• Hughes, J.S., X. Huo, L. Falk, B. Coburn, A. Hurford, K. Lan, A.M. Morris and J. Wu. 2017. Benefits and unintended consequences of antimicrobial de-escalation. PLOS One 12(2):e0171218
• Hughes, J.S., A. Hurford, R.L. Finley, D.M. Patrick, J. Wu and A.M. Morris. 2016. How to measure the impacts of antibiotic resistance and antibiotic development on empiric therapy: new composite indices. BMJ Open 6:e012040.
• Hughes, J.S., C.A. Cobbold, K. Haynes, and G. Dwyer. 2015. The effects of forest spatial structure on insect outbreaks: insights from a simple host-parasitoid model. The American Naturalist 185(5):E130-E152. 
• Hughes, J.S., M.J. Fortin, V. Nealis, and J. Régnière. 2014. Pollen cone production in jack pine: spatial and temporal patterns subject to natural disturbance by the jack pine budworm. The Canadian Journal of Forest Research.  44(3): 195-211.
• Shore, T.L., A. Fall, W.G. Riel, J. Hughes and M. Eng. 2008. Methods to assess landscape scale risk of bark beetle infestation to support forest management decisions. Forest Encyclopedia Network: Environmental Threats: Pests/Biota: Native. USDA Forest Service, Asheville, NC. Online pub.
  
• Hughes, J.S., A. Fall, L. Safranyik, and K. Lertzman. 2007. Modeling the effect of landscape pattern on mountain pine beetles. Natural Resources Canada, CanadianForest Service, Pacific Forestry Centre, Victoria, British Columbia. Information Report BC-X-407.
  
• Schlesier, L., J. Hughes, A. Fall, and M. S. T. Carpendale. 2006. The LuMPB Key: A Multiple View Interface to Explore High Dimensional Mountain Pine Beetle Simulation Data. In Proceedings of the Fourth International Conference on Coordinated and Multiple Views in Exploratory Visualization (CMV 2006, July 4th, 2006, London, Great Britain), pages 31-41, 2006. IEEE Press.
• Hughes, J.S. and S.P. Otto. 1999. Ecology and the evolution of biphasic life cycles. The American Naturalist 154(3): 306-320.

Conference presentations

• Hughes, J.A, L. Frid, M. Suitor, T. Hegel. A population demography modeling tool to explore harvest management scenarios for the Fortymile caribou herd. Poster at the 17th North American Caribou Workshop. Oct 2018. Ottawa, ON.
• Hughes, J.S., A. Hurford, D.M. Patrick, J. Wu and A.M. Morris. Monitoring the net clinical impact of resistance: composite indices show improvement in our ability to cover severe device-associated infections in an academic ICU since 2000. Incubator poster at AMMI Canada. Apr 2016. Vancouver, BC.
• Dresser L., J.S. Hughes, M. McIntyre, S. Nelson, N. Ferguson, S. Lapinsky, N. Lazar, S. Mehta, L. Burry, J. Singh, C. Bell and A.M. Morris. Antimicrobial stewardship programs reduce daily prescribing variability in academic ICUs. Oral presentation at AMMI Canada. Apr 2016. Vancouver, BC.
• Dresser L., J.S. Hughes, M. McIntyre, S. Nelson, N. Ferguson, S. Lapinsky, N. Lazar, S. Mehta, L. Burry, J. Singh, C. Bell and A.M. Morris. Antimicrobial stewardship programs reduce daily prescribing variability in academic ICUs. Oral poster at the Critical Care Canada Forum. Oct 2015. Toronto, ON.
• Hughes, J.S., A. Hurford, R.L. Finley, D.M. Patrick, J. Wu and A.M. Morris. How to measure antibiotic resistance using empiric therapy indices. Poster at IDWeek. Oct 2015. San Diego, CA.
• Hughes, J.S., A. Hurford, J. Wu and A.M. Morris. 2015. Constructing Syndrome-Specific Antibiograms for Catheter-Associated Bloodstream Infections Using Uncertainty Estimation and Colour. Poster at the Interscience Conference on Antimicrobial Agents and Chemotherapy. September 2014. Washington, DC
• Hughes, J., C. Cobbold, B. Cooke, G. Dwyer, K. Haynes, and M. Pineda-Krch. 2011. The effect of landscape configuration on forest insect outbreak dynamics – insights from a simple host-parasitoid model. Presentation to the North American Forest Ecology Workshop. June 2011. Roanoke, VA.
• Hughes, J. and M.J. Fortin. 2010. Does density-dependent dispersal explain mountain pine beetle spread? Performance of models across years and regions in BC (Canada). Presentation to The Ecology Society of America. Aug 1-6. Pittsburgh, PA.
• Fortin, M.J. and J. Hughes. 2010. Statistics needed to study global change: Which ones to use? Invited presentation to The Ecology Society of America. Aug 1-6. Pittsburgh, PA.
• Hughes, J., M.J. Fortin and V. Nealis. 2010. Untangling reciprocal interactions in space-time data: the effects of jack pine budworm defoliation on jack pine flowering. Presentation to The Canadian Society for Ecology and Evolution. May 9-12. Quebec, QC.
• Hughes, J., M. Eng, A. Fall, M.J. Fortin, A. Walton, T. Shore, B. Riel. 2008. Lessons from an applied mountain pine beetle model: Simple answers are important, interesting questions remain. Invited presentation to The International Association of Landscape Ecology – U.S. Chapter. Apr 6-10, 2008. Madison, WI.
• Hughes, J.S., A. Fall, T. Shore, B. Riel, M. Eng, and P. Hall. 2005. Understanding landscape pattern and mountain pine beetle management in British Columbia. Poster for The Ecological Society of America. Aug 8 to 12. Montreal, QC.
• Hughes, J.S., A. Fall, T. Shore, B. Riel, M. Eng and P. Hall. 2005. Generalizing specific models and landscape conditions to gain insight into landscape scale interactions between forest patterns, mountain pine beetles and management. Presentation to The International Union of Forest Research Organizations Meeting on Forest Insect Epidemics. July 11-14. Prince George, BC.
• Hughes, J., A. Fall, and K. Lertzman. 2003. Modeling the effect of landscape pattern on mountain pine beetles. Presentation to The International Association of Landscape Ecology – U.S. Chapter. Apr 2-6. Banff, AB.
• Hughes, J., A. Fall, M.J. Fortin, and K. Lertzman. 2001. Predicting the effect of pattern on congregative dispersal: A comparison of landscape indices. Presentation to The International Association of Landscape Ecology – U.S. Chapter. Apr 25-29. Pheonix, Arizona.

Reports

• Hughes, J.S., L. Frid and C. Daniel. 2017. Simulating the Fortymile caribou herd using DG-Sim. Prepared by Apex Resource Management Solutions for Environment Yukon.
• Frid, L., J.S. Hughes and C. Daniel. 2017. Forest management guide for Great Lakes – St. Lawrence landscapes: review of simulated range of natural variation. Prepared by Apex Resource Management Solutions for The Ontario Ministry of Natural Resources and Forestry
• Frid, L., C. Daniel and J.S. Hughes. 2017. Using ST-Sim as the LANDFIRE update engine. Prepared by Apex Resource Management Solutions for The Nature Conservancy LANDFIRE Project.
• Hughes, J.S., M. Eng and A. Fall. 2006. Provincial-level projection of the current mountain pine beetle outbreak Appendix 3: Mountain pine beetle projection. British Columbia Ministry of Forests Technical Report, Victoria.
• Eng, M., A. Fall, J. Hughes, T.L. Shore, W.G. Riel, P. Hall, A. Walton. 2005. Provincial-Level Projection of the Current Mountain Pine Beetle Outbreak: An Overview of the Model (BCMPB v2) and Results of Year 2 of the Project. Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, B.C. Mountain Pine Beetle Initiative Working Paper 2005-20.
• Hughes, J. and R. Drever. 2001. Salvaging solutions: science-based management of BC’s pine beetle outbreak. Commissioned By the David Suzuki Foundation, Forest Watch of British Columbia (a project of the Sierra Legal Defence Fund), and the Canadian Parks and Wilderness Society – B.C. Chapter. Vancouver, B.C.