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ORCIDBenjamin P. Vandervalk
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2010 – 2019
- 2018
[j12]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): 1697-1704 (2018)- [j11]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): 234:1-234:10 (2018) - [j10]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): 393:1-393:10 (2018) - 2017
- [j9]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): 1782-1788 (2017) - [j8]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): 2789 (2017) - 2016
- [j7]Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol:
ntHash: recursive nucleotide hashing. Bioinform. 32(22): 3492-3494 (2016) - 2015
- [j6]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: 230:1-230:8 (2015) - 2014
- [c10]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: 15-22 - [c9]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: 51-58 - 2013
- [j5]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:
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data. Bioinform. 29(12): 1492-1497 (2013) - [i2]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 abs/1305.4455 (2013) - 2012
- [j4]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist language-neutral query composer. BMC Bioinform. 13(S-1): S2 (2012) - [c8]Ian Wood, Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
OWL-DL Domain-Models as Abstract Workflows. ISoLA (2) 2012: 56-66 - 2011
- [j3]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: 8 (2011) - [c7]Benjamin P. Vandervalk, Michel Dumontier, E. Luke McCarthy, Mark D. Wilkinson:
SADI for GMOD: Semantic Web Services for Model Organism Databases. CSWS 2011: 70-75 - 2010
- [j2]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): S7 (2010) - [c6]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: 301-312 - [c5]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
SHARE & The Semantic Web - This Time it's Personal! OWLED 2010 - [c4]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist Language-Neutral Query Composer. SWAT4LS 2010 - [i1]E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist Language-Neutral Query Composer. CoRR abs/1012.1666 (2010)
2000 – 2009
- 2009
- [j1]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
Moby and Moby 2: Creatures of the Deep (Web). Briefings Bioinform. 10(2): 114-128 (2009) - [c3]Mark D. Wilkinson, Benjamin P. Vandervalk, E. Luke McCarthy:
SADI Semantic Web Services - 'cause you can't always GET what you want!. APSCC 2009: 13-18 - [c2]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
SHARE: A Semantic Web Query Engine for Bioinformatics. ASWC 2009: 367-369 - [c1]Benjamin P. Vandervalk, E. Luke McCarthy, Mark D. Wilkinson:
Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. CSE (1) 2009: 330-337
Coauthor Index
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