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Author: Sergey Koren

Rankings

  • All-time downloads: 202,530 (rank: 396 )
  • Categories:
    • bioinformatics: 83,688 (rank: 9 )
    • genetics: 481 (rank: 28,989 (tie) )
    • genomics: 116,246 (rank: 36 )
    • microbiology: 2,115 (rank: 8,107 (tie) )

Downloads per author, site-wide

Preprints

The complete sequence of a human genome

genomics more details view paper
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    • Site-wide: 199
    • In genomics: 7
  • Year to date:
    • Site-wide: 58
  • Since beginning of last month:
    • Site-wide: 108

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

genomics more details view paper
  • Downloaded 13,466 times
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    • Site-wide: 705
    • In genomics: 41
  • Year to date:
    • Site-wide: 5,341
  • Since beginning of last month:
    • Site-wide: 9,408

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

bioinformatics more details view paper
  • Downloaded 11,987 times
  • Download rankings, all-time:
    • Site-wide: 826
    • In bioinformatics: 32
  • Year to date:
    • Site-wide: 20,435
  • Since beginning of last month:
    • Site-wide: 25,779

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

bioinformatics more details view paper
  • Downloaded 9,216 times
  • Download rankings, all-time:
    • Site-wide: 1,154
    • In bioinformatics: 58
  • Year to date:
    • Site-wide: 5,678
  • Since beginning of last month:
    • Site-wide: 9,411

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

bioinformatics more details view paper
  • Downloaded 8,551 times
  • Download rankings, all-time:
    • Site-wide: 1,271
    • In bioinformatics: 68
  • Year to date:
    • Site-wide: 29,088
  • Since beginning of last month:
    • Site-wide: 74,748

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

bioinformatics more details view paper
  • Downloaded 6,944 times
  • Download rankings, all-time:
    • Site-wide: 1,628
    • In bioinformatics: 93
  • Year to date:
    • Site-wide: 25,663
  • Since beginning of last month:
    • Site-wide: 31,534

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 6,833 times
  • Download rankings, all-time:
    • Site-wide: 1,671
    • In bioinformatics: 95
  • Year to date:
    • Site-wide: 41,851
  • Since beginning of last month:
    • Site-wide: 55,022

Mash: fast genome and metagenome distance estimation using MinHash

bioinformatics more details view paper
  • Downloaded 6,779 times
  • Download rankings, all-time:
    • Site-wide: 1,694
    • In bioinformatics: 99
  • Year to date:
    • Site-wide: 48,778
  • Since beginning of last month:
    • Site-wide: 74,591

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

bioinformatics more details view paper
  • Downloaded 6,673 times
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    • Site-wide: 1,728
    • In bioinformatics: 104
  • Year to date:
    • Site-wide: 12,639
  • Since beginning of last month:
    • Site-wide: 31,711

Complete assembly of parental haplotypes with trio binning

genomics more details view paper
  • Downloaded 6,441 times
  • Download rankings, all-time:
    • Site-wide: 1,816
    • In genomics: 146
  • Year to date:
    • Site-wide: 20,138
  • Since beginning of last month:
    • Site-wide: 19,592

A robust benchmark for germline structural variant detection

genomics more details view paper
  • Downloaded 6,313 times
  • Download rankings, all-time:
    • Site-wide: 1,871
    • In genomics: 149
  • Year to date:
    • Site-wide: 5,614
  • Since beginning of last month:
    • Site-wide: 9,562

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

genomics more details view paper
  • Downloaded 5,903 times
  • Download rankings, all-time:
    • Site-wide: 2,038
    • In genomics: 168
  • Year to date:
    • Site-wide: 1,989
  • Since beginning of last month:
    • Site-wide: 12,375

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

genomics more details view paper
  • Downloaded 4,739 times
  • Download rankings, all-time:
    • Site-wide: 2,762
    • In genomics: 268
  • Year to date:
    • Site-wide: 11,826
  • Since beginning of last month:
    • Site-wide: 26,733

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

bioinformatics more details view paper
  • Downloaded 4,706 times
  • Download rankings, all-time:
    • Site-wide: 2,784
    • In bioinformatics: 217
  • Year to date:
    • Site-wide: 21,904
  • Since beginning of last month:
    • Site-wide: 38,302

The structure, function, and evolution of a complete human chromosome 8

genomics more details view paper
  • Downloaded 3,951 times
  • Download rankings, all-time:
    • Site-wide: 3,562
    • In genomics: 361
  • Year to date:
    • Site-wide: 2,611
  • Since beginning of last month:
    • Site-wide: 20,916

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

genomics more details view paper
  • Downloaded 3,710 times
  • Download rankings, all-time:
    • Site-wide: 3,874
    • In genomics: 386
  • Year to date:
    • Site-wide: 56,270
  • Since beginning of last month:
    • Site-wide: 45,707

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

bioinformatics more details view paper
  • Downloaded 3,594 times
  • Download rankings, all-time:
    • Site-wide: 4,048
    • In bioinformatics: 370
  • Year to date:
    • Site-wide: 8,869
  • Since beginning of last month:
    • Site-wide: 18,412

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

genomics more details view paper
  • Downloaded 3,406 times
  • Download rankings, all-time:
    • Site-wide: 4,365
    • In genomics: 437
  • Year to date:
    • Site-wide: 69,479
  • Since beginning of last month:
    • Site-wide: 88,617

Epigenetic Patterns in a Complete Human Genome

genomics more details view paper
  • Downloaded 3,025 times
  • Download rankings, all-time:
    • Site-wide: 5,161
    • In genomics: 514
  • Year to date:
    • Site-wide: 989
  • Since beginning of last month:
    • Site-wide: 1,321

A complete reference genome improves analysis of human genetic variation

genomics more details view paper
  • Downloaded 2,920 times
  • Download rankings, all-time:
    • Site-wide: 5,438
    • In genomics: 544
  • Year to date:
    • Site-wide: 1,032
  • Since beginning of last month:
    • Site-wide: 746

A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps

bioinformatics more details view paper
  • Downloaded 2,274 times
  • Download rankings, all-time:
    • Site-wide: 7,840
    • In bioinformatics: 868
  • Year to date:
    • Site-wide: 67,877
  • Since beginning of last month:
    • Site-wide: 131,415

Automated ensemble assembly and validation of microbial genomes

bioinformatics more details view paper
  • Downloaded 2,060 times
  • Download rankings, all-time:
    • Site-wide: 9,026
    • In bioinformatics: 1,004
  • Year to date:
    • Site-wide: 138,644
  • Since beginning of last month:
    • Site-wide: 139,335

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

genomics more details view paper
  • Downloaded 2,057 times
  • Download rankings, all-time:
    • Site-wide: 9,044
    • In genomics: 908
  • Year to date:
    • Site-wide: 99,476
  • Since beginning of last month:
    • Site-wide: 140,053

The whale shark genome reveals patterns of vertebrate gene family evolution

genomics more details view paper
  • Downloaded 1,976 times
  • Download rankings, all-time:
    • Site-wide: 9,584
    • In genomics: 954
  • Year to date:
    • Site-wide: 11,580
  • Since beginning of last month:
    • Site-wide: 15,794

A long read mapping method for highly repetitive reference sequences

bioinformatics more details view paper
  • Downloaded 1,923 times
  • Download rankings, all-time:
    • Site-wide: 9,980
    • In bioinformatics: 1,145
  • Year to date:
    • Site-wide: 3,273
  • Since beginning of last month:
    • Site-wide: 9,031

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

genomics more details view paper
  • Downloaded 1,783 times
  • Download rankings, all-time:
    • Site-wide: 11,184
    • In genomics: 1,121
  • Year to date:
    • Site-wide: 36,646
  • Since beginning of last month:
    • Site-wide: 75,737

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

genomics more details view paper
  • Downloaded 1,767 times
  • Download rankings, all-time:
    • Site-wide: 11,340
    • In genomics: 1,131
  • Year to date:
    • Site-wide: 20,544
  • Since beginning of last month:
    • Site-wide: 20,203

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

bioinformatics more details view paper
  • Downloaded 1,726 times
  • Download rankings, all-time:
    • Site-wide: 11,727
    • In bioinformatics: 1,324
  • Year to date:
    • Site-wide: 18,247
  • Since beginning of last month:
    • Site-wide: 30,832

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

bioinformatics more details view paper
  • Downloaded 1,720 times
  • Download rankings, all-time:
    • Site-wide: 11,796
    • In bioinformatics: 1,336
  • Year to date:
    • Site-wide: 121,495
  • Since beginning of last month:
    • Site-wide: 131,195

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

bioinformatics more details view paper
  • Downloaded 1,706 times
  • Download rankings, all-time:
    • Site-wide: 11,929
    • In bioinformatics: 1,349
  • Year to date:
    • Site-wide: 92,498
  • Since beginning of last month:
    • Site-wide: 111,639

Segmental duplications and their variation in a complete human genome

genomics more details view paper
  • Downloaded 1,673 times
  • Download rankings, all-time:
    • Site-wide: 12,280
    • In genomics: 1,239
  • Year to date:
    • Site-wide: 2,111
  • Since beginning of last month:
    • Site-wide: 2,877

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

genomics more details view paper
  • Downloaded 1,663 times
  • Download rankings, all-time:
    • Site-wide: 12,391
    • In genomics: 1,254
  • Year to date:
    • Site-wide: 49,200
  • Since beginning of last month:
    • Site-wide: 68,653

De novo long-read assembly of a complex animal genome

genomics more details view paper
  • Downloaded 1,613 times
  • Download rankings, all-time:
    • Site-wide: 12,952
    • In genomics: 1,304
  • Year to date:
    • Site-wide: 151,196
  • Since beginning of last month:
    • Site-wide: 140,651

Complete genomic and epigenetic maps of human centromeres

genomics more details view paper
  • Downloaded 1,604 times
  • Download rankings, all-time:
    • Site-wide: 13,055
    • In genomics: 1,312
  • Year to date:
    • Site-wide: 2,238
  • Since beginning of last month:
    • Site-wide: 1,213

Scaffolding of long read assemblies using long range contact information

genomics more details view paper
  • Downloaded 1,545 times
  • Download rankings, all-time:
    • Site-wide: 13,755
    • In genomics: 1,385
  • Year to date:
    • Site-wide: 116,863
  • Since beginning of last month:
    • Site-wide: 145,930

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

bioinformatics more details view paper
  • Downloaded 1,531 times
  • Download rankings, all-time:
    • Site-wide: 13,963
    • In bioinformatics: 1,582
  • Year to date:
    • Site-wide: 116,321
  • Since beginning of last month:
    • Site-wide: 129,665

MetaCompass: Reference-guided Assembly of Metagenomes

bioinformatics more details view paper
  • Downloaded 1,493 times
  • Download rankings, all-time:
    • Site-wide: 14,551
    • In bioinformatics: 1,648
  • Year to date:
    • Site-wide: 40,440
  • Since beginning of last month:
    • Site-wide: 24,834

Weighted minimizer sampling improves long read mapping

bioinformatics more details view paper
  • Downloaded 1,450 times
  • Download rankings, all-time:
    • Site-wide: 15,232
    • In bioinformatics: 1,728
  • Year to date:
    • Site-wide: 32,538
  • Since beginning of last month:
    • Site-wide: 61,214

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

genomics more details view paper
  • Downloaded 1,345 times
  • Download rankings, all-time:
    • Site-wide: 17,073
    • In genomics: 1,653
  • Year to date:
    • Site-wide: 33,343
  • Since beginning of last month:
    • Site-wide: 68,643

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 1,218 times
  • Download rankings, all-time:
    • Site-wide: 19,769
    • In microbiology: 1,155
  • Year to date:
    • Site-wide: 141,791
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    • Site-wide: 156,051

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

genomics more details view paper
  • Downloaded 1,129 times
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    • Site-wide: 22,135
    • In genomics: 2,075
  • Year to date:
    • Site-wide: 89,903
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    • Site-wide: 80,727

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

genomics more details view paper
  • Downloaded 1,101 times
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    • Site-wide: 22,960
    • In genomics: 2,153
  • Year to date:
    • Site-wide: 3,786
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    • Site-wide: 2,957

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

genomics more details view paper
  • Downloaded 1,023 times
  • Download rankings, all-time:
    • Site-wide: 25,650
    • In genomics: 2,348
  • Year to date:
    • Site-wide: 12,736
  • Since beginning of last month:
    • Site-wide: 26,174

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

genomics more details view paper
  • Downloaded 940 times
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    • Site-wide: 29,024
    • In genomics: 2,564
  • Year to date:
    • Site-wide: 88,534
  • Since beginning of last month:
    • Site-wide: 77,169

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

microbiology more details view paper
  • Downloaded 897 times
  • Download rankings, all-time:
    • Site-wide: 30,981
    • In microbiology: 1,826
  • Year to date:
    • Site-wide: 98,576
  • Since beginning of last month:
    • Site-wide: 147,710

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 892 times
  • Download rankings, all-time:
    • Site-wide: 31,257
    • In genomics: 2,697
  • Year to date:
    • Site-wide: 136,770
  • Since beginning of last month:
    • Site-wide: 113,773

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

bioinformatics more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 35,575
    • In bioinformatics: 3,859
  • Year to date:
    • Site-wide: 100,019
  • Since beginning of last month:
    • Site-wide: 131,141

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

bioinformatics more details view paper
  • Downloaded 665 times
  • Download rankings, all-time:
    • Site-wide: 46,982
    • In bioinformatics: 4,868
  • Year to date:
    • Site-wide: 93,645
  • Since beginning of last month:
    • Site-wide: 104,941

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

bioinformatics more details view paper
  • Downloaded 624 times
  • Download rankings, all-time:
    • Site-wide: 51,096
    • In bioinformatics: 5,172
  • Year to date:
    • Site-wide: 142,566
  • Since beginning of last month:
    • Site-wide: 153,328

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

genomics more details view paper
  • Downloaded 567 times
  • Download rankings, all-time:
    • Site-wide: 57,598
    • In genomics: 4,255
  • Year to date:
    • Site-wide: 84,664
  • Since beginning of last month:
    • Site-wide: 104,951

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

genomics more details view paper
  • Downloaded 551 times
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    • Site-wide: 59,561
    • In genomics: 4,360
  • Year to date:
    • Site-wide: 25,455
  • Since beginning of last month:
    • Site-wide: 27,050

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 481 times
  • Download rankings, all-time:
    • Site-wide: 69,640
    • In genetics: 3,010
  • Year to date:
    • Site-wide: 157,245
  • Since beginning of last month:
    • Site-wide: 145,936

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

bioinformatics more details view paper
  • Downloaded 419 times
  • Download rankings, all-time:
    • Site-wide: 80,476
    • In bioinformatics: 7,349
  • Year to date:
    • Site-wide: 16,088
  • Since beginning of last month:
    • Site-wide: 10,376

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