Presentations and Publications

Listed on this page:

Talks

  1. Fiona Brinkman. Integrating Data. Integrating Communities 15th Annual Child Health Research Days: Navigating the Information Avalanche. Oct 22-24, 2019. Winnipeg, MB, Canada.

  2. Fiona Brinkman. The power, the promise - and the pitfalls - of microbiome analyses. Sept 12-13, 2019. Chicago, BC, Canada.

  3. Fiona Brinkman. Bioinformatics, Big Data, and Big Opportunities for One Health Solutions. Genome BC Annual General Meeting. June 7, 2019. Vancouver, BC, Canada.

  4. Fiona Brinkman. Integrated, network-based analysis in infectious disease.. Symposium: Defeating antibiotic resistant organisms with alternatives to antibiotics May 15. 2019. Vancouver, BC, Canada.

  5. Fiona Brinkman. Computational development for multi-omic linkages. April 3, 2019. Calgary, AB, Canada.

  6. Fiona Brinkman. Aiding disease detectives. Royal Society of Canada Pacific Chapter. Feb 21, 2019. Vancouver, BC, Canada.

  7. Fiona Brinkman. Making predictions using microbiomes and microchips. Omics Meeting. November 28, 2018, Burnaby, BC, Canada.

  8. Fiona Brinkman. Open data takes center stage in the fight against infectious diseases. Canadian Bioinformatics Workshop on Genomic Epidemiology. July 10, 2018, Toronto, ON, Canada.

  9. Fiona Brinkman. Towards better risk assessment of antimicrobial resistance gene spread – insights from analyses of mobile gene puddles. Integrated Rapid Infectious Disease Analysis AGM. June 22, 2018, Winnipeg, MN, Canada.

  10. Fiona Brinkman. IRIDA.ca: Panel Presentations and Discussion: Supporting Research Platforms & Portals.CANHEIT-TECC 2018. June 19, 2018.

  11. Fiona Brinkman. Using evolutionary theory to direct development of more sustainable approaches for infectious disease control. FAB Lab, SFU, Burnaby, BC, Canada. May 18, 2018.

  12. Fiona Brinkman. Microbiome Analysis in a One Health, Evolutionary, Context. Microbiome Seminar Series, April 18, 2018, Vancouver, BC, Canada.

  13. Aaron Petkau, A long time ago in a #useGalaxy far, far away, …, Microbial Bioinfo Slack Virtual Lab Talks, March 5, 2018.

  14. Fiona Brinkman.Bugs and Bioinformatics. Women in Bioinformatics event (also an event organizer), February 1, 2018. Vancouver, BC, Canada.

  15. Damion Dooley. IoF for Food, Flavor and People Phenotype Development. IC3-Foods Conference. November 8, 2017. San Diego, USA.

  16. Gary Van Domselaar, Progress in Bioinformatics Infrastructure for Canada’s Public Health Genomics Program, Department of Medical Microbiology Seminar Series, Nov 8, 2017.

  17. Andrew McArthur. Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. Brock University (Invited Talk). October 20, 2017. St. Catharines, Canada.

  18. Emma Griffiths. ISO WG 25 Part 3: Metadata and Sequence Repository. International Organization for Standards (ISO) Face-to-Face Meeting. October 5-6, 2017. Washington DC, USA.

  19. Damion Dooley.   The Genomic Epidemiology Ontology and GEEM Ontology Reusability Platform. Joint Ontology Workshop. September 23, 2017. Bozen-Bolzano, Italy.

  20. Gary Van Domselaar, Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety. Global Summit on Regulatory Science, September 20, 2017. Brasilia, Brazil.

  21. Tom Matthews, IRIDA overview, CPHLN annual meeting (NML), September 19, 2017. Winnipeg, Manitoba, Canada.

  22. Fiona Brinkman. Capitalizing on Pseudomonas genomics: From Broad Studies to the Broad Street. 16th International Conference on Pseudomonas,September 5-9, 2017. Liverpool, UK.

  23. Fiona Brinkman. Tools and data integration challenges for genomic epidemiology. Centers for Disease Control and Prevention, July 27, 2016. Atlanta, Georgia, USA.

  24. Fiona Brinkman. Enabling global genomic epidemiology - a key tool for public health and microbiology research. CSM (Canadian Society of Microbiologists) 67th Annual Conference, June 20-23, 2017. Waterloo, ON, Canada.

  25. William Hsiao. Public Health Microbiology in the Genomics Age. ImmunoBC Conference. June 9, 2017. Vancouver, Canada.

  26. Damion Dooley. The FoodOn Food Ontology. GetWell.IO & Ripe.IO Meeting. June 8-9, 2017. San Francisco, USA.

  27. Damion Dooley. GenEpiO and GLOPID-R’s Decision Tree. GLOPID-R Meeting. May 16, 2017. London, UK.

  28. Damion Dooley. FoodOn and the Semantic Web of Food. Seeds and Chips Sustainable Food Conference. May 8-11, 2017. USA.

  29. Fiona Brinkman. Open Bioinformatics Takes Centre Stage in Infectious Disease. Canadian Bioinformatics Workshop: Genomic Epidemiology, May 1-3, 2016. Vancouver, BC, Canada.

  30. Andrew McArthur. Bioinformatics of antimicrobial resistance in the age of molecular epidemiology. Toronto Bioinformatics Users Group (TorBUG). April 26, 2017. Toronto, Canada.

  31. Damion Dooley. GenEpiO and Tuberculosis contextual data component V2. Infectious Disease Modelling Conference. April 16-18. 2017. USA.

  32. Damion Dooley. The Genomic Epidemiology Ontology and Proof Sheet Application. Critical Path to TB Drug Regimens (CPTR) Annual Workshop. March 22, 2017. USA.

  33. Gary Van Domselaar, Progress in the development of bioinformatics best practices for microbial forensics International Microbial Forensics AGM, March 21, 2017. Winnipeg Canada.

  34. Emma Griffiths. GenEpiO: Enabling data interoperability for infectious disease surveillance, investigation and control. Microbial Forensics Symposium. March 20, 2017. Winnipeg, Canada.

  35. Emma Griffiths. GenEpiO: Enabling Genomic, Clinical and Epidemiological Data Standardization, Interoperability and Integration. USDA-FSIS teleconference. February 8, 2017. Vancouver, Canada.

  36. William Hsiao. The application of WGS as a tool to strengthen foodborne disease surveillance and response in developing countries. WHO & PAHO Conference. January 10-13, 2017. USA.

  37. Fiona Brinkman. The emerging role of bioinformatics and open data in the fight against infectious disease. Mini-Symposium: Bioinformatics for Infectious Disease Control, Dec 12, 2016. Burnaby, BC, Canada.

  38. Fiona Brinkman. Overcoming data integration and visualization challenges in microbial genomics. Department of Genome Sciences, November 9, 2016, University of Washington, Seattle, Washington, USA.

  39. Gary Van Domselaar, IRIDA Presentation to CBRNE PoC Detection Group, BADD Group (NML), Oct 27, 2016. Winnipeg, Manitoba, Canada 2016.

  40. Emma Griffiths. FoodON Use Cases: Food Allergy. International Conference on Biological Ontology & BioCreative.  August 1-4, 2016.  Corvallis, Oregon. USA.  (Download)

  41. Aaron Petkau.  Outbreak surveillance and investigation using IRIDA and SNVPhyl.  Galaxy Community Conference 2016.  June 25-29, 2016; Bloomington, IN, USA.  (Download)

  42. Fiona Brinkman.  Integrating Data, Integrating Domains.  May 29-June 1 2016.  AllerGen Conference, Bioinformatics Workshop, Vancouver, Canada.

  43. Robert Beiko.  Phylogeography with GenGIS.  3rd EMBO Conference on Visualizing Biological Data (VIZBI 2016).  March 11, 2016;  Heidelberg, Germany.  (Download)

  44. William Hsiao.  IRIDA: Canada’s federated platform for genomic epidemiology. 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal. (Download)

  45. Emma Griffiths.  IRIDA’s Genomic Epidemiology Application Ontology (GenEpiO): Genomic, Clinical and Epidemiological Data Standardization and Integration.  11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal. (Download)

  46. Eduardo Taboada. The EpiQuant framework for assessing epidemiologic and genetic concordance: Towards improved use of genomic data in epidemiological applications. 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal. (Download)

  47. Eduardo Taboada. Utility Of The Salmonella In Sillico Typing Resource (SISTR) To Outbreak Investigations. 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal. (Download)

  48. Eduardo Taboada. Mitigating the effects of sequence data quality on strain typeability: towards the development of robust core genome MLST (cgMLST) schemes. 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal. (Download)

  49. Chad Laing. Biomarker discovery for phenotypic groups In Escherichia coli using SuperPhy. 11th International Meeting on Microbial Epidemiological Markers (IMMEM XI).  March 9 - 12, 2016.  Estoril, Portugal.

  50. Thomas Matthews. Bioinformatics Best Practices at the NML. 2016 International Microbial Forensics Symposium. Feb 24 2016; USA

  51. Fiona Brinkman.  Microbial investigations using the IRIDA federated approach.  Pacific Symposium on Biocomputing. Jan 4-8, 2016; Hawaii,  United States

  52. Bhavjinder Dhillon.  Exploring the evolution of antimicrobial resistance using IslandViewer 3.  VanBUG Vancouver Bioinformatics User Group;  October 8, 2015; Vancouver, Canada.  (Download)

  53. Eduardo Taboada.  The Salmonella In Silico Typing Resource (SISTR): Rapid Analysis of Salmonella Draft Genome Sequence Data. 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens; September 24-27, 2015;  Washington, D.C., USA

  54. Aaron Petkau.  Phylogenetic reconstruction and outbreak investigation using IRIDA and SNVPhyl. 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens; September 24-27, 2015;  Washington, D.C., USA.  (Download)

  55. Fiona Brinkman.  Perspectives on linking internationally – Canada and www.irida.ca.  FDA GenomeTrakr Meeting; September 23-24 2015; Washington DC, USA.  (Download)

  56. Aaron Petkau. Genomic data management at Canada’s National Microbiology Laboratory with IRIDA and Galaxy. Galaxy Admins Web Meetup; August 20, 2015. (Slides/Video).

  57. Damion Dooley.  Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers.  Bioinformatics Open Source Conference/23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); July 10-14, 2015; Dublin, Ireland. (Download).

  58. Melanie Courtot.  The IRIDA project: standards for public health genomic epidemiology to improve infectious disease outbreak detection and investigation. 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); July 10-14, 2015; Dublin, Ireland.

  59. Aaron Petkau. IRIDA: A Genomic Epidemiology Platform Built on top of Galaxy.  Galaxy Community Conference 2015; July 8 2015;  United Kingdom. (Download)

  60. Fiona Brinkman. Integrated Rapid Infectious Disease Analysis (IRIDA) for public health.  Scottish National Microbiology Reference Laboratories; June 30, 2015; Scotland.

  61. William Hsiao.  How Can We Make Genomic Epidemiology a Widespread Reality?  Genome Atlantic; June 23, 2015; Halifax, Canada.

  62. Gary Van Domselaar. Quality Assurance of High Throughput Sequencing in the Diagnostic Laboratory. XVII International Symposium of the World Organization for Animal Health, World Association of Veterinary Laboratory Diagnostician;  June 17, 2015, Saskatoon, Canada.

  63. Robert Beiko.  Microbial genomics for rapid investigation of infectious disease.  Statistical and Computational Analytics for Big Data; June 12, 2015; Halifax, Canada.

  64. William Hsiao. How Can We Make Genomic Epidemiology a Widespread Reality? BCCDC Grand Rounds; May 26, 2015; Vancouver, Canada.

  65. Fiona Brinkman.  Keynote: “Integrating Bioinformatics Data. Integrating Bioinformatics Communities. Alberta Bioinformatics Symposium; May 21, 2015; Alberta, Canada.

  66. Gary Van Domselaar.   The use of WGS data for surveillance systems: the Canadian experience.  Global Microbial Identifier Network; May 11-13, 2015;  Beijing, China. (Download)

  67. William Hsiao.  IRIDA: Canada’s federated platform for genomic epidemiology.  ABPHM 2015; May 7, 2015; Cambridge, United Kingdom. (Download)

  68. Melanie Courtot.  Standards for public health genomic epidemiology to improve infectious disease outbreak detection and investigation.  Biocuration 2015; May 23-26, 2015; Beijing, China

  69. Julie Shay.  Genomic island prediction in IslandViewer and the significance of draft genome analysis.  Simon Fraser University Department of Molecular Biology and Biochemistry Graduate Colloquium; April 14, 2015; Burnaby, Canada.

  70. Fiona Brinkman.  IRIDA: Integrated Rapid Infectious Disease Analysis: Transforming public health with bioinformatics. IRMACS - 10th Anniversary; April 10, 2015.  Burnaby, Canada.

  71. Fiona Brinkman. Harnessing the power of bioinformatic platforms.  Big Data - For Heart and Lung Basic, Clinical, and Translational Research Meeting.  March 26, 2015.  Canada.

  72. William Hsiao.  Effective use of ontology for data standardization: an example in molecular epidemiology.  BC Centre for Disease Control; November 18, 2014; Vancouver, Canada.

  73. Fiona Brinkman.  Evolution of microbial pathogens and our microbiome: Implications for biodiversity.  McMaster University; October 27, 2014; Hamilton, Canada.

  74. Fiona Brinkman.  Omic analyses aiding more holistic, sustainable infectious disease control  - and environmental monitoring. University of Victoria; October 10, 2014; Victoria, Canada.

 

Posters

  1. Kara Tsang and Andrew McArthur. Encoding the efflux pump phenomena. 2nd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines. October 8-11, 2017. Washington DC, USA.

  2. Damion Dooley. GenEpiO: an Ontology for Genomic Epidemiology Data Integration and Harmonization. Applied Bioinformatics and Public Health Microbiology Conference. May 17-19, 2017. Hinxton, Cambridge, UK.

  3. Dalia Alghamdi. FoodOn: A Semantic Ontology Approach for mapping Foodborne Disease Metadata. International Conference on Biomedical Ontologies. September 13-15, 2017. Newcastle, UK.

  4. Gurinder Gosal. Text Mining Foodborne Pathogen Isolate Sample Descriptions for Ontology Term Mapping. IC3-Foods 2017. November 8, 2017.

  5. Emma Griffiths. Ontolo – what? Harmonization, integration and exchange of WGS contextual information using GenEpiO and GE2M. 2nd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines. October 8-11, 2017. Washington DC, USA.

  6. Emma Griffiths. Creating a standardized genomic epidemiology ontology for tuberculosis in Canada: challenges and opportunities. The Union TB NAR. February 24, 2017. Vancouver, Canada.

  7. Aaron Petkau.  Outbreak surveillance and investigation using IRIDA and SNVPhyl.  Galaxy Community Conference 2016.  June 25-29, 2016; Bloomington, IN, USA.  (Download)

  8. Emma Griffiths. GenEpiO: The Genomic Epidemiology Application Ontology for Standardization and Integration of Microbial Genomic, Clinical and Epidemiological Data.  American Society for Microbiology (ASM) Microbe.  June 16–20, 2016; Boston, MA, USA. (Download)

  9. Claire Bertelli.  Improving the Prediction and the Comparison of Genomic Islands in Draft and Complete Genomes. American Society for Microbiology (ASM) Microbe.  June 16–20, 2016; Boston, MA, USA.

  10. Julie Shay.  The utility of draft bacterial genomes for gene function analysis and genomic island prediction.  Great Lakes Bioinformatics and Canadian Computational Biology Conference.  May 16-19, 2016.  University of Toronto.  Canada. (Download)

  11. Claire Bertelli, Adrian C Lim, Gemma Hoad, Geoffrey L Winsor and Fiona S L Brinkman.  Enabling phyletic-based comparison and visualization of genomic islands for tens to hundreds of microbial genomes.  Great Lakes Bioinformatics and Canadian Computational Biology Conference.  May 16-19, 2016.  University of Toronto.  Canada.

  12. Emma Griffiths.  FoodON: A Global Farm-to-Fork Food Ontology. International Food Ontology (FoodON) Consortium.  May 28, 2016.  (Download)

  13. Emma Griffiths, Mélanie Courtot, Damion Dooley, Josh Adam, Franklin Bristow, João A Carriço, Bhavjinder K. Dhillon, Matthew Laird, Thomas Matthews, Aaron Petkau, Geoff Winsor, the IRIDA Ontology Advisory Group, Lynn M Schriml, Eduardo Taboada, Gary Van Domselaar, Morag Graham, Fiona Brinkman and William Hsiao. GenEpiO: The Genomic Epidemiology Application Ontology for the Standardization and Integration of Microbial Genomic, Clinical and Epidemiological Data. Biocuration; April 10-14, 2016; Geneva, Switzerland.  (Download)

  14. Damion M. Dooley, Aaron J. Petkau, Franklin Bristow, Gary Van Domselaar, William W.L. Hsiao.  A Scripting Language For Standardized Evaluation Of Quality Metrics In Galaxy And Command-line Driven Workflows. Estoril, Portugal.  (Download)

  15. Emma Griffiths, Mélanie Courtot, Damion Dooley, Josh Adam, Franklin Bristow, João A Carriço, Bhavjinder K. Dhillon, Matthew Laird, Thomas Matthews, Aaron Petkau, Geoff Winsor, the IRIDA Ontology Advisory Group, Lynn M Schriml, Eduardo Taboada, Gary Van Domselaar, Morag Graham, Fiona Brinkman and William Hsiao. Needs Assessment and Ontology Development for Integrating Whole Genome Sequencing into Routine Outbreak Investigations. 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens; September 24-27, 2015;  Washington, D.C., USA.  (Download)

  16.  Franklin Bristow, Josh Adam, João André Carriço, Mélanie Courtot, Bhavjinder Dhillon, Damion Dooley, Emma Griffiths, Judy Isaac-Renton, Alex Keddy, Peter Kruczkiewicz, Matthew Laird, Andrew MacArthur, Thomas Matthews, Aaron Petkau, Lynn Schriml, Julie Shay, Eduardo Taboada, Patrick Tang, Joel Thiessen, Geoff Winsor, Robert G. Beiko, Morag Graham, Gary Van Domselaar, William Hsiao,The IRIDA Consortium and Fiona Brinkman. A Federated Platform Enabling Richer Genomic Epidemiology Analysis in a Public Health Environment. 1st ASM Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens; September 24-27, 2015;  Washington, D.C., USA.  (Download)

  17. Courtot M, Griffiths E, Dooley D, Adam J, Bristow F, Carriço JA, Dhillon B, Laird M, Lo R, Matthews T, Petkau A, Winsor G, Schriml L, Graham M, Van Domselaar G, Brinkman F, and Hsiao W. The IRIDA genomic epidemiology ontology: Standards to improve infectious disease outbreak detection and investigation. Poster presented at: 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); July 10-14, 2015; Dublin, Ireland. (Download)

  18. Dooley D, Bristow F, Adam, J, Carriço JA, Courtot M, Dhillon, B, Griffiths E, Isaac-Renton J, Keddy A, Kruczkiewicz P, Laird M, Matthews T, Petkau A, Schriml L, Shay J, Taboada E, Tang P, Thiessen J, Winsor G, Beiko RG, Graham M, Van Domselaar G, Hsiao W, The IRIDA Consortium, and Brinkman F. IRIDA: Canada’s federated platform for genomic epidemiology. Poster presented at: 23rd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB); July 10-14, 2015; Dublin, Ireland. (Download)

  19. Petkau A, Bristow F, Matthews T, Adam J, Mabon P, Enns E, Cabral J, Thiessen J, Sieffert C, Knox N, Dooley D, Griffiths E, Winsor G, Laird M, Courtot M, Kruczkiewicz P, Keddy A, Beiko RG, Hsiao W, Van Domselaar G, and Brinkman F. IRIDA: A Genomic Epidemiology Platform Built on top of Galaxy. Poster presented at: Galaxy Community Conference 2015; July 6-8, 2015; Norwich, UK. (Download)

  20. Bristow F, Adam, J, Carriço JA, Courtot M, Dhillon, B, Dooley D, Griffiths E, Isaac-Renton J, Keddy A, Kruczkiewicz P, Laird M, Matthews T, Petkau A, Schriml L, Shay J, Taboada E, Tang P, Thiessen J, Winsor G, Beiko RG, Graham M, Van Domselaar G, Hsiao W, The IRIDA Consortium, and Brinkman F. IRIDA: Canada’s federated platform for genomic epidemiology. Poster presented at: The 8th Meeting of the Global Microbial Identifier; May 11-13, 2015; Beijing, China. (Download)

  21. Nasha J, Yoshida C, Miao D, Kruczkiewicz P & Taboada E.  The effect of whole genome sequencing and assembly upon in silico serotyping of Salmonella enterica using the SISTR platform.  Poster presented at: ABPHM 2015; May 6-8, 2015; UK. (Download)

  22. Shay J, Dhillon B, Laird M,  Winsor G, Griffiths E, Berry C, Knox N, Petkau A,Reimer A, Langille M, Van Domselaar G, Brinkman F.  IslandViewer: More Flexible, Integrated Prediction and Visualization of Genomic Islands, Virulence Factors, and Antimicrobial Resistance Genes in Bacterial Genomes.  Poster presented at Genome BC; May 8, 2015; Vancouver, Canada.  (Download)

  23. Shay J, Dhillon B, Laird M,  Winsor G, Griffiths E, Berry C, Knox N, Petkau A,Reimer A, Langille M, Van Domselaar G, Brinkman F.  IslandViewer: More Flexible, Integrated Prediction and Visualization of Genomic Islands, Virulence Factors, and Antimicrobial Resistance Genes in Bacterial Genomes.  Poster presented at American Society for Microbiology General Meeting; May 30-Jun 2, 2015; New Orleans, USA.  (Download)

  24. Courtot M, Dooley D, Griffiths E, Adam J, Bristow F, Carriço JA, Dhillon B, Laird M, Matthews T, Petkau A, Silva M, Winsor G, the IRIDA Ontology Advisory Group, Schriml L, Van Domselaar G, Brinkman F, and Hsiao W. IRIDA: Standards for public health genomic epidemiology to improve infections disease outbreak and investigation. Poster presented at: The 8th International Biocuration Conference; April 23-26, 2015; Beijing, China. (Download)

  25. Hsiao W, Bristow F, Matthews T, Adam J, Carriço JA, Courtot M, Dhillon B, Dooley D, Griffiths E, Isaac-Renton J, Keddy A, Kruczkiewicz P, Laird M, Petkau A, Schriml L, Shay J, Taboada E, Tang P, Winsor G, Beiko RG, Graham M, Van Domselaar G, The IRIDA Consortium, and Brinkman F. IRIDA: Canada’s federated platform for genomic epidemiology. Poster presented at: BC Centre for Disease Control Research Week; November 17-21, 2014; Vancouver, Canada. (Download)

  26. Courtot M, Dooley D, Griffiths E, Adam J, Bristow F, Carriço JA, Dhillon B, Laird M, Matthews T, Petkau A, Silva M, Winsor G, The IRIDA Ontology Advisory Group, Schriml L, Van Domselaar G, Brinkman F, Hsiao W. Design and implementation of an ontology for public health epidemiology. Poster presented at: BC Centre for Disease Control Research Week; November 17-21, 2014; Vancouver, Canada. (Download)

  27. Laird M, Bristow F, Chiu T, Courtot M, Dhillon B, Griffiths E, Langille M, Shay J, Whiteside M, Winsor G, Van Domselaar G, Hsiao W, and Brinkman F. Comparison and visualization of large datasets of microbial genomes. Poster presented at: Biological Data Science; November 5-8, 2014; Cold Spring Harbor, USA. (Download)

  28. Hsiao W, Bristow F, Matthews T, Adam J, Carriço JA, Courtot M, Dhillon B, Dooley D, Griffiths E, Isaac-Renton J, Keddy A, Kruczkiewicz P, Laird M, Petkau A, Schriml L, Shay J, Taboada E, Tang P, Winsor G, Beiko RG, Graham M, Van Domselaar G, The IRIDA Consortium, and Brinkman F. IRIDA: Canada’s federated platform for genomic epidemiology. Poster presented at: Genome Informatics 2014; September 21-24, 2014; Cambridge, UK. (Download)

  29. Bristow F, Matthews T, Adam J, Carriço JA, Courtot M, Dhillon B, Dooley D, Griffiths E, Isaac-Renton J, Keddy A, Kruczkiewicz P, Laird M, Petkau A, Schriml L, Shay J, Taboada E, Tang P, Winsor G, Beiko RG, Graham M, Van Domselaar G, Hsiao W, The IRIDA Consortium, and Brinkman F. IRIDA: Canada’s federated platform for genomic epidemiology. Poster presented at: The 7th Meeting of the Global Microbial Identifier; September 11-12, 2014; York, UK. (Download)

  30. Courtot M, Dooley D, Griffiths E, Adam J, Bristow F, Carriço JA, Dhillon B, Laird M, Matthews T, Petkau A, Silva M, Winsor G, The IRIDA Ontology Advisory Group, Schriml L, Van Domselaar G, Brinkman F, Hsiao W. Design and implementation of an ontology for public health epidemiology. Poster presented at: The 7th Meeting of the Global Microbial Identifier; September 11-12, 2014; York, UK. (Download)

  31. Dhillon B, Laird M, Shay J, Chiu T, Langille M, Reimer A, Knox N, Petkau A, Berry C, Brinkman F. IslandViewer and IslandPlot: genomic island identification and analysis with improved annotation and more flexible, dynamic visualization. Poster presented at: The 7th Meeting of the Global Microbial Identifier; September 11-12, 2014; York, UK. (Download)

  32. Petkau A, Keddy A, Slusky L, Mabon P, Bristow F, Matthews T, Adam J, Carriço JA, Katz LS, Reimer A, Knox N, Courtot M, Graham M, Hsiao W, Brinkman F, Beiko RG, Van Domselaar G. Outbreak investigation with IRIDA’s SNVPhyl pipeline and GenGIS. Poster presented at: The 7th Meeting of the Global Microbial Identifier; September 11-12, 2014; York, UK. (Download)

  33. Petkau A, Bristow F, Matthews T, Adam J, Dooley D, Griffiths E, Winsor G, Laird M, Courtot M, Hsiao W, Van Domselaar G, Brinkman F. Integration of Galaxy with IRIDA, a Genomic Epidemiology Platform. Poster presented at: The 2014 Galaxy Community Conference; June 30-July 2;Baltimore, MD, USA. (Download)

 

Publications

  1. Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L. MentaLiST - A fast MLST caller for large MLST schemes. Microb Genom. 2018 Jan 10. doi: 10.1099/mgen.0.000146.  https://www.ncbi.nlm.nih.gov/pubmed/29319471

  2. Dooley D, Griffiths E, Gosal G, Brinkman B, Hsiao W. The Genomic Epidemiology Ontology and GEEM Ontology Reusability Platform. ICBO Conference Preceedings. 2018.  (http://ceur-ws.org/Vol-2050/ODLS_paper_12.pdf)

  3. Carriço JA, Rossi M, Moran-Gilad J, Van Domselaar G, Ramirez M. A primer on microbial bioinformatics for nonbioinformaticians. Clin Microbiol Infect. 2018 Jan 5. pii: S1198-743X(17)30709-7. doi: 10.1016/j.cmi.2017.12.015.  (https://www.ncbi.nlm.nih.gov/pubmed/29309933)

  4. Bertelli C, Laird MR, Williams KP, Simon Fraser University Research Computing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017 Jul 3;45(W1):W30-W35. doi: 10.1093/nar/gkx343.  (https://www.ncbi.nlm.nih.gov/pubmed/28472413)

  5. Griffiths E, Dooley D, Graham M, Van Domselaar G, Brinkman FSL, Hsiao WWL. Context Is Everything: Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance. Front Microbiol. 2017; 8: 1068. Published online 2017 Jun 26. doi: 10.3389/fmicb.2017.01068  (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483436/)

  6. Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom. 2017 Jun 8;3(6):e000116. doi: 10.1099/mgen.0.000116. eCollection 2017 Jun 30.  (https://www.ncbi.nlm.nih.gov/pubmed/29026651)

  7. Taboada EN, Graham MR, Carriço JA, Van Domselaar G. Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol. 2017 May 23;8:909. doi: 10.3389/fmicb.2017.00909. eCollection 2017.  (https://www.ncbi.nlm.nih.gov/pubmed/28588568)

  8. Miller RR, Langille MGI, Montoya V, Crisan A, Stefanovic A, Hoang L, Patrick DM, Romney M, Tyrrell G, Jones SJM, Brinkman FSL, Tang P. Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009. Can J Infect Dis Med Microbiol. 2016; 2016: 5381871. Published online 2016 April 14. doi: 10.1155/2016/5381871  (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4904568/)

  9. Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FS, Truelstrup Hansen L, Wang S. Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress. Front Microbiol. 2017 Mar 8;8:369. doi: 10.3389/fmicb.2017.00369. eCollection 2017. (https://www.ncbi.nlm.nih.gov/pubmed/28337186)

  10. Lambert D, Pightling A, Griffiths E,Van Domselaar G,  Evans P, Berthelet S, Craig D, Chandry PS, Stones R, Brinkman F, Angers-Loustau A, Kreysa J, Tong W, Blais B.  Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety.   J. AOAC International. Appeared or available online: Thu Jan 19 00:00:00 GMT 2017 (https://www.ncbi.nlm.nih.gov/pubmed/28105974)

  11. McArthur AG, Tsang KK. Antimicrobial resistance surveillance in the genomic age. Ann N Y Acad Sci. 2017 Jan;1388(1):78-91. doi: 10.1111/nyas.13289. Epub 2016 Nov 22.  (https://www.ncbi.nlm.nih.gov/pubmed/27875856)

  12. Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FSL, Wright GD, McArthur AG. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2017 Jan 4;45(D1):D566-D573. doi: 10.1093/nar/gkw1004. Epub 2016 Oct 26. (https://www.ncbi.nlm.nih.gov/pubmed/27789705)

  13. Lynch T, Petkau A, Knox N, Graham M, Van Domselaar G. A Primer on Infectious Disease Bacterial Genomics. Clin Microbiol Rev. 2016 Oct;29(4):881-913. doi: 10.1128/CMR.00001-16. Epub 2016 Sep 7. (https://www.ncbi.nlm.nih.gov/pubmed/28590251)

  14. Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA. PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic Acids Res. first published online April 29, 2016; doi: 10.1093/nar/gkw359. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987911/)

  15. Miller RR, MGI Langille, V Montoya, A Crisan, A Stefanovic, I Martin, L Hoang, DM Patrick, M Romney, G Tyrrell, SJM Jones, FSL Brinkman, P Tang. Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009. Can J Infect Dis Med Microbiol. 2016;2016:5381871. doi: 10.1155/2016/5381871. Epub 2016 Apr ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4904568/)

  16. Whiteside MD, Laing CR, Manji A, Kruczkiewicz P, Taboada EN, Gannon VPJ. SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli. BMC Microbiol.  BMC Microbiol. 2016 Apr 12;16:65. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828761/)

  17. Yoshida CE, Kruczkiewicz P,  Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies; PLOS One first published online January 22 2016; DOI: 10.1371/journal.pone.0147101  (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101)

  18. Winsor GL, Griffiths EJ, Lo R, Dhillon BK, Shay JA, Brinkman FS. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Nucleic Acids Research 44:D646-53. [Epub ahead of Print]. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702867/)

  19. Marinier E, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, The LiDS-NG Consortium, Van Domselaar G.  Neptune: A Tool for Rapid Genomic Signature Discovery. bioRxiv.  posted online Nov. 18, 2015.  (http://biorxiv.org/content/biorxiv/early/2015/11/18/032227.full.pdf)

  20. Dooley, D., Petkau, A., Van Domselaar G., and Hsiao, W.  Sequence database versioning for command line and Galaxy bioinformatics servers. Bioinformatics. 2015. First published online: December 12, 2015 doi: 10.1093/bioinformatics/btv724 (http://bioinformatics.oxfordjournals.org/content/early/2015/12/11/bioinformatics.btv724.full.pdf+html)

  21. Laird MR, Langille MG, Brinkman FS.  GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications.  Bioinformatics. 2015 first published online June 20, 2015 doi:10.1093/bioinformatics/btv376 (http://bioinformatics.oxfordjournals.org/content/early/2015/07/13/bioinformatics.btv376.long)

  22. Dhillon, B.K., Laird, M.R., Shay, J.A., Winsor, G.L., Lo, R., Nizam, F., Pereira, S.K., Waglechner, N., McArthur A.G., Langille, M.G.I., and Brinkman, F.S.L. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Research. 2015 (Published online before press: doi: 10.1093/nar/gkv401, http://nar.oxfordjournals.org/content/early/2015/04/27/nar.gkv401.full)

  23. Brinkman, F.S.L., Gardy,  J.L., and  Meulien  P.  Big Ideas, Big Data: How genomics will change our world. Policy Magazine (November-December 2014 issue) (http://policymagazine.ca/pdf/10/PolicyMagazineNovember-DecemberMeulienBrinkmanGardy-14.pdf)

  24. Vaz, C., Francisco, A.P., Silva, M., Jolley, K.A., Bray, J.E., Pouseele, H., Rothganger, J., Ramirez, M., and Carriço J.A.  TypOn: the microbial typing ontology.  Journal of Biomedical Semantics 2014, 5:43 (http://www.jbiomedsem.com/content/5/1/43)

  25. Carlsten C, Brauer M, Brinkman F, Brook J, Daley D, McNagny K, Pui M, Royce D, Takaro T, Denburg J.  Genes, the environment and personalized medicine: We need to harness both environmental and genetic data to maximize personal and population health. EMBO Reports 2014 Jun 6. pii: e201438480. (http://onlinelibrary.wiley.com/doi/10.15252/embr.201438480/pdf)

  26. Didelot X, Gardy J, and Colijn C. Bayesian inference of infectious disease transmission from whole-genome sequence data. Mol Biol Evol. 2014 Apr. (http://www.ncbi.nlm.nih.gov/pubmed/24714079)

  27. Courtot M, Brinkman RR, and Ruttenberg A. The logic of surveillance guidelines: An analysis of vaccine adverse event reports from an ontological perspective. PLoS One. 2014 Mar; 9(3). (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0092632)

  28. Pesquita C, Ferreira J, Couto F, and Silva M. The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. J Biomed Semantics. 2014 Jan; 5(1):4. (http://www.jbiomedsem.com/content/5/1/4)

  29. Dhillon BK, Chiu TA, Laird MR, Langille MG, and Brinkman FS. IslandViewer update: Improved genomic island discovery and visualization. Nucleic Acids Res. 2013 Jul; 41(Web Server issue):W129-132. (http://www.ncbi.nlm.nih.gov/pubmed/23677610)

  30. Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, Knox N, Frace M, Boncy J, Graham M, Hammer BK, Boucher Y, Bashir A, Hanage WP, Van Domselaar G, and Tarr CL. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 2013 July; 4(4):e00398-13. (http://mbio.asm.org/content/4/4/e00398-13.abstract)

  31. Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MG, and Beiko RG. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One. 2013 Jul;8(7):e69885. (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069885)

  32. Smith SE, Showers-Corneli P, Dardenne CN, Harpending HH, Martin DP, Beiko RG. Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution. PLoS One. 2012 Nov; 7(11):e50070. (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0050070)

  33. Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, Rempel S, Moore R, Zhao Y, Holt R, Varhol R, Birol I, Lem M, Sharma MK, Elwood K, Jones SJ, Brinkman FS, Brunham RC, and Tang P. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011 Feb; 364(8):730-739. (http://www.ncbi.nlm.nih.gov/pubmed/21345102)

  34. Reimer AR, Van Domselaar G, Stroika S, Walker M, Kent H, Tarr C, Talkington D, Rowe L, Olsen-Rasmussen M, Frace M, Sammons S, Dahourou GA, Boncy J, Smith AM, Mabon P, Petkau A, Graham M, Gilmour MW, Gerner-Smidt P, and Vibrio cholerae Outbreak Genomics Task Force. Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa. Emerg. Infect. Dis. 2011  November; 17(11):2113–2121. (http://www.ncbi.nlm.nih.gov/pubmed/22099115)

  35. MacDonald NJ, Beiko RG. Efficient learning of microbial genotype-phenotype association rules. Bioinformatics. 2010 Aug; 26(15):1834-40. (http://bioinformatics.oxfordjournals.org/content/26/15/1834.abstract)

  36. Petkau A, Stuart-Edwards M, Stothard P, and Van Domselaar G. Interactive microbial genome visualization with GView. Bioinformatics. 2010 October; 26(24): 3125-3126. (http://bioinformatics.oxfordjournals.org/content/26/24/3125)

  37. Brinkman R, Courtot M, Derom D, Fostel J, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoekert CJ, Turner JA, Zheng J, and the OBI Consortium. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 June; 1(Suppl 1):S7. (http://www.jbiomedsem.com/content/1/S1/S7)

  38. Langille MG, Hsiao WW, and Brinkman FS. Detecting genomic islands using bioinformatics approaches. Nat Rev Microbiol. 2010 May; 8(5):373-382. (http://www.ncbi.nlm.nih.gov/pubmed/20395967)

  39. Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko RG. GenGIS: A geospatial information system for genomic data. Genome Res. 2009 Oct; 19(10):1896-904. (http://genome.cshlp.org/content/19/10/1896)