Benjamin P. Vandervalk

According to our database, Benjamin P. Vandervalk authored at least 21 papers between 2009 and 2018.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2018

Tigmint: correcting assembly errors using linked reads from large molecules.

Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Benjamin P. Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Jörg Bohlmann, Steven J. M. Jones, Inanç Birol

BMC Bioinform., 2018

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanç Birol, René L. Warren

BMC Bioinform., 2018

ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data.

Hamza Khan, Hamid Mohamadi, Benjamin P. Vandervalk, René L. Warren, Justin Chu, Inanç Birol

Bioinform., 2018

2017

Kollector: transcript-informed, targeted de novo assembly of gene loci.

Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol

Bioinform., 2017

2016

ntHash: recursive nucleotide hashing.

Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol

Bioinform., 2016

2015

Sealer: a scalable gap-closing application for finishing draft genomes.

Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Inanç Birol

BMC Bioinform., 2015

2014

Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph.

Benjamin P. Vandervalk, Shaun D. Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean A. Attali, Justin Chu, René L. Warren, Inanç Birol

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Spaced seed data structures.

Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P. Vandervalk, Shaun D. Jackman, René L. Warren

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013

SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

CoRR, 2013

Assembling the 20 Gb white spruce (<i>Picea glauca</i>) genome from whole-genome shotgun sequencing data.

Inanç Birol, Anthony Raymond, Shaun D. Jackman, Stephen Pleasance, Robin Coope, Greg A. Taylor, Macaire Man Saint Yuen, Christopher I. Keeling, Dana Brand, Benjamin P. Vandervalk, Heather Kirk, Pawan Pandoh, Richard A. Moore, Yongjun Zhao, Andrew J. Mungall, Barry Jaquish, Alvin Yanchuk, Carol Ritland, Brian Boyle, Jean Bousquet, Kermit Ritland, John MacKay, Jörg Bohlmann, Steven J. M. Jones

Bioinform., 2013

2012

SPARQL Assist language-neutral query composer.

E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson

BMC Bioinform., 2012

OWL-DL Domain-Models as Abstract Workflows.

Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies, 2012

2011

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy

J. Biomed. Semant., 2011

SADI for GMOD: Semantic Web Services for Model Organism Databases.

Benjamin P. Vandervalk, Michel Dumontier, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 3rd Canadian Semantic Web Symposium (CSWS2011), 2011

2010

SADI, SHARE, and the in silico scientific method.

Mark D. Wilkinson, E. Luke McCarthy, Benjamin P. Vandervalk, David Withers, Edward A. Kawas, Soroush Samadian

BMC Bioinform., 2010

SHARE & The Semantic Web - This Time it's Personal!

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 7th International Workshop on OWL: Experiences and Directions (OWLED 2010), 2010

Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins.

David Withers, Edward A. Kawas, E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson

Proceedings of the Leveraging Applications of Formal Methods, Verification, and Validation, 2010

2009

Moby and Moby 2: Creatures of the Deep (Web).

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Briefings Bioinform., 2009

Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm.

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the 12th IEEE International Conference on Computational Science and Engineering, 2009

SHARE: A Semantic Web Query Engine for Bioinformatics.

Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson

Proceedings of the Semantic Web, Fourth Asian Conference, 2009

SADI Semantic Web Services - 'cause you can't always GET what you want!.

Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy

Proceedings of the 4th IEEE Asia-Pacific Services Computing Conference, 2009