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Author: Michael C. Schatz

Rankings

  • All-time downloads: 119,108 (rank: 96 out of 333,545)
  • Categories:
    • bioinformatics: 93,090 (rank: 1 out of 28,762)
    • genomics: 25,927 (rank: 249 out of 36,844)
    • microbiology: 91 (rank: 33,883 (tie) out of 35,415)

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Preprints

Third-generation sequencing and the future of genomics

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

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    • In genomics: 31 out of 5,050
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    • Site-wide: 695 out of 76,880

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing

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Accurate detection of complex structural variations using single molecule sequencing

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A robust benchmark for germline structural variant detection

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Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

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Fast and accurate reference-guided scaffolding of draft genomes

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    • In bioinformatics: 280 out of 7,428
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Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly

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    • In bioinformatics: 290 out of 7,428
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    • Site-wide: 43,726 out of 76,880

Ribbon: Visualizing complex genome alignments and structural variation

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    • In bioinformatics: 304 out of 7,428
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    • Site-wide: 7,125 out of 76,880
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    • Site-wide: 6,937 out of 76,880

The next 20 years of genome research

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    • In bioinformatics: 307 out of 7,428
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    • Site-wide: 45,857 out of 76,880

SplitMEM: Graphical pan-genome analysis with suffix skips

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    • In bioinformatics: 428 out of 7,428
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Reducing INDEL calling errors in whole-genome and exome sequencing data

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    • In bioinformatics: 432 out of 7,428
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    • Site-wide: 45,009 out of 76,880
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    • Site-wide: 37,543 out of 76,880

Interactive analysis and quality assessment of single-cell copy-number variations

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    • In bioinformatics: 459 out of 7,428
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    • Site-wide: 54,692 out of 76,880
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    • Site-wide: 58,046 out of 76,880

Addressing confounding artifacts in reconstruction of gene co-expression networks

genomics more details view paper
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    • Site-wide: 2,611 out of 76,880
    • In genomics: 523 out of 5,050
  • Year to date:
    • Site-wide: 26,949 out of 76,880
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    • Site-wide: 23,012 out of 76,880

Indel variant analysis of short-read sequencing data with Scalpel

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    • In bioinformatics: 524 out of 7,428
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    • Site-wide: 61,069 out of 76,880
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    • Site-wide: 51,099 out of 76,880

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

genomics more details view paper
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    • In genomics: 546 out of 5,050
  • Year to date:
    • Site-wide: 119 out of 76,880
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    • Site-wide: 98 out of 76,880

Metassembler: Merging and optimizing de novo genome assemblies

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    • In bioinformatics: 709 out of 7,428
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Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

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    • Site-wide: 4,132 out of 76,880
    • In bioinformatics: 806 out of 7,428
  • Year to date:
    • Site-wide: 1,310 out of 76,880
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    • Site-wide: 1,934 out of 76,880

GenomeScope: Fast reference-free genome profiling from short reads

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    • In bioinformatics: 832 out of 7,428
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    • Site-wide: 44,033 out of 76,880
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    • Site-wide: 38,175 out of 76,880

Paragraph: A graph-based structural variant genotyper for short-read sequence data

genomics more details view paper
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    • In genomics: 757 out of 5,050
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    • Site-wide: 6,437 out of 76,880

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

genomics more details view paper
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    • In genomics: 772 out of 5,050
  • Year to date:
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    • Site-wide: 57,623 out of 76,880

The DOE Systems Biology Knowledgebase (KBase)

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    • In bioinformatics: 914 out of 7,428
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GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

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    • In bioinformatics: 1,110 out of 7,428
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    • Site-wide: 1,902 out of 76,880

Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution

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Assemblytics: a web analytics tool for the detection of assembly-based variants

genomics more details view paper
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    • In genomics: 1,088 out of 5,050
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    • Site-wide: 40,692 out of 76,880

LRSim: a Linked Reads Simulator generating insights for better genome partitioning

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    • In bioinformatics: 1,271 out of 7,428
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Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

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    • In bioinformatics: 1,403 out of 7,428
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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

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    • In bioinformatics: 1,452 out of 7,428
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    • Site-wide: 67,933 out of 76,880

Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

genomics more details view paper
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    • In genomics: 1,307 out of 5,050
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    • Site-wide: 61,217 out of 76,880

SplitThreader: Exploration and analysis of rearrangements in cancer genomes

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    • In bioinformatics: 1,707 out of 7,428
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    • Site-wide: 43,540 out of 76,880

Samovar: Single-sample mosaic SNV calling with linked reads

genomics more details view paper
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    • Site-wide: 10,887 out of 76,880
    • In genomics: 1,566 out of 5,050
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    • Site-wide: 36,889 out of 76,880

iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone

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SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants

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First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)

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Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

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    • Site-wide: 73,550 out of 76,880

Sapling: Accelerating Suffix Array Queries with Learned Data Models

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Vargas: heuristic-free alignment for assessing linear and graph read aligners

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    • Site-wide: 12,508 out of 76,880

Recovering rearranged cancer chromosomes from karyotype graphs

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    • Site-wide: 68,846 out of 76,880

Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

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    • In bioinformatics: 6,379 out of 7,428
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    • Site-wide: 14,186 out of 76,880

A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor

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    • Site-wide: 73,499 out of 76,880
    • In microbiology: 5,918 out of 6,357
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  • Since beginning of last month:
    • Site-wide: 7,623 out of 76,880

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