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Author: Benedict Paten

Rankings

  • All-time downloads: 74,862 (rank: 442 out of 361,790)
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    • bioinformatics: 45,475 (rank: 56 out of 31,267)
    • evolutionary biology: 470 (rank: 10,095 (tie) out of 18,767)
    • genomics: 28,917 (rank: 251 out of 39,123)

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Preprints

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

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Genome Graphs

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

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

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

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

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Computational Pan-Genomics: Status, Promises and Challenges

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

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Alignathon: A competitive assessment of whole genome alignment methods.

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Haplotype-aware genotyping from noisy long reads

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Linear Assembly of a Human Y Centromere

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

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Cytosine Variant Calling with High-throughput Nanopore Sequencing

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Chromosome assembly of large and complex genomes using multiple references

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

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A fully phased accurate assembly of an individual human genome

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    • In bioinformatics: 926 out of 8,053
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Genotyping structural variants in pangenome graphs using the vg toolkit

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

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

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The UCSC Genome Browser database: 2016 update

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Genome Graphs and the Evolution of Genome Inference

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

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Superbubbles, Ultrabubbles and Cacti

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A Flow Procedure for the Linearization of Genome Sequence Graphs.

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

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Haplotype-aware graph indexes

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

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

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Modelling haplotypes with respect to reference cohort variation graphs

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ProTECT: Prediction of T-cell Epitopes for Cancer Therapy

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Describing the Local Structure of Sequence Graphs

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Succinct dynamic variation graphs

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A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

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Distance Indexing and Seed Clustering in Sequence Graphs

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A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

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