publications.bib

@article{jackman2017abyss,
  title={ABySS 2.0: Resource-efficient Assembly of Large Genomes using a Bloom Filter},
  author={Jackman, Shaun D and Vandervalk, Benjamin P and Mohamadi, Hamid and Chu, Justin and Yeo, Sarah and Hammond, S Austin and Jahesh, Golnaz and Khan, Hamza and Coombe, Lauren and Warren, Rene L and others},
  journal={Genome Research},
  volume={27},
  number={5},
  pages={768--777},
  url = {https://genome.cshlp.org/content/27/5/768},
  year={2017},
  publisher={Cold Spring Harbor Lab}
}
@article{vandervalk2015konnector,
  title={Konnector v2. 0: Pseudo-long Reads from Paired-end Sequencing Data},
  author={Vandervalk, Benjamin P and Yang, Chen and Xue, Zhuyi and Raghavan, Karthika and Chu, Justin and Mohamadi, Hamid and Jackman, Shaun D and Chiu, Readman and Warren, Rene L and Birol, Inanc},
  journal={BMC Medical Genomics},
  volume={8},
  number={3},
  pages={S1},
  url = {https://doi.org/10.1186/1755-8794-8-S3-S1},
  year={2015},
  publisher={BioMed Central}
}
@inproceedings{vandervalk2014konnector,
  title={Konnector: Connecting Paired-end Reads using a Bloom Filter de Bruijn Graph},
  author={Vandervalk, Benjamin P and Jackman, Shaun D and Raymond, Anthony and Mohamadi, Hamid and Yang, Chen and Attali, Dean A and Chu, Justin and Warren, Rene L and Birol, Inanc},
  booktitle={Bioinformatics and Biomedicine (BIBM) 2014},
  pages={51--58},
  url = {https://doi.org/10.1109/BIBM.2014.6999126},
  year={2014},
  organization={IEEE}
}
@article{Spruce,
author = {Birol, Inanc and Raymond, Anthony and Jackman, Shaun D. and Pleasance, Stephen and Coope, Robin and Taylor, Greg A. and Macaire Man Saint Yuen and Keeling, Christopher I. and Brand, Dana and Vandervalk, Benjamin P. and Kirk, Heather and Pandoh, Pawan and Moore, Richard A. and Zhao, Yongjun and Mungall, Andrew J. and Jaquish, Barry and Yanchuk, Alvin and Ritland, Carol and Boyle, Brian and Bousquet, Jean and Ritland, Kermit and MacKay, John and Bohlmann, Jorg and Jones, Steven J. M. },
title = {{Assembling the 20 Gb White Spruce (Picea glauca) Genome From Whole-Genome Shotgun Sequencing Data}},
journal = {Bioinformatics}
publisher = {Oxford Journals},
month = {Dec},	  
pages = {1492-1497},
volume = {29(12)},
url = {http://dx.doi.org/10.1093/bioinformatics/btt178},
year = {2013}
}
@article{HealthLens,
author = {Vandervalk, Ben and McCarthy, E. Luke and Cruz-Toledo, Jose and Klein, Arjom and Baker, Christopher J. and Dumontier, Michel and Wilkinson, Mark D.},
title = {{The SADI Personal Health Lens: A Web Browser-Based System for Identifying Personally Relevant Drug Interactions}},
journal = {JMIR Research Protocols}
publisher = {JMIR Publications},
month = {Jan-Jun},	  
pages = {e14},
volume = {2(1)},
url = {http://dx.doi.org/10.2196/resprot.2315},
year = {2013}
}
@article{ISoLAWorkflow, 
author = {Wood, Ian and Vandervalk, Ben and McCarthy, Luke and Wilkinson, Mark D.},
affiliation = {Institute for Heart + Lung Health, St. Paul’s Hospital, University of British Columbia, Vancouver, BC, Canada},
title = {OWL-DL Domain-Models as Abstract Workflows},
booktitle = {Leveraging Applications of Formal Methods, Verification and Validation: Applications and Case Studies},
series = {Lecture Notes in Computer Science},
editor = {Margaria, Tiziana and Steffen, Bernhard},
publisher = {Springer Berlin / Heidelberg},
isbn = {978-3-642-34031-4},
keyword = {Computer Science},
pages = {56-66},
volume = {7610},
url = {http://dx.doi.org/10.1007/978-3-642-34032-1_6},
note = {10.1007/978-3-642-34032-1_6},
year = {2012}
}
@inproceedings{Vandervalk2011b,
author = {Vandervalk, Ben and Dumontier, Michel and McCarthy, E. Luke and Wilkinson, Mark D.},
booktitle = {Proceedings of the Canadian Semantic Web Symposium (CSWS) 2011},
keywords = {BenVV},
title = {{SADI for GMOD: Semantic Web Services for Model Organism Databases}},
url = {http://ceur-ws.org/Vol-774/ben.pdf},
year = {2011}
}
@inproceedings{Vandervalk2010,
author = {Vandervalk, Benjamin and McCarthy, E. Luke and Wilkinson, Mark D.},
booktitle = {Proceedings of OWL Experiences and Directions (OWLED) 2010},
keywords = {BenVV},
title = {{SHARE \& The Semantic Web - This Time it's Personal!}},
url = {http://www.webont.org/owled/2010/papers/owled2010\_submission\_22.pdf},
year = {2010}
}
@article{Vandervalk2009c,
abstract = {Facile and meaningful integration of data from disparate resources is the ‘holy grail’ of bioinformatics. Some resources have begun to address this problem by providing their data using Semantic Web standards, specifically the Resource Description Framework (RDF) and the Web Ontology Language (OWL). Unfortunately, adoption of Semantic Web standards has been slow overall, and even in cases where the standards are being utilized, interconnectivity between resources is rare. In response, we have seen the emergence of centralized ‘semantic warehouses’ that collect public data from third parties, integrate it, translate it into OWL/RDF and provide it to the community as a unified and queryable resource. One limitation of the warehouse approach is that queries are confined to the resources that have been selected for inclusion. A related problem, perhaps of greater concern, is that the majority of bioinformatics data exists in the ‘Deep Web’—that is, the data does not exist until an application or analytical tool is invoked, and therefore does not have a predictable Web address. The inability to utilize Uniform Resource Identifiers (URIs) to address this data is a barrier to its accessibility via URI-centric Semantic Web technologies. Here we examine ‘The State of the Union’ for the adoption of Semantic Web standards in the health care and life sciences domain by key bioinformatics resources, explore the nature and connectivity of several community-driven semantic warehousing projects, and report on our own progress with the CardioSHARE/Moby-2 project, which aims to make the resources of the Deep Web transparently accessible through SPARQL queries.},
annote = {10.1093/bib/bbn051},
author = {Vandervalk, Ben and McCarthy, E. Luke and Wilkinson, Mark D.},
issn = {1467-5463},
journal = {Briefings in Bioinformatics},
keywords = {BenVV},
month = jan,
number = {2},
pages = {114},
title = {{Moby and Moby 2: Creatures of the Deep (Web)}},
url = {http://dx.doi.org/10.1093/bib/bbn051},
volume = {10},
year = {2009}
}
@inproceedings{Vandervalk2009a,
annote = {10.1109/cse.2009.144},
author = {Vandervalk, Ben and McCarthy, E. Luke and Wilkinson, Mark D.},
booktitle = {Proceedings of the IEEE International Conference on Computational Science and Engineering (CSE) 2009},
keywords = {BenVV},
pages = {330--337},
title = {{Optimization of Distributed SPARQL Queries Using Edmonds' Algorithm and Prim's Algorithm}},
url = {http://dx.doi.org/10.1109/cse.2009.144},
volume = {1},
year = {2009}
}
@inproceedings{Vandervalk2009b,
abstract = {Driven by the goal of automating data analyses in the field of bioinformatics, SHARE (Semantic Health and Research Environment) is a specialized SPARQL engine that resolves queries against Web Services and SPARQL endpoints. Developed in conjunction with SHARE, SADI (Semantic Automated Discovery and Integration) is a standard for native-RDF services that facilitates the automated assembly of services into workflows, thereby eliminating the need for ad hoc scripting in the construction of a bioinformatics analysis pipeline.},
annote = {10.1007/978-3-642-10871-6\_27},
author = {Vandervalk, Ben and McCarthy, E. Luke and Wilkinson, Mark D.},
booktitle = {Proceedings of the Asian Semantic Web Conference (ASWC) 2009},
keywords = {BenVV},
pages = {367--369},
title = {{SHARE: A Semantic Web Query Engine for Bioinformatics}},
url = {http://dx.doi.org/10.1007/978-3-642-10871-6\_27},
volume = {5926},
year = {2009}
}
@article{Wilkinson2011,
abstract = {ABSTRACT: BACKGROUND: The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. CONCLUSIONS: SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies.},
author = {Wilkinson, Mark D. and Vandervalk, Benjamin and McCarthy, E. Luke},
doi = {10.1186/2041-1480-2-8},
issn = {2041-1480},
journal = {Journal of Biomedical Semantics},
keywords = {API,SADI},
mendeley-tags = {API,SADI},
month = oct,
number = {1},
pages = {8},
pmid = {22024447},
title = {{The Semantic Automated Discovery and Integration (SADI) Web Service Design-Pattern, API and Reference Implementation}},
url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212890/?tool=pmcentrez\&rendertype=abstract},
volume = {2},
year = {2011}
}
@article{Wilkinson2010,
abstract = {Background The emergence and uptake of Semantic Web technologies by the Life Sciences provides exciting opportunities for exploring novel ways to conduct in silico science. Web Service Workflows are already becoming first-class objects in �the new way�, and serve as explicit, shareable, referenceable representations of how an experiment was done. In turn, Semantic Web Service projects aim to facilitate workflow construction by biological domain-experts such that workflows can be edited, re-purposed, and re-published by non-informaticians. However the aspects of the scientific method relating to explicit discourse, disagreement, and hypothesis generation have remained relatively impervious to new technologies. Results Here we present SADI and SHARE - a novel Semantic Web Service framework, and a reference implementation of its client libraries. Together, SADI and SHARE allow the semi- or fully-automatic discovery and pipelining of Semantic Web Services in response to ad hoc user queries. Conclusions The semantic behaviours exhibited by SADI and SHARE extend the functionalities provided by Description Logic Reasoners such that novel assertions can be automatically added to a data-set without logical reasoning, but rather by analytical or annotative services. This behaviour might be applied to achieve the �semantification� of those aspects of the in silico scientific method that are not yet supported by Semantic Web technologies. We support this suggestion using an example in the clinical research space.},
annote = {10.1186/1471-2105-11-s12-s7},
author = {Wilkinson, Mark D. and McCarthy, E. Luke and Vandervalk, Benjamin and Withers, David and Kawas, Edward and Samadian, Soroush},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {BenVV},
number = {Suppl 12},
pages = {S7},
title = {{SADI, SHARE, and the In Silico Scientific Method}},
url = {http://dx.doi.org/10.1186/1471-2105-11-s12-s7},
volume = {11},
year = {2010}
}