Publications

Latest publications can be found on my Google scholar page.

Refereed journal publications

Soo RM, Skennerton CT, Sekiguchi Y Imelfort M, Parch SJ, Denis PG, Steen JA, Parks DH, Tyson GW, Hugenholtz P. 2014. An expanded genomic representation of the phylum cyanobacteria. Genome Biology and Evolution, 6, 1031-45.

Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. 2013. GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework. PLoS ONE, July, 2013.

Parks DH and Beiko RG. 2012. Measuring community similarity with phylogenetic networks. Molecular Biology and Evolution, August, 2012.

Parks DH and Beiko RG. 2012. Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. ISME J, August, 2012.

MacDonald NJ, Parks DH, Beiko RG. 2012. Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Research, Advanced access, April 24, 2012.

Parks DH, MacDonald NJ, Beiko RG. 2011. Classifying short genomic fragments from novel lineages using composition and homology. BMC Bioinformatics, 12:328.

Parks DH and Beiko RG. 2010. Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-21. (website)

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartman M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: Open source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537-41. (website)

Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG. 2009. GenGIS: A geospatial information system for genomic data. Genome Research, 19, 1896-904. (website)

Parks DH and Levine MD. 2010. Is local colour normalization good enough for local appearance-based classification? Machine Vision and Applications, 21, 789-796. First published online in January, 2009 (DOI: 10.1007/s00138-009-0186-y).

Refereed conference publications

Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. 17th International Conference on Geoinformatics, Fairfax, VA. Received CPGIS 2009 Best Student Paper Award.

Parks DH and Fels S. 2008. Evaluation of background subtraction algorithms with post-processing. IEEE International Conference on Advanced Video and Signal-based Surveillance, Fairfax, Virginia.

Afrah A, Miller G, Parks DH, Finke M, Fels S. 2008. Hive: A distributed system for vision processing. Proc. 2nd International Conference on Distributed Smart Cameras, Palo Alto, California.

Parks DH and Levine MD. 2006. McGill object detection suite. Third Canadian Conference on Computer and Robot Vision (CRV06), Quebec City, Quebec. (website)

Book chapters

Parks DH and Beiko RG. 2013. STAMP: Statistical analysis of metagenomic profiles. Encyclopedia of Metagenomics.

Beiko RG and Parks DH. 2013. Rapid identification of high- confidence taxonomic assignments for metagenomic data. Encyclopedia of Metagenomics.

Invited presentations

Parks DH. 2015. K-mers in metagenomics. University of Queensland's Winter School in Mathematical & Computational Biology, Brisbane, Australia.

Parks DH and Beiko RG. 2010. Using β-diversity to study the influence of geographic proximity and habitat on the composition of marine microbial communities. 95th Ecological Society of America Annual Meeting, Pittsburgh, Pennsylvania.

Oral conference presentations

Parks DH. 2014. CheckM: assessing the quality of genomes from pure strains, single-cell genomics, and metagenomic data. ISME15, Seoul, South Korea.

Parks DH, Imelfort M, Tyson GW. 2013. Identifying genomes from spatiotemporal metagenomic samples. iEvoBio, Snowbird, Utah.

Parks DH. 2012. GenGIS 2: Geospatial analysis of genetic and genomic datasets. iEvoBio, Ottawa, Canada.

Parks DH. 2011. GenGIS: A geospatial information system for genomic data. Society for Molecular Biology and Evolution, Kyoto, Japan.

Parks DH, MacDonald NJ, Beiko RG. 2009. A rapid data acquisition pipeline for visualizing the 2009 A/H1N1 influenza pandemic. Atlantic Provinces Council on the Sciences (APICS), Halifax, Nova Scotia. (slides)

Parks DH and Beiko RG. 2009. Quantitative visualizations of hierarchically organized data in a geographic context. 17th International Conference on Geoinformatics, Fairfax, VA. Received CPGIS 2009 Best Student Paper Award.

Parks DH and Fels S. 2008. Evaluation of background subtraction algorithms with post-processing. IEEE International Conference on Advanced Video and Signal-based Surveillance, Santa Fe, New Mexico.

Other talks

Parks, DH 2012. Extending phylogenetic beta-diversity measures to split systems. Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia.

Parks, DH 2009. Investigating microbial biogeography using GenGIS. Comparative Genomics and Evolutionary Bioinformatics, Halifax, Nova Scotia.

Poster presentations

Parks DH and Beiko RG. 2012. Applying network-based measures of phylogenetic beta diversity. Society for Molecular Biology and Evolution (SMBE), Dublin, Ireland.

Parks DH and Beiko RG. 2011. Quantifying beta-diversity over phylogenetic trees and networks. Society for Molecular Biology and Evolution (SMBE), Kyoto, Japan.

Parks DH and Beiko RG. 2011. Statistical analysis of metagenomic profiles. Society for Molecular Biology and Evolution (SMBE), Kyoto, Japan.

Parks DH and Beiko RG. 2010. Investigating viral and microbial biogeography using GenGIS. International Society for Microbial Ecology (ISME), Seattle, Washington.

Parks DH and Beiko RG. 2010. GenGIS: a visualization framework for exploring georeferenced genomic and metagenomic data sets. EMBO Workshop on Visualizing Biological Data (VizBi), Heidelberg, Germany.

Parks DH and Beiko RG. 2009. Exploring marine microbial community diversity. Canadian Society for Ecology and Evolution (CSEE) and the Genetics Society of Canada (GSC) Conference, Halifax, Nova Scotia.

Wong DHJ, Parks DH, Churcher S, Beiko RG. 2009. Exploring the world of microbes using new genomic methods and software tools. 5th Annual Environment and Sustainability Research Symposium, Halifax, Nova Scotia.

Thesis

Parks DH. 2012. Georeferenced trees and the phylogenetic similarity of biological communities. PhD. Thesis, Dalhousie University.

Parks DH. 2006. Object detection and analysis using coherency filtering. MEng. Thesis, McGill University. Also available at Amazon.

Non-refereed contributions

MacDonald NJ, Parks DH, Beiko RG. 2009. SeqMonitor: Influenza analysis pipeline and visualization. PLoS Currents: Influenza, RRN1040.

Parks DH, MacDonald, NJ, Beiko RG. 2009. Tracking the evolution and geographic spread of influenza A. PLoS Currents: Influenza, RRN1014.

Parks DH 2008. Analyzing the structure of a motion capture database under a similarity metric. CPSC533C: Information Visualization, University of British Columbia.

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