J. Simpson

Publications72
h-index34
Citations13,979
Highly Influential Citations1,185
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ABySS: a parallel assembler for short read sequence data.
Widespread adoption of massively parallel deoxyribonucleic acid (DNA) sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the… Expand
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Efficient de novo assembly of large genomes using compressed data structures.
De novo genome sequence assembly is important both to generate new sequence assemblies for previously uncharacterized genomes and to identify the genome sequence of individuals in a… Expand
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A complete bacterial genome assembled de novo using only nanopore sequencing data
We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then… Expand
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Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the… Expand
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
TLDR
We provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). Expand
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Nanopore sequencing and assembly of a human genome with ultra-long reads
Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However… Expand
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Detecting DNA cytosine methylation using nanopore sequencing
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford… Expand
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Trait Variation in Yeast Is Defined by Population History
A fundamental goal in biology is to achieve a mechanistic understanding of how and to what extent ecological variation imposes selection for distinct traits and favors the fixation of specific… Expand
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Efficient construction of an assembly string graph using the FM-index
TLDR
We use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster than previously described algorithms. Expand
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Real-time, portable genome sequencing for Ebola surveillance
The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to… Expand
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