SADI Semantic Web Services - 'cause you can't always GET what you want!. - Mark D. Wilkinson; Benjamin P. Vandervalk; E. Luke McCarthy (APSCC, 2009)

SHARE: A Semantic Web Query Engine for Bioinformatics. - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (ASWC, 2009)

Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm. - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (CSE (1), 2009)

Moby and Moby 2: Creatures of the Deep (Web). - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (Briefings Bioinform., 2009)

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 (ISoLA (1), 2010)

SHARE & The Semantic Web - This Time it's Personal! - Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (OWLED, 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)

SADI for GMOD: Semantic Web Services for Model Organism Databases. - Benjamin P. Vandervalk; Michel Dumontier; E. Luke McCarthy; Mark D. Wilkinson (CSWS, 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)

OWL-DL Domain-Models as Abstract Workflows. - Ian Wood; Benjamin P. Vandervalk; E. Luke McCarthy; Mark D. Wilkinson (ISoLA (2), 2012)

SPARQL Assist language-neutral query composer. - E. Luke McCarthy; Benjamin P. Vandervalk; Mark D. Wilkinson (BMC Bioinform., 2012)

Assembling the 20 Gb white spruce (Picea glauca) 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; et al. (Bioinform., 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)

Spaced seed data structures. - Inanç Birol; Hamid Mohamadi; Anthony Raymond; Karthika Raghavan; Justin Chu; Benjamin P. Vandervalk; Shaun D. Jackman; René L. Warren (BIBM, 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 (BIBM, 2014)

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)

ntHash: recursive nucleotide hashing. - Hamid Mohamadi; Justin Chu; Benjamin P. Vandervalk; Inanç Birol (Bioinform., 2016)

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)

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)

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)

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)