomics: 35,504 (rank: 140 out of 30,302)

Downloads per author, site-wide

Preprints

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

genomics more details view paper

No bioRxiv download data for this paper yet.

Nanopore sequencing and assembly of a human genome with ultra-long reads

genomics more details view paper
  • Downloaded 12,838 times
  • Download rankings, all-time:
    • Site-wide: 59 out of 57,553
    • In genomics: 17 out of 4,033
  • Year to date:
    • Site-wide: 3,650 out of 57,553
  • Since beginning of last month:
    • Site-wide: 5,910 out of 57,553

Genome Graphs

bioinformatics more details view paper
  • Downloaded 7,415 times
  • Download rankings, all-time:
    • Site-wide: 170 out of 57,553
    • In bioinformatics: 31 out of 5,869
  • Year to date:
    • Site-wide: 882 out of 57,553
  • Since beginning of last month:
    • Site-wide: 1,663 out of 57,553

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

genomics more details view paper
  • Downloaded 6,017 times
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    • Site-wide: 260 out of 57,553
    • In genomics: 77 out of 4,033
  • Year to date:
    • Site-wide: 155 out of 57,553
  • Since beginning of last month:
    • Site-wide: 299 out of 57,553

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

bioinformatics more details view paper
  • Downloaded 5,611 times
  • Download rankings, all-time:
    • Site-wide: 307 out of 57,553
    • In bioinformatics: 58 out of 5,869
  • Year to date:
    • Site-wide: 3,158 out of 57,553
  • Since beginning of last month:
    • Site-wide: 3,518 out of 57,553

Computational Pan-Genomics: Status, Promises and Challenges

genomics more details view paper
  • Downloaded 3,996 times
  • Download rankings, all-time:
    • Site-wide: 572 out of 57,553
    • In genomics: 153 out of 4,033
  • Year to date:
    • Site-wide: 9,989 out of 57,553
  • Since beginning of last month:
    • Site-wide: 10,337 out of 57,553

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

genomics more details view paper
  • Downloaded 3,365 times
  • Download rankings, all-time:
    • Site-wide: 808 out of 57,553
    • In genomics: 210 out of 4,033
  • Year to date:
    • Site-wide: 5,295 out of 57,553
  • Since beginning of last month:
    • Site-wide: 11,239 out of 57,553

Alignathon: A competitive assessment of whole genome alignment methods.

bioinformatics more details view paper
  • Downloaded 3,071 times
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    • In bioinformatics: 193 out of 5,869
  • Year to date:
    • Site-wide: 19,536 out of 57,553
  • Since beginning of last month:
    • Site-wide: 23,013 out of 57,553

Linear Assembly of a Human Y Centromere

genomics more details view paper
  • Downloaded 2,481 times
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    • In genomics: 328 out of 4,033
  • Year to date:
    • Site-wide: 25,981 out of 57,553
  • Since beginning of last month:
    • Site-wide: 24,976 out of 57,553

Haplotype-aware genotyping from noisy long reads

bioinformatics more details view paper
  • Downloaded 2,286 times
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    • Site-wide: 1,626 out of 57,553
    • In bioinformatics: 327 out of 5,869
  • Year to date:
    • Site-wide: 1,656 out of 57,553
  • Since beginning of last month:
    • Site-wide: 3,422 out of 57,553

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

bioinformatics more details view paper
  • Downloaded 1,929 times
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    • Site-wide: 2,181 out of 57,553
    • In bioinformatics: 449 out of 5,869
  • Year to date:
    • Site-wide: 302 out of 57,553
  • Since beginning of last month:
    • Site-wide: 21 out of 57,553

Cytosine Variant Calling with High-throughput Nanopore Sequencing

genomics more details view paper
  • Downloaded 1,919 times
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    • Site-wide: 2,201 out of 57,553
    • In genomics: 471 out of 4,033
  • Year to date:
    • Site-wide: 33,085 out of 57,553
  • Since beginning of last month:
    • Site-wide: 29,848 out of 57,553

Chromosome assembly of large and complex genomes using multiple references

bioinformatics more details view paper
  • Downloaded 1,580 times
  • Download rankings, all-time:
    • Site-wide: 3,061 out of 57,553
    • In bioinformatics: 623 out of 5,869
  • Year to date:
    • Site-wide: 32,734 out of 57,553
  • Since beginning of last month:
    • Site-wide: 23,796 out of 57,553

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

bioinformatics more details view paper
  • Downloaded 1,435 times
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    • Site-wide: 3,590 out of 57,553
    • In bioinformatics: 720 out of 5,869
  • Year to date:
    • Site-wide: 5,128 out of 57,553
  • Since beginning of last month:
    • Site-wide: 13,391 out of 57,553

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

bioinformatics more details view paper
  • Downloaded 1,330 times
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    • Site-wide: 4,071 out of 57,553
    • In bioinformatics: 811 out of 5,869
  • Year to date:
    • Site-wide: 40,914 out of 57,553
  • Since beginning of last month:
    • Site-wide: 42,650 out of 57,553

Genome Graphs and the Evolution of Genome Inference

bioinformatics more details view paper
  • Downloaded 1,226 times
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    • Site-wide: 4,629 out of 57,553
    • In bioinformatics: 922 out of 5,869
  • Year to date:
    • Site-wide: 42,157 out of 57,553
  • Since beginning of last month:
    • Site-wide: 35,415 out of 57,553

The UCSC Genome Browser database: 2016 update

genomics more details view paper
  • Downloaded 1,217 times
  • Download rankings, all-time:
    • Site-wide: 4,689 out of 57,553
    • In genomics: 829 out of 4,033
  • Year to date:
    • Site-wide: 54,309 out of 57,553
  • Since beginning of last month:
    • Site-wide: 45,830 out of 57,553

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

genomics more details view paper
  • Downloaded 1,120 times
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    • Site-wide: 5,366 out of 57,553
    • In genomics: 920 out of 4,033
  • Year to date:
    • Site-wide: 10,401 out of 57,553
  • Since beginning of last month:
    • Site-wide: 10,104 out of 57,553

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

genomics more details view paper
  • Downloaded 1,006 times
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    • Site-wide: 6,424 out of 57,553
    • In genomics: 1,066 out of 4,033
  • Year to date:
    • Site-wide: 49,926 out of 57,553
  • Since beginning of last month:
    • Site-wide: 40,952 out of 57,553

Superbubbles, Ultrabubbles and Cacti

bioinformatics more details view paper
  • Downloaded 928 times
  • Download rankings, all-time:
    • Site-wide: 7,305 out of 57,553
    • In bioinformatics: 1,320 out of 5,869
  • Year to date:
    • Site-wide: 27,757 out of 57,553
  • Since beginning of last month:
    • Site-wide: 36,204 out of 57,553

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

bioinformatics more details view paper
  • Downloaded 925 times
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    • Site-wide: 7,350 out of 57,553
    • In bioinformatics: 1,324 out of 5,869
  • Year to date:
    • Site-wide: 1,229 out of 57,553
  • Since beginning of last month:
    • Site-wide: 80 out of 57,553

A Flow Procedure for the Linearization of Genome Sequence Graphs.

bioinformatics more details view paper
  • Downloaded 857 times
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    • Site-wide: 8,255 out of 57,553
    • In bioinformatics: 1,469 out of 5,869
  • Year to date:
    • Site-wide: 36,053 out of 57,553
  • Since beginning of last month:
    • Site-wide: 44,214 out of 57,553

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

genomics more details view paper
  • Downloaded 611 times
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    • Site-wide: 13,430 out of 57,553
    • In genomics: 1,798 out of 4,033
  • Year to date:
    • Site-wide: 2,528 out of 57,553
  • Since beginning of last month:
    • Site-wide: 6,664 out of 57,553

Genotyping structural variants in pangenome graphs using the vg toolkit

bioinformatics more details view paper
  • Downloaded 578 times
  • Download rankings, all-time:
    • Site-wide: 14,522 out of 57,553
    • In bioinformatics: 2,335 out of 5,869
  • Year to date:
    • Site-wide: 2,801 out of 57,553
  • Since beginning of last month:
    • Site-wide: 1,227 out of 57,553

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

genomics more details view paper
  • Downloaded 544 times
  • Download rankings, all-time:
    • Site-wide: 15,747 out of 57,553
    • In genomics: 2,005 out of 4,033
  • Year to date:
    • Site-wide: 46,510 out of 57,553
  • Since beginning of last month:
    • Site-wide: 48,425 out of 57,553

Haplotype-aware graph indexes

bioinformatics more details view paper
  • Downloaded 495 times
  • Download rankings, all-time:
    • Site-wide: 17,734 out of 57,553
    • In bioinformatics: 2,689 out of 5,869
  • Year to date:
    • Site-wide: 3,660 out of 57,553
  • Since beginning of last month:
    • Site-wide: 11,211 out of 57,553

Modelling haplotypes with respect to reference cohort variation graphs

genomics more details view paper
  • Downloaded 390 times
  • Download rankings, all-time:
    • Site-wide: 23,181 out of 57,553
    • In genomics: 2,526 out of 4,033
  • Year to date:
    • Site-wide: 48,733 out of 57,553
  • Since beginning of last month:
    • Site-wide: 47,629 out of 57,553

Describing the Local Structure of Sequence Graphs

bioinformatics more details view paper
  • Downloaded 375 times
  • Download rankings, all-time:
    • Site-wide: 24,185 out of 57,553
    • In bioinformatics: 3,365 out of 5,869
  • Year to date:
    • Site-wide: 54,787 out of 57,553
  • Since beginning of last month:
    • Site-wide: 52,258 out of 57,553

An average-case sublinear exact Li and Stephens forward algorithm

bioinformatics more details view paper
  • Downloaded 325 times
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    • Site-wide: 27,813 out of 57,553
    • In bioinformatics: 3,721 out of 5,869
  • Year to date:
    • Site-wide: 33,263 out of 57,553
  • Since beginning of last month:
    • Site-wide: 30,585 out of 57,553

ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

bioinformatics more details view paper
  • Downloaded 279 times
  • Download rankings, all-time:
    • Site-wide: 31,759 out of 57,553
    • In bioinformatics: 4,073 out of 5,869
  • Year to date:
    • Site-wide: 9,293 out of 57,553
  • Since beginning of last month:
    • Site-wide: 674 out of 57,553

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

evolutionary biology more details view paper
  • Downloaded 278 times
  • Download rankings, all-time:
    • Site-wide: 31,866 out of 57,553
    • In evolutionary biology: 2,453 out of 3,945
  • Year to date:
    • Site-wide: 23,376 out of 57,553
  • Since beginning of last month:
    • Site-wide: 12,974 out of 57,553

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

bioinformatics more details view paper
  • Downloaded 191 times
  • Download rankings, all-time:
    • Site-wide: 41,183 out of 57,553
    • In bioinformatics: 4,798 out of 5,869
  • Year to date:
    • Site-wide: 15,962 out of 57,553
  • Since beginning of last month:
    • Site-wide: 8,138 out of 57,553

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