Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 60,240 bioRxiv papers from 267,843 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: 91,631 (rank: 73 out of 268,131)
  • Categories:
    • bioinformatics: 55,241 (rank: 11 out of 23,906)
    • genetics: 340 (rank: 18,781 (tie) out of 27,088)
    • genomics: 34,399 (rank: 158 out of 31,268)
    • microbiology: 1,651 (rank: 1,393 (tie) out of 27,515)

Downloads per author, site-wide

Preprints

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

bioinformatics more details view paper
  • Downloaded 10,731 times
  • Download rankings, all-time:
    • Site-wide: 91 out of 60,323
    • In bioinformatics: 16 out of 6,082
  • Year to date:
    • Site-wide: 3,375 out of 60,323
  • Since beginning of last month:
    • Site-wide: 2,801 out of 60,323

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

genomics more details view paper
  • Downloaded 9,284 times
  • Download rankings, all-time:
    • Site-wide: 118 out of 60,323
    • In genomics: 39 out of 4,185
  • Year to date:
    • Site-wide: 16 out of 60,323
  • Since beginning of last month:
    • Site-wide: 82 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 7,533 times
  • Download rankings, all-time:
    • Site-wide: 174 out of 60,323
    • In bioinformatics: 30 out of 6,082
  • Year to date:
    • Site-wide: 4,941 out of 60,323
  • Since beginning of last month:
    • Site-wide: 7,012 out of 60,323

Mash: fast genome and metagenome distance estimation using MinHash

bioinformatics more details view paper
  • Downloaded 6,326 times
  • Download rankings, all-time:
    • Site-wide: 251 out of 60,323
    • In bioinformatics: 46 out of 6,082
  • Year to date:
    • Site-wide: 15,232 out of 60,323
  • Since beginning of last month:
    • Site-wide: 9,861 out of 60,323

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 6,126 times
  • Download rankings, all-time:
    • Site-wide: 264 out of 60,323
    • In bioinformatics: 47 out of 6,082
  • Year to date:
    • Site-wide: 4,018 out of 60,323
  • Since beginning of last month:
    • Site-wide: 6,276 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 5,816 times
  • Download rankings, all-time:
    • Site-wide: 301 out of 60,323
    • In bioinformatics: 56 out of 6,082
  • Year to date:
    • Site-wide: 271 out of 60,323
  • Since beginning of last month:
    • Site-wide: 852 out of 60,323

Complete assembly of parental haplotypes with trio binning

genomics more details view paper
  • Downloaded 4,979 times
  • Download rankings, all-time:
    • Site-wide: 385 out of 60,323
    • In genomics: 102 out of 4,185
  • Year to date:
    • Site-wide: 738 out of 60,323
  • Since beginning of last month:
    • Site-wide: 1,889 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 3,663 times
  • Download rankings, all-time:
    • Site-wide: 721 out of 60,323
    • In bioinformatics: 138 out of 6,082
  • Year to date:
    • Site-wide: 4,492 out of 60,323
  • Since beginning of last month:
    • Site-wide: 6,720 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 3,245 times
  • Download rankings, all-time:
    • Site-wide: 898 out of 60,323
    • In bioinformatics: 179 out of 6,082
  • Year to date:
    • Site-wide: 133 out of 60,323
  • Since beginning of last month:
    • Site-wide: 16 out of 60,323

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

genomics more details view paper
  • Downloaded 3,052 times
  • Download rankings, all-time:
    • Site-wide: 1,003 out of 60,323
    • In genomics: 249 out of 4,185
  • Year to date:
    • Site-wide: 23,587 out of 60,323
  • Since beginning of last month:
    • Site-wide: 24,637 out of 60,323

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

genomics more details view paper
  • Downloaded 3,034 times
  • Download rankings, all-time:
    • Site-wide: 1,015 out of 60,323
    • In genomics: 250 out of 4,185
  • Year to date:
    • Site-wide: 3,891 out of 60,323
  • Since beginning of last month:
    • Site-wide: 3,850 out of 60,323

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

genomics more details view paper
  • Downloaded 2,593 times
  • Download rankings, all-time:
    • Site-wide: 1,349 out of 60,323
    • In genomics: 316 out of 4,185
  • Year to date:
    • Site-wide: 1,224 out of 60,323
  • Since beginning of last month:
    • Site-wide: 1,511 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 2,298 times
  • Download rankings, all-time:
    • Site-wide: 1,690 out of 60,323
    • In bioinformatics: 340 out of 6,082
  • Year to date:
    • Site-wide: 248 out of 60,323
  • Since beginning of last month:
    • Site-wide: 13 out of 60,323

A robust benchmark for germline structural variant detection

genomics more details view paper
  • Downloaded 2,103 times
  • Download rankings, all-time:
    • Site-wide: 1,958 out of 60,323
    • In genomics: 433 out of 4,185
  • Year to date:
    • Site-wide: 307 out of 60,323
  • Since beginning of last month:
    • Site-wide: 287 out of 60,323

Automated ensemble assembly and validation of microbial genomes

bioinformatics more details view paper
  • Downloaded 1,904 times
  • Download rankings, all-time:
    • Site-wide: 2,341 out of 60,323
    • In bioinformatics: 483 out of 6,082
  • Year to date:
    • Site-wide: 56,802 out of 60,323
  • Since beginning of last month:
    • Site-wide: 48,014 out of 60,323

A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps

bioinformatics more details view paper
  • Downloaded 1,783 times
  • Download rankings, all-time:
    • Site-wide: 2,625 out of 60,323
    • In bioinformatics: 530 out of 6,082
  • Year to date:
    • Site-wide: 8,614 out of 60,323
  • Since beginning of last month:
    • Site-wide: 17,006 out of 60,323

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

genomics more details view paper
  • Downloaded 1,697 times
  • Download rankings, all-time:
    • Site-wide: 2,859 out of 60,323
    • In genomics: 575 out of 4,185
  • Year to date:
    • Site-wide: 3,498 out of 60,323
  • Since beginning of last month:
    • Site-wide: 12,040 out of 60,323

De novo long-read assembly of a complex animal genome

genomics more details view paper
  • Downloaded 1,485 times
  • Download rankings, all-time:
    • Site-wide: 3,574 out of 60,323
    • In genomics: 672 out of 4,185
  • Year to date:
    • Site-wide: 40,257 out of 60,323
  • Since beginning of last month:
    • Site-wide: 55,440 out of 60,323

Scaffolding of long read assemblies using long range contact information

genomics more details view paper
  • Downloaded 1,350 times
  • Download rankings, all-time:
    • Site-wide: 4,190 out of 60,323
    • In genomics: 767 out of 4,185
  • Year to date:
    • Site-wide: 39,569 out of 60,323
  • Since beginning of last month:
    • Site-wide: 35,657 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 1,297 times
  • Download rankings, all-time:
    • Site-wide: 4,470 out of 60,323
    • In bioinformatics: 888 out of 6,082
  • Year to date:
    • Site-wide: 21,187 out of 60,323
  • Since beginning of last month:
    • Site-wide: 13,089 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 1,280 times
  • Download rankings, all-time:
    • Site-wide: 4,543 out of 60,323
    • In bioinformatics: 903 out of 6,082
  • Year to date:
    • Site-wide: 7,404 out of 60,323
  • Since beginning of last month:
    • Site-wide: 10,436 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 1,173 times
  • Download rankings, all-time:
    • Site-wide: 5,246 out of 60,323
    • In bioinformatics: 1,011 out of 6,082
  • Year to date:
    • Site-wide: 988 out of 60,323
  • Since beginning of last month:
    • Site-wide: 1,127 out of 60,323

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

genomics more details view paper
  • Downloaded 1,142 times
  • Download rankings, all-time:
    • Site-wide: 5,491 out of 60,323
    • In genomics: 938 out of 4,185
  • Year to date:
    • Site-wide: 28,890 out of 60,323
  • Since beginning of last month:
    • Site-wide: 17,600 out of 60,323

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 1,038 times
  • Download rankings, all-time:
    • Site-wide: 6,456 out of 60,323
    • In microbiology: 250 out of 4,833
  • Year to date:
    • Site-wide: 2,776 out of 60,323
  • Since beginning of last month:
    • Site-wide: 16,328 out of 60,323

MetaCompass: Reference-guided Assembly of Metagenomes

bioinformatics more details view paper
  • Downloaded 846 times
  • Download rankings, all-time:
    • Site-wide: 8,895 out of 60,323
    • In bioinformatics: 1,557 out of 6,082
  • Year to date:
    • Site-wide: 17,283 out of 60,323
  • Since beginning of last month:
    • Site-wide: 17,024 out of 60,323

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 734 times
  • Download rankings, all-time:
    • Site-wide: 10,979 out of 60,323
    • In genomics: 1,579 out of 4,185
  • Year to date:
    • Site-wide: 43,241 out of 60,323
  • Since beginning of last month:
    • Site-wide: 46,313 out of 60,323

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

genomics more details view paper
  • Downloaded 690 times
  • Download rankings, all-time:
    • Site-wide: 12,026 out of 60,323
    • In genomics: 1,676 out of 4,185
  • Year to date:
    • Site-wide: 6,922 out of 60,323
  • Since beginning of last month:
    • Site-wide: 12,170 out of 60,323

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

microbiology more details view paper
  • Downloaded 613 times
  • Download rankings, all-time:
    • Site-wide: 14,125 out of 60,323
    • In microbiology: 702 out of 4,833
  • Year to date:
    • Site-wide: 25,056 out of 60,323
  • Since beginning of last month:
    • Site-wide: 41,777 out of 60,323

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

genomics more details view paper
  • Downloaded 601 times
  • Download rankings, all-time:
    • Site-wide: 14,525 out of 60,323
    • In genomics: 1,901 out of 4,185
  • Year to date:
    • Site-wide: 3,189 out of 60,323
  • Since beginning of last month:
    • Site-wide: 1,344 out of 60,323

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

genomics more details view paper
  • Downloaded 568 times
  • Download rankings, all-time:
    • Site-wide: 15,672 out of 60,323
    • In genomics: 1,991 out of 4,185
  • Year to date:
    • Site-wide: 3,504 out of 60,323
  • Since beginning of last month:
    • Site-wide: 2,988 out of 60,323

The whale shark genome reveals patterns of vertebrate gene family evolution

genomics more details view paper
  • Downloaded 565 times
  • Download rankings, all-time:
    • Site-wide: 15,799 out of 60,323
    • In genomics: 2,000 out of 4,185
  • Year to date:
    • Site-wide: 3,540 out of 60,323
  • Since beginning of last month:
    • Site-wide: 3,494 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 554 times
  • Download rankings, all-time:
    • Site-wide: 16,195 out of 60,323
    • In bioinformatics: 2,532 out of 6,082
  • Year to date:
    • Site-wide: 13,125 out of 60,323
  • Since beginning of last month:
    • Site-wide: 23,781 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 455 times
  • Download rankings, all-time:
    • Site-wide: 20,685 out of 60,323
    • In bioinformatics: 3,026 out of 6,082
  • Year to date:
    • Site-wide: 9,763 out of 60,323
  • Since beginning of last month:
    • Site-wide: 19,325 out of 60,323

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 340 times
  • Download rankings, all-time:
    • Site-wide: 28,150 out of 60,323
    • In genetics: 1,824 out of 3,443
  • Year to date:
    • Site-wide: 52,808 out of 60,323
  • Since beginning of last month:
    • Site-wide: 54,742 out of 60,323

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

genomics more details view paper
  • Downloaded 334 times
  • Download rankings, all-time:
    • Site-wide: 28,630 out of 60,323
    • In genomics: 2,864 out of 4,185
  • Year to date:
    • Site-wide: 8,430 out of 60,323
  • Since beginning of last month:
    • Site-wide: 518 out of 60,323

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

bioinformatics more details view paper
  • Downloaded 211 times
  • Download rankings, all-time:
    • Site-wide: 41,078 out of 60,323
    • In bioinformatics: 4,813 out of 6,082
  • Year to date:
    • Site-wide: 16,678 out of 60,323
  • Since beginning of last month:
    • Site-wide: 1,175 out of 60,323

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

genomics more details view paper
  • Downloaded 188 times
  • Download rankings, all-time:
    • Site-wide: 43,828 out of 60,323
    • In genomics: 3,609 out of 4,185
  • Year to date:
    • Site-wide: 19,364 out of 60,323
  • Since beginning of last month:
    • Site-wide: 10,026 out of 60,323

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


News