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Author: Sergey Koren

Rankings

  • All-time downloads: 189,117 (rank: 375 )
  • Categories:
    • bioinformatics: 81,755 (rank: 10 )
    • genetics: 474 (rank: 27,819 (tie) )
    • genomics: 104,798 (rank: 46 )
    • microbiology: 2,090 (rank: 7,498 (tie) )

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Preprints

Merfin: improved variant filtering and polishing via k-mer validation

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The complete sequence of a human genome

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    • Site-wide: 223
    • In genomics: 10
  • Year to date:
    • Site-wide: 43
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Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

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  • Downloaded 13,235 times
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    • Site-wide: 640
    • In genomics: 40
  • Year to date:
    • Site-wide: 5,595
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Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

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  • Downloaded 11,886 times
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    • Site-wide: 744
    • In bioinformatics: 30
  • Year to date:
    • Site-wide: 20,869
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Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

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  • Downloaded 9,007 times
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    • Site-wide: 1,066
    • In bioinformatics: 58
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Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

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  • Downloaded 8,488 times
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    • Site-wide: 1,151
    • In bioinformatics: 65
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    • Site-wide: 26,408
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

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  • Downloaded 6,844 times
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    • Site-wide: 1,499
    • In bioinformatics: 93
  • Year to date:
    • Site-wide: 27,859
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    • Site-wide: 44,977

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

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  • Downloaded 6,784 times
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    • Site-wide: 1,518
    • In bioinformatics: 94
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    • Site-wide: 95,141

Mash: fast genome and metagenome distance estimation using MinHash

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  • Downloaded 6,723 times
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    • Site-wide: 1,538
    • In bioinformatics: 95
  • Year to date:
    • Site-wide: 47,988
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Telomere-to-telomere assembly of a complete human X chromosome

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  • Downloaded 6,568 times
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    • Site-wide: 1,591
    • In bioinformatics: 101
  • Year to date:
    • Site-wide: 11,615
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Complete assembly of parental haplotypes with trio binning

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  • Downloaded 6,335 times
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    • Site-wide: 1,666
    • In genomics: 140
  • Year to date:
    • Site-wide: 21,195
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    • Site-wide: 17,557

A robust benchmark for germline structural variant detection

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  • Downloaded 6,132 times
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    • Site-wide: 1,756
    • In genomics: 150
  • Year to date:
    • Site-wide: 5,322
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    • Site-wide: 4,324

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

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  • Downloaded 5,770 times
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    • Site-wide: 1,904
    • In genomics: 164
  • Year to date:
    • Site-wide: 1,516
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A fast approximate algorithm for mapping long reads to large reference databases

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  • Downloaded 4,658 times
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    • Site-wide: 2,561
    • In bioinformatics: 212
  • Year to date:
    • Site-wide: 17,417
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Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

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  • Downloaded 4,648 times
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    • Site-wide: 2,564
    • In genomics: 259
  • Year to date:
    • Site-wide: 10,279
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The structure, function, and evolution of a complete human chromosome 8

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  • Downloaded 3,819 times
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    • Site-wide: 3,404
    • In genomics: 356
  • Year to date:
    • Site-wide: 2,044
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    • Site-wide: 4,423

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

genomics more details view paper
  • Downloaded 3,674 times
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    • Site-wide: 3,591
    • In genomics: 379
  • Year to date:
    • Site-wide: 49,218
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    • Site-wide: 56,262

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

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  • Downloaded 3,445 times
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    • Site-wide: 3,915
    • In bioinformatics: 379
  • Year to date:
    • Site-wide: 8,672
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    • Site-wide: 13,686

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

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  • Downloaded 3,375 times
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    • Site-wide: 4,042
    • In genomics: 421
  • Year to date:
    • Site-wide: 60,535
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    • Site-wide: 32,732

A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps

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  • Downloaded 2,239 times
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    • Site-wide: 7,333
    • In bioinformatics: 836
  • Year to date:
    • Site-wide: 61,312
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    • Site-wide: 124,545

Epigenetic Patterns in a Complete Human Genome

genomics more details view paper
  • Downloaded 2,236 times
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    • Site-wide: 7,350
    • In genomics: 771
  • Year to date:
    • Site-wide: 995
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    • Site-wide: 720

Automated ensemble assembly and validation of microbial genomes

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  • Downloaded 2,046 times
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    • Site-wide: 8,322
    • In bioinformatics: 947
  • Year to date:
    • Site-wide: 126,091
  • Since beginning of last month:
    • Site-wide: 94,980

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

genomics more details view paper
  • Downloaded 2,031 times
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    • Site-wide: 8,428
    • In genomics: 879
  • Year to date:
    • Site-wide: 91,693
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    • Site-wide: 118,279

The whale shark genome reveals patterns of vertebrate gene family evolution

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  • Downloaded 1,794 times
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    • Site-wide: 10,154
    • In genomics: 1,052
  • Year to date:
    • Site-wide: 14,037
  • Since beginning of last month:
    • Site-wide: 18,741

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

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  • Downloaded 1,720 times
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    • Site-wide: 10,794
    • In genomics: 1,121
  • Year to date:
    • Site-wide: 35,070
  • Since beginning of last month:
    • Site-wide: 29,768

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

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  • Downloaded 1,703 times
  • Download rankings, all-time:
    • Site-wide: 10,965
    • In bioinformatics: 1,279
  • Year to date:
    • Site-wide: 108,636
  • Since beginning of last month:
    • Site-wide: 122,494

A complete reference genome improves analysis of human genetic variation

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  • Downloaded 1,685 times
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    • Site-wide: 11,130
    • In genomics: 1,155
  • Year to date:
    • Site-wide: 1,441
  • Since beginning of last month:
    • Site-wide: 100

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

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  • Downloaded 1,679 times
  • Download rankings, all-time:
    • Site-wide: 11,188
    • In bioinformatics: 1,311
  • Year to date:
    • Site-wide: 84,451
  • Since beginning of last month:
    • Site-wide: 112,075

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

genomics more details view paper
  • Downloaded 1,679 times
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    • Site-wide: 11,184
    • In genomics: 1,163
  • Year to date:
    • Site-wide: 19,595
  • Since beginning of last month:
    • Site-wide: 21,372

A long read mapping method for highly repetitive reference sequences

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  • Downloaded 1,677 times
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    • Site-wide: 11,212
    • In bioinformatics: 1,314
  • Year to date:
    • Site-wide: 3,048
  • Since beginning of last month:
    • Site-wide: 2,172

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

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  • Downloaded 1,645 times
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    • Site-wide: 11,558
    • In bioinformatics: 1,352
  • Year to date:
    • Site-wide: 16,454
  • Since beginning of last month:
    • Site-wide: 53,776

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

genomics more details view paper
  • Downloaded 1,625 times
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    • Site-wide: 11,751
    • In genomics: 1,213
  • Year to date:
    • Site-wide: 42,138
  • Since beginning of last month:
    • Site-wide: 99,811

De novo long-read assembly of a complex animal genome

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  • Downloaded 1,600 times
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    • Site-wide: 12,016
    • In genomics: 1,244
  • Year to date:
    • Site-wide: 142,322
  • Since beginning of last month:
    • Site-wide: 135,955

Scaffolding of long read assemblies using long range contact information

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  • Downloaded 1,520 times
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    • Site-wide: 12,883
    • In genomics: 1,333
  • Year to date:
    • Site-wide: 113,982
  • Since beginning of last month:
    • Site-wide: 94,535

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

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  • Downloaded 1,507 times
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    • Site-wide: 13,073
    • In bioinformatics: 1,509
  • Year to date:
    • Site-wide: 111,499
  • Since beginning of last month:
    • Site-wide: 137,229

MetaCompass: Reference-guided Assembly of Metagenomes

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  • Downloaded 1,420 times
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    • Site-wide: 14,340
    • In bioinformatics: 1,668
  • Year to date:
    • Site-wide: 43,142
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    • Site-wide: 16,563

Weighted minimizer sampling improves long read mapping

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  • Downloaded 1,410 times
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    • Site-wide: 14,477
    • In bioinformatics: 1,688
  • Year to date:
    • Site-wide: 26,291
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    • Site-wide: 22,320

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

genomics more details view paper
  • Downloaded 1,270 times
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    • Site-wide: 16,980
    • In genomics: 1,671
  • Year to date:
    • Site-wide: 33,712
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    • Site-wide: 50,187

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 1,209 times
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    • Site-wide: 18,254
    • In microbiology: 1,057
  • Year to date:
    • Site-wide: 122,522
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    • Site-wide: 93,243

Segmental duplications and their variation in a complete human genome

genomics more details view paper
  • Downloaded 1,185 times
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    • Site-wide: 18,788
    • In genomics: 1,840
  • Year to date:
    • Site-wide: 2,322
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    • Site-wide: 1,326

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

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  • Downloaded 1,090 times
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    • Site-wide: 21,258
    • In genomics: 2,047
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    • Site-wide: 93,824
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Complete genomic and epigenetic maps of human centromeres

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  • Downloaded 1,003 times
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    • Site-wide: 23,992
    • In genomics: 2,260
  • Year to date:
    • Site-wide: 2,939
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Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

genomics more details view paper
  • Downloaded 938 times
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    • Site-wide: 26,511
    • In genomics: 2,439
  • Year to date:
    • Site-wide: 10,952
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Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

genomics more details view paper
  • Downloaded 908 times
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    • Site-wide: 27,732
    • In genomics: 2,522
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    • Site-wide: 84,727
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Amycomicin: a potent and specific antibiotic discovered with a targeted interaction screen

microbiology more details view paper
  • Downloaded 881 times
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    • Site-wide: 28,953
    • In microbiology: 1,709
  • Year to date:
    • Site-wide: 81,259
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    • Site-wide: 128,489

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 877 times
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    • Site-wide: 29,131
    • In genomics: 2,606
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    • Site-wide: 125,234
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    • Site-wide: 110,349

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

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  • Downloaded 779 times
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    • Site-wide: 34,348
    • In bioinformatics: 3,768
  • Year to date:
    • Site-wide: 103,683
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    • Site-wide: 96,333

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

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  • Downloaded 648 times
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    • Site-wide: 44,041
    • In genomics: 3,536
  • Year to date:
    • Site-wide: 5,535
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    • Site-wide: 312

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

bioinformatics more details view paper
  • Downloaded 631 times
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    • Site-wide: 45,558
    • In bioinformatics: 4,760
  • Year to date:
    • Site-wide: 93,015
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    • Site-wide: 129,231

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

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  • Downloaded 616 times
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    • Site-wide: 46,922
    • In bioinformatics: 4,893
  • Year to date:
    • Site-wide: 122,539
  • Since beginning of last month:
    • Site-wide: 129,656

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

genomics more details view paper
  • Downloaded 545 times
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    • Site-wide: 54,591
    • In genomics: 4,127
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    • Site-wide: 71,621
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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 474 times
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    • Site-wide: 63,956
    • In genetics: 2,835
  • Year to date:
    • Site-wide: 145,065
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    • Site-wide: 145,911

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

genomics more details view paper
  • Downloaded 449 times
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    • Site-wide: 67,764
    • In genomics: 4,780
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