jennifer gardy

jennifer [dot] gardy [at] bccdc [dot] ca

new job! as of june 2009, i'm now a researcher at the bc centre for disease control!

latest update: august 2009.

+ research interests
in 2005, i finished my phd in the f.s.l. brinkman laboratory, where i studied computational methods for protein subcellular localization prediction in bacteria. during my time there, i developed psortb - the most precise bacterial localization prediction tool available - and created the psort.org localization resource site. i also worked on development of the psortdb dataset and website. all that work on localiation has made me very good at reading maps.

from january 2006 - may 2009, i was a postdoctoral fellow in the r.e.w. hancock laboratory at the university of british columbia , where i was part of a large, international research project examining the mammalian innate immune system. i was part of the team working on innatedb, a comprehensive biomolecular interaction and pathway database designed to facilitate systems-level analysis of mammalian datasets. my principal role was in the development of the cerebral cytoscape plugin, which provides a subcellular localization context to network layout, and makes navigating and comparing multiple quantitative datasets in a network context easy as pie. and we all like pie.

now i'm at the bc centre for disease control. a colleague and i are leading their new genome research lab and are bringing a new genomics/bioinformatics perspective to the centre's public health and infectious disease work. our current work is focused on the molecular evolution of emerging outbreak situations, both bacterial and viral. we'll be on zombies too, if that ever happens.

science communication is my other passion, and i've done a pile of writing (most recently for the globe & mail) and some television. you can still catch me hosting project x in reruns on cbc at odd and unusual hours.

+ academic background

  • Postdoctoral Fellowship, R.E.W. Hancock Lab. Centre for Microbial Diseases & Immunity Research. University of British Columbia. Vancouver, BC. January 2006 - present.
  • PhD, F.S.L. Brinkman Lab. Dept. of Molecular Biology and Biochemistry. Simon Fraser University. Burnaby, BC. September, 2001 – December, 2005.
  • Graduate Certificate in Biotechnology. McGill University. Montreal, QC. January, 2001 – May, 2001.
  • B.Sc., Cell Biology and Genetics. University of British Columbia. Vancouver, BC. September, 1996 – May, 2000.
  • Science Communications Workshop. The Banff Centre. Banff, AB. August, 2006
  • BCST1170: Introduction to Broadcast Journalism. British Columbia Institute of Technology. Vancouver, BC. September, 2005 – November, 2005.

+ publications

+ other publications

+ invited talks

  • Gardy JL. Perspectives on protein subcellular localiation prediction: lessons from PSORTb and friends. Invited keynote address. Protein Structure Prediction Workshop. Aug. 26-29, 2009. Budapest, Hungary.
  • Gardy JL. Getting the most out of your conference experience. Pre-conference workshop for the International Conference on Mathematical Biology & Annual Meeting of the Society for Mathematical Biology. July 25, 2009. Vancouver, BC, Canada.
  • Gardy JL. An Insider’s Guide to Networking. MITACS Soft Skills Workshop Series. Nov. 17, 2008. Vancouver, BC, Canada. PrioNet SYPA Day. Mar. 1, 2009. Edmonton, AB, Canada.
  • Gardy JL. Cold Flu & You. Government of Canada – 2008 Alberta Human Resources Professionals’ Workshop. Oct. 8, 2008. Banff, AB, Canada.
  • Gardy JL. Cerebral: A Cytoscape plugin for the network-based visualization of datasets from multiple experimental conditions. 9th Annual BioPathways Meeting. July 19, 2008. Toronto, ON, Canada.
  • Gardy JL. Cerebral: A Cytoscape plugin for the network-based visualization of datasets from multiple experimental conditions. 2008 Cytoscape Retreat. July 18, 2008. Toronto, ON, Canada.
  • Gardy JL. Science presentation skills for the graduate student. SFU/MITACS Soft Skills Workshop Series. Multiple sessions – May 2008-present. Vancouver, BC, Canada.
  • Gardy JL. Making the most of your graduate training. UBC Science: Vivien M. Srivastava Career Mentoring Workshop. May 3, 2008. Vancouver, BC, Canada.
  • Gardy JL. Immune interaction databases: the present, the problems, the future. Biodefense Immune Modeling Summer School. June 22, 2007. Pittsburgh, PA, USA.
  • Gardy JL. Bioinformatics resources for the systems-level analysis of innate immunity: the InnateDB interaction database and a novel method for the pathway-like layout of biological networks. 9th Annual Conference on Computational Genomics. Oct. 31, 2006. Baltimore, BD, USA.
  • Gardy JL. Evolution of microbial cellular networks: Insights from improved genome-wide prediction of orthologs and protein subcellular localization. 4th RECOMB Comparative Genomics Satellite Workshop. Sept. 25, 2006. Montreal, QC, Canada.
  • Gardy JL. An interdisciplinary approach to bioinformatics: the PSORTb software for protein localization prediction. IRMACS: The Interdisciplinary Colloqium. Nov. 10, 2005. Burnaby, BC, Canada.
  • Gardy JL. Updates from the protein localization prediction front: PSORTb, PSORTdb and perspectives on predictive methods. Vancouver Bioinformatics Users Group (VanBug) monthly seminar series. Sept. 9, 2004. Vancouver, BC, Canada.
  • Gardy JL. PSORTb: an open source meta-analysis tool for protein localization prediction. 5th Annual Bioinformatics Open Source Conference (BOSC). Jul. 29-30 2004. Glasgow, Scotland.
  • Gardy JL. Analysis and prediction of protein subcellular localization for Gram-negative bacteria. American Society for Microbiology Northwest Branch Meeting. Aug. 7-10, 2003. Vancouver, BC, Canada.
  • Gardy JL. Computational prediction of subcellular localization in Gram-negative bacteria. 2nd ASM/TIGR Conference on Microbial Genomes. Feb. 10-13, 2002. Las Vegas, NV, USA.

+ posters personally presented (excludes posters presented by others on which i was listed as an author)

  • Gardy JL, Lynn DJ, Hancock REW, Brinkman FSL. InnateDB and Cerebral Facilitate the Systems-Level Analysis of Large Datasets: Case Studies. 17th International Conference on Intelligent Systems for Molecular Biology. June 27-July 2, Stockholm, Sweden.
  • Gardy JL, Barsky A, Kincaid R, Munzner T, Hancock REW. Cerebral: Visual Comparison of Multiple Qualitative Datasets in a Network Context permits Novel Insights into Pathogenesis. Keystone Symposium on Emerging Infectious Diseases. Oct. 23-26, Bangkok, Thailand.
  • Gardy JL, Barsky A, Kincaid R, Munzner T, Hancock REW. Cerebral 2.0: a Cytoscape plugin for the network-based visualization of datasets from multiple experimental conditions. 16th International Conference on Intelligent Systems for Molecular Biology. July 17-23, Toronto, Ontario, Canada.
  • Gardy JL, Lynn D, Winsor G, Barsky A, Roche F, Chan T, Laird M, Chan C, Shah N, Richard N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside M, Munzner T, Hancock REW, Brinkman FSL. InnateDB & Cerebral: user-friendly tools for the systems-level analysis of innate immunity. Experimental Biology 2008. April 4-9, 2008. San Diego, CA, USA.
  • Gardy JL, Brown KL, Mookherjee N, Hokamp K, Roche FM, Speert DP, Falsafi R, Acab MR, Lo R, Brinkman FSL, Hancock REW. A systems biology approach to understanding innate immunity: Immunomodulatory effects of the host defence peptide LL-37 and contrasting gene expression defects in patients with inflammatory disorders. Keystone Symposium - Systems Biology: Integrating Biology, Technology and Computation. Mar. 5-10, 2006. Taos, NM, USA.
  • Gardy JL, Brinkman FSL. Comparative analysis of computationally predicted bacterial protein subcellular localization: perspectives on network complexity and the need for more diverse training data. 13th International Conference on Intelligent Systems for Molecular Biology. June 26 - 29, 2005. Detroit, MI, USA.
  • Gardy JL, Brinkman FSL. Comparative Genomics of Bacterial Protein Subcellular Localization: Resources and Analysis. The International Conference on Microbial Genomes. April 13-17, 2005. Halifax, NS, Canada.
  • Gardy JL, Chen F, Walsh CJ, Laird MR, Rey S, Ester M, Brinkman FSL. PSORT-B: Improved Prediction of Subcellular Localization and Insights Gained from Comparative Analysis of Bacterial Proteomes. 12th International Conference on Intelligent Systems for Molecular Biology. July 31 - August 4, 2004. Glasgow, Scotland.
  • Gardy JL, Walsh CJ, Rey S, Laird MR, Brinkman FSL. Prediction of Subcellular Localization and Insights Gained from Comparative Analysis of Bacterial Proteomes. 54th Annual General Meeting of the Canadian Society of Microbiologists. June 20-23, 2004. Edmonton, AB, Canada.
  • Gardy JL, Laird MR, Rey S, Spencer CA, Walsh CJ, Brinkman FSL. PSORT-B: Improving and Comparing Subcellular Localization Prediction for Bacteria. ASM 104th Annual General Meeting. May 22-27, 2004. New Orleans, LA, USA.
  • Gardy JL, Chen F, Walsh CJ, Laird MR, Rey S, Ester M, Brinkman FSL. PSORT-B: Improved Prediction of Subcellular Localization and Insights Gained from Comparative Analysis of Bacterial Proteomes. TIGR Genomes 2004. April 14-17, 2004. Hinxton, England.
  • Gardy JL, Spencer CA, Rey S, Brinkman FSL. PSORT-B: A Web-Based Method for Bacterial Subcellular Localization Prediction. ASM NW Branch Meeting. Aug. 7-10, 2003. Vancouver, BC, Canada.
  • Gardy JL, Spencer CA, Rey S, Brinkman FSL. PSORT-B: A Web-Based Method for Bacterial Subcellular Localization Prediction. 11th International Conference on Intelligent Systems for Molecular Biology, June 29-July 3, 2003. Brisbane, Australia.
  • Gardy JL, She R, Chen F, Wang K, Ester M, Brinkman FSL. Identifying Bacterial Outer Membrane Proteins Using Frequent Subsequences: A Data Mining Approach. 11th International Conference on Intelligent Systems for Molecular Biology, June 29-July 3, 2003. Brisbane, Australia.
  • Gardy JL, Spencer CA, Ho Sui SJ, Hsing MM, Ester M, Brinkman FSL. Prediction of Protein Subcellular Localization in Gram-negative Bacteria: An Updated Version of PSORT. 10th International Conference on Intelligent Systems for Molecular Biology, Aug. 3-7, 2002. Edmonton, AB, Canada.

+ teaching

  • May, 2009: Introduction to Marine Science Filmmaking (Bamfield Marine Science Centre). Guest lecturer (1 lecture)
  • 2007-present: MICB 404 – Selected Topics in Pathogenesis (University of British Columbia). Guest lecturer (2 lectures)
  • June 2007: Canadian Bioinformatics Workshops-Bioinformatics (Vancouver, BC) - Lead instructor
  • February 2006: Canadian Bioinformatics Workshops-Bioinformatics (Toronto, ON) - Lead instructor
  • February 2005: Canadian Bioinformatics Workshops-Bioinformatics (Vancouver, BC) - Co-lead instructor
  • February 2004: Canadian Bioinformatics Workshops-Bioinformatics (Vancouver, BC) - Co-lead instructor
  • September 2003: MBB 441/841-Bioinformatics (Simon Fraser University) - Teaching assistant
  • May 2003: Canadian Bioinformatics Workshops-Bioinformatics (Ottawa, ON) - Co-lead instructor
  • March 2003: Canadian Bioinformatics Workshops-Bioinformatics (Vancouver, BC) - Instructor
  • September 2002: MBB 441/841-Bioinformatics (Simon Fraser University) - Teaching assistant
  • February 2002: Canadian Bioinformatics Workshops-Bioinformatics (Vancouver, BC) - Instructor

+ funding

  • 2007-2010: Canadian Institutes for Health Research Postdoctoral Fellowship (co-funding from Sanofi Pasteur) - Novel Alternatives to Antibiotics ($135,000)
  • 2006-2008: Michael Smith Foundation for Health Research Postdoctoral Fellowship ($78,000)
  • 2005-2006: Canadian Institutes for Health Research Canada Graduate Scholarship ($70,000)
  • April 2005: TIGR Student Travel Award ($1300)
  • 2004-2006: Michael Smith Foundation for Health Research Senior Graduate Studentship ($45,000)
  • Spring 2004: SFU Graduate Fellowship ($6000)
  • July 2003: Burroughs-Wellcome Canadian Proteomics Workshop Award ($1600)
  • Summer 2003: Macmillan-Bloedel MBB Graduate Scholarship ($4800)
  • Spring 2003: SFU Graduate Fellowship ($4800)
  • Feb. 2002: American Society for Microbiology Student Travel Fellowship ($500)
  • Feb. 2002: Burroughs-Wellcome Canadian Bioinformatics Workshop Award ($2200)

+ awards

  • July 2006: PSORTb v.2.0 manuscript selected as a New Hot Paper in the field of Computer Science by Thomson's Essential Science Indicators (Top 0.1% of citations in a bimonthly period)
  • May 2006: Governor General's Gold Medal (Top Graduating PhD Student at SFU)
  • July 2003: Intelligent Systems for Molecular Biology Best Poster Award
  • May 2003: SFU Faculty of Science Excellence in Teaching Award

+ television appearances

  • Urban Rush (Shaw Television): Regular guest. Multiple episodes. Feb. 2008– present.
  • Project X (CBC Television): Co-host. 8 episodes. Feb.-Apr. 2008.
  • The Leading Edge (Knowledge Network): Guest. 1 episode. Sept. 2007





    i have a secret webpage at jennifergardy.com!