Madeleine Bonsma-Fisher
Toronto, ON | m.bonsma@utoronto.ca
EDUCATION
University of Toronto, Toronto, ON – 2015 to 2022
PhD, Physics
Supervisor: Sidhartha Goyal
Thesis: “Population dynamics of CRISPR adaptive immunity in communities of bacteria and phages: A window into another world
University of Toronto, Toronto, ON – 2014 to 2015
MSc, Physics
Supervisor: Sidhartha Goyal
Thesis: “Analyzing Prokaryote-Phage Interactions Using the CRISPR locus”
University of Waterloo, Waterloo, ON – 2009 to 2014
BSc, Honours Co-operative Physics
Minor: Biology
Honours Thesis: “Analyzing Oscillations in the Rat Ventral Striatum”
RESEARCH
Postdoctoral
University of Toronto, Toronto, ON
Data Sciences Institute – 2022
Graduate
University of Toronto, Toronto, ON
Biophysics Group, Department of Physics – 2014 to 2022
phageParser Open Source Project
Project Lead – 2015 to 2022
Undergraduate
University of Waterloo, Waterloo, ON
Computational Neuroscience Group, Department of Biology – 2013-2014
Supervised by Dr. Matthijs van der Meer.
Dalhousie University, Halifax, NS
DREAMS Undergraduate Visiting Research Assistant – Summer 2013
Supervised by Dr. Jeff Dahn.
Institute for Quantum Computing, University of Waterloo, Waterloo, ON
Undergraduate Research Assistant – Fall 2012
Supervised by Dr. Kevin Resch.
Vineland Research and Innovation Centre, Vineland, ON
Research Assistant – Summer 2010
Industry
Sensors & Software Inc., Mississauga, ON
R&D Applications Testing Assistant – Winter 2011 & Winter 2012
Christie Digital Systems Inc., Kitchener, ON
Optical Engineering Assistant – Fall 2011
PUBLICATIONS
Refereed publications
M. Bonsma-Fisher, S. Goyal
Dynamics of immune memory and learning in bacterial communities. Under review at eLife.
L. W. Johnston, M. Bonsma-Fisher, J. Ostblom, A. R. Hasan, J. S. Santangelo, L. Coome, L. Tran, E. Sales de Andrade, S. Mahallati.
A graduate student-led participatory live-coding quantitative methods course in R: Experiences on initiating, developing, and teaching. The Journal of Open Source Education, 2(16), 49 (2019).
M. Bonsma-Fisher, D. Soutiere, S. Goyal.
How adaptive immunity constrains the composition and fate of large bacterial populations. PNAS (2018). DOI: 10.1073/pnas.1802887115. Full text PDF
L. Vermeyden, X. Ma, J. Lavoie, M. Bonsma, U. Sinha, R. Laflamme, K. J. Resch.
Experimental test of environment-assisted invariance. Physical Review A, 91, 012120 (2015).
L. Vermeyden*, M. Bonsma*, C. Noel, J.M. Donohue, E. Wolfe, K. J. Resch.
Experimental violation of three families of Bell inequalities. Physical Review A, 87, 032105 (2013). *These authors contributed equally to this work.
Other publications
M. Bonsma-Fisher and D. Roberston. Ottawa’s Winter Cycling Network: An analysis of expansion opportunities using Strava Ridership Data. Report circulated to Ottawa City Council.
M. Bonsma-Fisher and A. Hasan. Working with plant phenology data and fitting a nonlinear model using least squares in R. NEON Faculty Mentoring Network, QUBES Educational Resources. doi:10.25334/Q4Q73D
M. Bonsma-Fisher. Working with spreadsheet-style data in Python with pandas and seaborn. QUBES Educational Resources. doi:10.25334/Q4PF1D
M. Bonsma-Fisher. The Importance of Working Open. Medium.
SELECTED PRESENTATIONS
Invited Talks and Panels
M. Bonsma-Fisher.
Immune memory in the CRISPR arms race
MicrobeTO Seminar Series, Toronto, Canada – October 18, 2019
M. Bonsma-Fisher, A. Hasan, J. S. Santangelo.
Let them learn R – and reproducible, collaborative, quantitative science
GTA R User Group, Toronto, Canada – October 16, 2019
M. Bonsma-Fisher.
Open CRISPR: leveraging open source for scientific discovery
Free Software and Open Source Symposium 2018, Toronto, Canada – October 25, 2018 [Keynote]
M. Bonsma.
Are You Open?
Shaking it Up: Making Open Science Work For You, Toronto, Canada – April 25, 2017 [Panelist]
M. Bonsma.
Using Personas and Pathways to Build Community
Mozilla Science Lab Working Open Workshop, Montreal, Canada – March 10, 2017
Contributed Talks and Workshops
M. Bonsma-Fisher and S. Goyal.
Diversity-generating host-disease coevolution with CRISPR adaptive immunity
Canadian Association of Physicists Congress, Hamilton, Canada – 2022
M. Bonsma-Fisher and S. Goyal.
Who lives, who dies: Average immunity predicts population outcomes in host-disease coevolution
Ontario Networking Event in Biophysics, Toronto, Canada – 2021
M. Bonsma-Fisher.
Working with data in Python
iSchool Master of Information Programming Bootcamp, Toronto, Canada – September 7, 2018 [Workshop]
M. Bonsma-Fisher, D. Soutiere, S. Goyal.
Adaptive immunity constrains the composition and fate of large bacterial populations
APS March Meeting, Los Angeles, USA – March 7, 2018
M. Bonsma-Fisher, D. Soutiere, S. Goyal.
The CRISPR-Cas system: a window into the microbial world
Physics Summer Colloquium, Toronto, Canada – June 22, 2017
M. Bonsma, D. Soutiere, S. Goyal.
Modelling the effect of CRISPR on bacteria-virus interactions
Ontario Networking Event in Biophysics, Mississauga, Canada – June 16, 2017;
M. Bonsma, S. Goyal.
Building bacteria-phage interaction networks using the CRISPR locus.
Women in Physics Canada Conference, Toronto, ON – July 31, 2015p;
Poster Sessions
M. Bonsma-Fisher, S. Goyal.
Signatures of co-evolution in the CRISPR adaptive immune system.
Canadian Society for Ecology and Evolution 2018, Guelph, Canada – July 19, 2018
M. Bonsma-Fisher, D. Soutiere, S. Goyal.
How adaptive immunity constrains the composition and fate of large bacterial populations.
Canadian Society for Ecology and Evolution 2018, Guelph, Canada – July 19, 2018
M. Bonsma-Fisher, D. Soutiere, S. Goyal.
Diversity and survival in the CRISPR adaptive immune system.
Ontario Networking Event in Biophysics, Mississauga, Canada – June 15, 2018
M. Bonsma, S. Goyal.
Building bacteria-phage interaction networks using the CRISPR locus.
The Ninth q-bio Conference, Blacksburg, VA – August 6, 2015
SELECTED AWARDS
Queen Elizabeth II Graduate Scholarship in Science and Technology – 2020-2021
NSERC Vanier Canada Graduate Scholarship, University of Toronto – 2016-2020
NSERC Gilles Brassard Doctoral Prize for Interdisciplinary Research – 2016-2017
NSERC Alexander Graham Bell Canada Graduate Scholarship – Doctoral – 2016-2017 [Declined]
Mozilla Network50 – 50 People Who Made the Internet a Better Place in 2016
Van Kranendonk Teaching Assistant Award, University of Toronto – 2015-2016
NSERC Canada Graduate Scholarship – Master’s, University of Toronto – 2015-2016
Ontario Graduate Scholarship, University of Toronto – 2014-2015
Mike Lazaridis Scholarship in Theoretical Physics, University of Waterloo (declined) – 2013
NSERC Undergraduate Student Research Award, University of Waterloo – 2012