Benjamin P. Vandervalk

Publication Activity (10 Years)

Years Active: 2009-2018
Publications (10 Years): 6

Top Topics

Genomic Sequences

Top Venues

Publications

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
Tigmint: correcting assembly errors using linked reads from large molecules. BMC Bioinform. 19 (1) (2018)
Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanç Birol, René L. Warren
ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. BMC Bioinform. 19 (1) (2018)
Hamza Khan, Hamid Mohamadi, Benjamin P. Vandervalk, René L. Warren, Justin Chu, Inanç Birol
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinform. 34 (10) (2018)
Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol
Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinform. 33 (12) (2017)
Erdi Kucuk, Justin Chu, Benjamin P. Vandervalk, S. Austin Hammond, René L. Warren, Inanç Birol
Kollector: transcript-informed, targeted de novo assembly of gene loci. Bioinform. 33 (17) (2017)
Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol
ntHash: recursive nucleotide hashing. Bioinform. 32 (22) (2016)
Daniel Paulino, René L. Warren, Benjamin P. Vandervalk, Anthony Raymond, Shaun D. Jackman, Inanç Birol
Sealer: a scalable gap-closing application for finishing draft genomes. BMC Bioinform. 16 (2015)
Inanç Birol, Hamid Mohamadi, Anthony Raymond, Karthika Raghavan, Justin Chu, Benjamin P. Vandervalk, Shaun D. Jackman, René L. Warren
Spaced seed data structures. BIBM (2014)
Benjamin P. Vandervalk, Shaun D. Jackman, Anthony Raymond, Hamid Mohamadi, Chen Yang, Dean A. Attali, Justin Chu, René L. Warren, Inanç Birol
Konnector: Connecting paired-end reads using a bloom filter de Bruijn graph. BIBM (2014)
Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
SHARE: A Web Service Based Framework for Distributed Querying and Reasoning on the Semantic Web CoRR (2013)
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
) genome from whole-genome shotgun sequencing data. Bioinform. 29 (12) (2013)
Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
OWL-DL Domain-Models as Abstract Workflows. ISoLA (2) (2012)
E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson
SPARQL Assist language-neutral query composer. BMC Bioinform. 13 (S-1) (2012)
Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy
The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation. J. Biomed. Semant. 2 (2011)
Benjamin P. Vandervalk, Michel Dumontier, E. Luke McCarthy, Mark D. Wilkinson
SADI for GMOD: Semantic Web Services for Model Organism Databases. CSWS (2011)
Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
SHARE & The Semantic Web - This Time it's Personal! OWLED (2010)
Mark D. Wilkinson, E. Luke McCarthy, Benjamin P. Vandervalk, David Withers, Edward A. Kawas, Soroush Samadian
SADI, SHARE, and the in silico scientific method. BMC Bioinform. 11 (S-12) (2010)
David Withers, Edward A. Kawas, E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson
Semantically-Guided Workflow Construction in Taverna: The SADI and BioMoby Plug-Ins. ISoLA (1) (2010)
E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson
SPARQL Assist Language-Neutral Query Composer. SWAT4LS (2010)
E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson
SPARQL Assist Language-Neutral Query Composer CoRR (2010)
Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy
SADI Semantic Web Services - 'cause you can't always GET what you want!. APSCC (2009)
Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
Moby and Moby 2: Creatures of the Deep (Web). Briefings Bioinform. 10 (2) (2009)
Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
SHARE: A Semantic Web Query Engine for Bioinformatics. ASWC (2009)
Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. CSE (1) (2009)