Publications by authors named "Benjamin Vandervalk"

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Tigmint: correcting assembly errors using linked reads from large molecules.
Shaun D Jackman, Lauren Coombe, Justin Chu, Rene L Warren, Benjamin P Vandervalk

BMC Bioinformatics· October 2018

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ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.
Lauren Coombe, Jessica Zhang, Benjamin P Vandervalk, Justin Chu, Shaun D Jackman

BMC Bioinformatics· June 2018

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ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.
Hamza Khan, Hamid Mohamadi, Benjamin P Vandervalk, Rene L Warren, Justin Chu

Bioinformatics· May 2018

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The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA.
S Austin Hammond, René L Warren, Benjamin P Vandervalk, Erdi Kucuk, Hamza Khan

Nat Commun· November 2017

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Kollector: transcript-informed, targeted de novo assembly of gene loci.
Erdi Kucuk, Justin Chu, Benjamin P Vandervalk, S Austin Hammond, René L Warren

Bioinformatics· September 2017

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Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data.
Lauren Coombe, René L Warren, Shaun D Jackman, Chen Yang, Benjamin P Vandervalk

PLoS One· August 2017

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Kollector: transcript-informed, targeted de novo assembly of gene loci.
Erdi Kucuk, Justin Chu, Benjamin P Vandervalk, S Austin Hammond, René L Warren

Bioinformatics· June 2017

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ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.
Shaun D Jackman, Benjamin P Vandervalk, Hamid Mohamadi, Justin Chu, Sarah Yeo

Genome Res· May 2017

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ntHash: recursive nucleotide hashing.
Hamid Mohamadi, Justin Chu, Benjamin P Vandervalk, Inanc Birol

Bioinformatics· November 2016

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LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.
René L Warren, Chen Yang, Benjamin P Vandervalk, Bahar Behsaz, Albert Lagman

Gigascience· July 2016

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Konnector v2.0: pseudo-long reads from paired-end sequencing data.
Benjamin P Vandervalk, Chen Yang, Zhuyi Xue, Karthika Raghavan, Justin Chu

BMC Med Genomics· July 2016

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DIDA: Distributed Indexing Dispatched Alignment.
Hamid Mohamadi, Benjamin P Vandervalk, Anthony Raymond, Shaun D Jackman, Justin Chu

PLoS One· April 2016

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Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.
Shaun D Jackman, René L Warren, Ewan A Gibb, Benjamin P Vandervalk, Hamid Mohamadi

Genome Biol Evol· December 2015

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Spaced Seed Data Structures for De Novo Assembly.
Inanç Birol, Justin Chu, Hamid Mohamadi, Shaun D Jackman, Karthika Raghavan, Benjamin P Vandervalk

Int J Genomics· November 2015

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Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.
René L Warren, Christopher I Keeling, Macaire Man Saint Yuen, Anthony Raymond, Greg A Taylor, Benjamin P Vandervalk

Plant J· July 2015

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Sealer: a scalable gap-closing application for finishing draft genomes.
Daniel Paulino, René L Warren, Benjamin P Vandervalk, Anthony Raymond, Shaun D Jackman

BMC Bioinformatics· July 2015

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Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Inanc Birol, Anthony Raymond, Shaun D Jackman, Stephen Pleasance, Robin Coope, Benjamin P Vandervalk

Bioinformatics· June 2013

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The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.
Mark D Wilkinson, Benjamin Vandervalk, Luke McCarthy

J Biomed Semantics· October 2011

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SADI, SHARE, and the in silico scientific method.
Mark D Wilkinson, Luke McCarthy, Benjamin Vandervalk, David Withers, Edward Kawas

BMC Bioinformatics· December 2010

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