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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 67,118 bioRxiv papers from 295,271 authors.

Author: Sergey Koren

  • ORCiD: http://orcid.org/0000-0002-1472-8962
  • Most recently observed institution: Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health

Rankings

  • All-time downloads: 100,003 (rank: 72 out of 295,271)
  • Categories:
    • bioinformatics: 59,595 (rank: 9 out of 25,734)
    • genetics: 366 (rank: 19,705 (tie) out of 29,454)
    • genomics: 38,346 (rank: 139 out of 33,640)
    • microbiology: 1,696 (rank: 1,623 (tie) out of 30,515)

Downloads per author, site-wide

Preprints

Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

bioinformatics more details view paper
  • Downloaded 10,932 times
  • Download rankings, all-time:
    • Site-wide: 100 out of 67,118
    • In bioinformatics: 17 out of 6,625
  • Year to date:
    • Site-wide: 2,986 out of 67,118
  • Since beginning of last month:
    • Site-wide: 4,527 out of 67,118

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

genomics more details view paper
  • Downloaded 10,156 times
  • Download rankings, all-time:
    • Site-wide: 111 out of 67,118
    • In genomics: 35 out of 4,561
  • Year to date:
    • Site-wide: 21 out of 67,118
  • Since beginning of last month:
    • Site-wide: 455 out of 67,118

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

bioinformatics more details view paper
  • Downloaded 7,634 times
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    • Site-wide: 199 out of 67,118
    • In bioinformatics: 33 out of 6,625
  • Year to date:
    • Site-wide: 5,260 out of 67,118
  • Since beginning of last month:
    • Site-wide: 10,413 out of 67,118

Mash: fast genome and metagenome distance estimation using MinHash

bioinformatics more details view paper
  • Downloaded 6,388 times
  • Download rankings, all-time:
    • Site-wide: 281 out of 67,118
    • In bioinformatics: 47 out of 6,625
  • Year to date:
    • Site-wide: 15,447 out of 67,118
  • Since beginning of last month:
    • Site-wide: 32,243 out of 67,118

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

bioinformatics more details view paper
  • Downloaded 6,221 times
  • Download rankings, all-time:
    • Site-wide: 295 out of 67,118
    • In bioinformatics: 48 out of 6,625
  • Year to date:
    • Site-wide: 4,450 out of 67,118
  • Since beginning of last month:
    • Site-wide: 11,806 out of 67,118

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

bioinformatics more details view paper
  • Downloaded 6,116 times
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    • Site-wide: 311 out of 67,118
    • In bioinformatics: 55 out of 6,625
  • Year to date:
    • Site-wide: 329 out of 67,118
  • Since beginning of last month:
    • Site-wide: 2,727 out of 67,118

Complete assembly of parental haplotypes with trio binning

genomics more details view paper
  • Downloaded 5,360 times
  • Download rankings, all-time:
    • Site-wide: 388 out of 67,118
    • In genomics: 100 out of 4,561
  • Year to date:
    • Site-wide: 701 out of 67,118
  • Since beginning of last month:
    • Site-wide: 1,578 out of 67,118

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

bioinformatics more details view paper
  • Downloaded 5,000 times
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    • Site-wide: 433 out of 67,118
    • In bioinformatics: 85 out of 6,625
  • Year to date:
    • Site-wide: 94 out of 67,118
  • Since beginning of last month:
    • Site-wide: 149 out of 67,118

A fast approximate algorithm for mapping long reads to large reference databases

bioinformatics more details view paper
  • Downloaded 3,797 times
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    • Site-wide: 759 out of 67,118
    • In bioinformatics: 149 out of 6,625
  • Year to date:
    • Site-wide: 4,387 out of 67,118
  • Since beginning of last month:
    • Site-wide: 6,264 out of 67,118

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

bioinformatics more details view paper
  • Downloaded 3,326 times
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    • Site-wide: 961 out of 67,118
    • In bioinformatics: 189 out of 6,625
  • Year to date:
    • Site-wide: 194 out of 67,118
  • Since beginning of last month:
    • Site-wide: 357 out of 67,118

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

genomics more details view paper
  • Downloaded 3,128 times
  • Download rankings, all-time:
    • Site-wide: 1,091 out of 67,118
    • In genomics: 260 out of 4,561
  • Year to date:
    • Site-wide: 4,355 out of 67,118
  • Since beginning of last month:
    • Site-wide: 8,032 out of 67,118

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

genomics more details view paper
  • Downloaded 3,080 times
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    • Site-wide: 1,123 out of 67,118
    • In genomics: 263 out of 4,561
  • Year to date:
    • Site-wide: 27,283 out of 67,118
  • Since beginning of last month:
    • Site-wide: 28,372 out of 67,118

A robust benchmark for germline structural variant detection

genomics more details view paper
  • Downloaded 2,957 times
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    • Site-wide: 1,212 out of 67,118
    • In genomics: 282 out of 4,561
  • Year to date:
    • Site-wide: 245 out of 67,118
  • Since beginning of last month:
    • Site-wide: 345 out of 67,118

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

genomics more details view paper
  • Downloaded 2,900 times
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    • Site-wide: 1,260 out of 67,118
    • In genomics: 290 out of 4,561
  • Year to date:
    • Site-wide: 1,143 out of 67,118
  • Since beginning of last month:
    • Site-wide: 1,894 out of 67,118

Automated ensemble assembly and validation of microbial genomes

bioinformatics more details view paper
  • Downloaded 1,912 times
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    • Site-wide: 2,625 out of 67,118
    • In bioinformatics: 524 out of 6,625
  • Year to date:
    • Site-wide: 64,543 out of 67,118
  • Since beginning of last month:
    • Site-wide: 63,069 out of 67,118

A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps

bioinformatics more details view paper
  • Downloaded 1,843 times
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    • Site-wide: 2,782 out of 67,118
    • In bioinformatics: 556 out of 6,625
  • Year to date:
    • Site-wide: 9,678 out of 67,118
  • Since beginning of last month:
    • Site-wide: 33,032 out of 67,118

De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

genomics more details view paper
  • Downloaded 1,742 times
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    • Site-wide: 3,066 out of 67,118
    • In genomics: 600 out of 4,561
  • Year to date:
    • Site-wide: 4,506 out of 67,118
  • Since beginning of last month:
    • Site-wide: 30,957 out of 67,118

De novo long-read assembly of a complex animal genome

genomics more details view paper
  • Downloaded 1,509 times
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    • Site-wide: 3,914 out of 67,118
    • In genomics: 716 out of 4,561
  • Year to date:
    • Site-wide: 44,430 out of 67,118
  • Since beginning of last month:
    • Site-wide: 34,162 out of 67,118

Mash Screen: High-throughput sequence containment estimation for genome discovery

bioinformatics more details view paper
  • Downloaded 1,470 times
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    • Site-wide: 4,102 out of 67,118
    • In bioinformatics: 810 out of 6,625
  • Year to date:
    • Site-wide: 968 out of 67,118
  • Since beginning of last month:
    • Site-wide: 3,291 out of 67,118

Scaffolding of long read assemblies using long range contact information

genomics more details view paper
  • Downloaded 1,361 times
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    • Site-wide: 4,653 out of 67,118
    • In genomics: 829 out of 4,561
  • Year to date:
    • Site-wide: 48,008 out of 67,118
  • Since beginning of last month:
    • Site-wide: 60,105 out of 67,118

MetaMaps - Strain-level metagenomic assignment and compositional estimation for long reads

bioinformatics more details view paper
  • Downloaded 1,346 times
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    • Site-wide: 4,732 out of 67,118
    • In bioinformatics: 916 out of 6,625
  • Year to date:
    • Site-wide: 8,302 out of 67,118
  • Since beginning of last month:
    • Site-wide: 18,503 out of 67,118

RefSeq database growth influences the accuracy of k-mer-based species identification

bioinformatics more details view paper
  • Downloaded 1,318 times
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    • Site-wide: 4,900 out of 67,118
    • In bioinformatics: 949 out of 6,625
  • Year to date:
    • Site-wide: 25,941 out of 67,118
  • Since beginning of last month:
    • Site-wide: 52,695 out of 67,118

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

genomics more details view paper
  • Downloaded 1,183 times
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    • Site-wide: 5,859 out of 67,118
    • In genomics: 988 out of 4,561
  • Year to date:
    • Site-wide: 29,975 out of 67,118
  • Since beginning of last month:
    • Site-wide: 25,563 out of 67,118

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

microbiology more details view paper
  • Downloaded 1,061 times
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    • Site-wide: 7,035 out of 67,118
    • In microbiology: 281 out of 5,414
  • Year to date:
    • Site-wide: 3,875 out of 67,118
  • Since beginning of last month:
    • Site-wide: 54,160 out of 67,118

MetaCompass: Reference-guided Assembly of Metagenomes

bioinformatics more details view paper
  • Downloaded 911 times
  • Download rankings, all-time:
    • Site-wide: 8,981 out of 67,118
    • In bioinformatics: 1,574 out of 6,625
  • Year to date:
    • Site-wide: 16,921 out of 67,118
  • Since beginning of last month:
    • Site-wide: 14,499 out of 67,118

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

genomics more details view paper
  • Downloaded 810 times
  • Download rankings, all-time:
    • Site-wide: 10,771 out of 67,118
    • In genomics: 1,567 out of 4,561
  • Year to date:
    • Site-wide: 6,440 out of 67,118
  • Since beginning of last month:
    • Site-wide: 8,129 out of 67,118

An improved pig reference genome sequence to enable pig genetics and genomics research

genomics more details view paper
  • Downloaded 798 times
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    • Site-wide: 10,994 out of 67,118
    • In genomics: 1,590 out of 4,561
  • Year to date:
    • Site-wide: 2,864 out of 67,118
  • Since beginning of last month:
    • Site-wide: 3,318 out of 67,118

The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research

genomics more details view paper
  • Downloaded 764 times
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    • Site-wide: 11,752 out of 67,118
    • In genomics: 1,668 out of 4,561
  • Year to date:
    • Site-wide: 3,112 out of 67,118
  • Since beginning of last month:
    • Site-wide: 4,922 out of 67,118

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation

genomics more details view paper
  • Downloaded 749 times
  • Download rankings, all-time:
    • Site-wide: 12,114 out of 67,118
    • In genomics: 1,702 out of 4,561
  • Year to date:
    • Site-wide: 50,392 out of 67,118
  • Since beginning of last month:
    • Site-wide: 51,883 out of 67,118

The whale shark genome reveals patterns of vertebrate gene family evolution

genomics more details view paper
  • Downloaded 749 times
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    • Site-wide: 12,105 out of 67,118
    • In genomics: 1,700 out of 4,561
  • Year to date:
    • Site-wide: 3,224 out of 67,118
  • Since beginning of last month:
    • Site-wide: 5,965 out of 67,118

Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen

microbiology more details view paper
  • Downloaded 635 times
  • Download rankings, all-time:
    • Site-wide: 15,293 out of 67,118
    • In microbiology: 764 out of 5,414
  • Year to date:
    • Site-wide: 29,730 out of 67,118
  • Since beginning of last month:
    • Site-wide: 50,770 out of 67,118

HLA*PRG:LA - HLA typing from linearly projected graph alignments

bioinformatics more details view paper
  • Downloaded 597 times
  • Download rankings, all-time:
    • Site-wide: 16,657 out of 67,118
    • In bioinformatics: 2,569 out of 6,625
  • Year to date:
    • Site-wide: 14,948 out of 67,118
  • Since beginning of last month:
    • Site-wide: 25,788 out of 67,118

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

genomics more details view paper
  • Downloaded 486 times
  • Download rankings, all-time:
    • Site-wide: 21,743 out of 67,118
    • In genomics: 2,459 out of 4,561
  • Year to date:
    • Site-wide: 6,682 out of 67,118
  • Since beginning of last month:
    • Site-wide: 8,297 out of 67,118

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

bioinformatics more details view paper
  • Downloaded 477 times
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    • Site-wide: 22,316 out of 67,118
    • In bioinformatics: 3,192 out of 6,625
  • Year to date:
    • Site-wide: 12,783 out of 67,118
  • Since beginning of last month:
    • Site-wide: 30,377 out of 67,118

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

genetics more details view paper
  • Downloaded 366 times
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    • Site-wide: 29,978 out of 67,118
    • In genetics: 1,904 out of 3,775
  • Year to date:
    • Site-wide: 55,134 out of 67,118
  • Since beginning of last month:
    • Site-wide: 21,040 out of 67,118

Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

genomics more details view paper
  • Downloaded 331 times
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    • Site-wide: 33,084 out of 67,118
    • In genomics: 3,178 out of 4,561
  • Year to date:
    • Site-wide: 12,588 out of 67,118
  • Since beginning of last month:
    • Site-wide: 342 out of 67,118

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

bioinformatics more details view paper
  • Downloaded 307 times
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    • Site-wide: 35,428 out of 67,118
    • In bioinformatics: 4,390 out of 6,625
  • Year to date:
    • Site-wide: 14,093 out of 67,118
  • Since beginning of last month:
    • Site-wide: 8,561 out of 67,118

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

genomics more details view paper
  • Downloaded 283 times
  • Download rankings, all-time:
    • Site-wide: 37,905 out of 67,118
    • In genomics: 3,413 out of 4,561
  • Year to date:
    • Site-wide: 15,808 out of 67,118
  • Since beginning of last month:
    • Site-wide: 14,744 out of 67,118

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