Education
PhD Bioinformatics (expected graduation Sept 2023), University of British Columbia
MSc Population and Public Health, University of British Columbia, May 2019
BSc Microbiology and Immunology, University of British Columbia, May 2014
Exchange Semester, University of Otago, Feb 2011
Publications
- McLaughlin, A., Montoya, V., Miller, R. L., Mordecai, G. J., Worobey, M., Poon, A. F. Y., & Joy, J. B. Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. eLife. (2022). doi: 10.7554/eLife.73896
- Miller, R. L., McLaughlin, A., Liang, R. H., Harding, J., Le, A. Q., Brumme, C. J., Montaner, J. S. G., & Joy, J. B. Phylogenetic prioritization of HIV-1 transmission clusters with viral lineage-level diversification rates. Evolution Medicine and Public Health. (2022). doi: 10.1093/emph/eoac026.
- McLaughlin, A., Sereda, P., Brumme, C. J., Brumme, Z. L., Barrios, R., Montaner, J. S. G., & Joy, J. B. Concordance of HIV transmission risk factors elucidated using viral diversification rate and phylogenetic clustering. Evolution Medicine and Public Health. (2021). doi: 10.1093/emph/eoab028
- MacPherson, A., Louca, S., McLaughlin, A., Joy, J. B., & Pennell, M. W. Unifying phylogenetic birth-death models in epidemiology and macroevolution. Systematic Biology (2021). doi: 10.1093/sysbio/syab049
- McLaughlin, A., Montoya, V., Miller, R. L., Mordecai, G. J., Worobey, M., Poon, A. F. Y., & Joy, J. B. Early and ongoing importations of SARS-COV-2 in Canada. [pre-print] medRxiv (2021). doi: 10.1101/2021.04.09.21255131
- Louca, S., McLaughlin, A., MacPherson, A., Joy, J. B., & Pennell, M. W. Fundamental identifiability limits in molecular epidemiology. Molecular Biology and Evolution. (2021). doi: 10.1093/molbev/msab149
- Louca, S., McLaughlin, A., MacPherson, A., Joy, J. B., & Pennell, M. W. Fundamental identifiability limits in molecular epidemiology. [pre-print] bioRxiv 18, 481-57 (2021). doi: 10.1101/2021.01.18.427170
- Montoya, V., McLaughlin, A., Mordecai G. J., Miller, R. L., Joy, J. B. Variable routes to genomic and host adaptation among coronaviruses. Journal of Evolutionary Biology. (2021). doi: 10.1111/jeb.13771
- MacPherson, A., Louca, S.,McLaughlin, A., Joy, J. B., & Pennell, M. W. A general birth-death-sampling model for epidemiology and macroevolution. bioRxiv 303, 327-19 (2020). doi: 10.1101/2020.10.10.334383
- McLaughlin, A., Sereda, P., Oliveira, N., Barrios, R., Brumme, C.J., Brumme, Z. L., Montaner, J. S. G., & Joy, J. B. Detection of HIV transmission hotspots in British Columbia, Canada: A novel framework for the prioritization and allocation of treatment and prevention resources. EBioMedicine 48, 405-413 (2019). doi: 10.1016/j.ebiom.2019.09.026
- Heggen, A., McLaughlin, A., Russell, G., & Zhang, A. T4 Bacteriophage may not inhibit transcription of T7 bacteriophage genes rpol and gp10a during co-infection of Escherichia coli. Journal of Experimental Microbiology and Immunology 18, 162-166 (2014)
Presentations
- McLaughlin, A.*, Toy, J., Hollebakken, R., Kalynyak, T., Cobarrubias, K., Dong, W., Trigg, J., Sereda, P., Brumme, Z. L., Brumme, C. J., Gustafson, R., Barrios, R., Montaner, J. S. G., & Joy, J. B. Differential reductions in HIV clusters’ effective reproductive number following population level interventions in British Columbia, Canada. Poster presentation at 11th International AIDS Society Conference on HIV Science; 2021 July 18-21; virtual.
- Louca, S., McLaughlin, A.*, MacPherson, A., Joy, J. B., & Pennell, M. W. Fundamental identifiability limits of phylodynamic birth-death models. Poster presentation at 18th Ecology and Evolution of Infectious Diseases; 2021 June 14-17; Montpellier, virtual.
- McLaughlin, A.*, Montoya, V., Miller, R. L., Mordecai, G. J., Worobey, M., Poon, A. F. Y., & Joy, J. B. Origins and dissemination of SARS-COV-2 in Canada. Oral presentation at 28th International Dynamics & Evolution of Human Viruses; 2021 May 5-7; virtual.
- Louca, S., McLaughlin, A.*, MacPherson, A., Joy, J. B., & Pennell, M. W. Fundamental identifiability limits of phylodynamic birth-death models. Oral presentation at 28th International Dynamics & Evolution of Human Viruses; 2021 May 5-7; virtual.
- Montoya, V.*, Mordecai G. J., Miller, R. L., McLaughlin, A., Joy, J. B. Variable routes to genomic and host adaptation among coronaviruses. Poster presentation at COVID-19 Dynamics & Evolution - Part 2; 2020 Oct 19-20; virtual.
- Miller, R. L.*, McLaughlin, A., Montoya, V., & Joy, J. B. Lineage-level diversification rates reflect longitudinal changes in COVID-19 epidemic characteristics. Poster presentation at COVID-19 Dynamics & Evolution - Part 2; 2020 Oct 19-20; virtual.
- McLaughlin, A.*, & Joy, J. B. Phylodynamic analyses reveal differential reductions in HIV cluster-specific reproduction number following provision of pre-exposure prophylaxis. Oral presentation at 27th International Dynamics & Evolution of HIV and Other Human Viruses; 2020 May 11-13; virtual.
- McLaughlin, A*. Epidemiological correlates of HIV lineage-level diversification rate. Oral presentation at 28th Annual Canadian Conference on HIV/AIDS Research; 2019 May 9-12; Saskatoon, SA.
- Joy, J. B.*, McLaughlin, A., Liang, R. H., Choi, J., Brumme, C.J., & Montaner, J. S. G.. A phylogenetic approach to prioritizing HIV transmission clusters. Poster presentation at 26th International HIV Dynamics & Evolution; 2019 Mar 24-27; Cascais, Portugal.
- McLaughlin, A.*, Kalynyak, T., Choi, J., & Joy, J. B. Epidemiological correlates of HIV lineage-level diversification rate. Poster presentation at Conference on Retroviruses and Opportunistic Infections; 2019 Mar 4-7; Seattle, MA.
- McLaughlin, A.*, Harrigan, P. R., Shoveller, J., & Joy, J. B. Phylodynamic method of identifying HIV-1 transmission foci in British Columbia. Poster presentation at 27th annual Canadian Conference on HIV/ AIDS Research; 2018 Apr 26-29; Vancouver, BC.
- McLaughlin, A.*, Harrigan, P. R., Shoveller, J., & Joy, J. B. Phylodynamic method of identifying HIV-1 transmission foci. Poster presentation at 25th International HIV Dynamics & Evolution; 2018 Apr 22-25; Leavenworth, WA.
- McLaughlin, A.*, Harrigan, P. R., Shoveller, J., & Joy, J. B. Phylodynamic methods of identifying foci of HIV-1 transmission. Poster presentation at Conference on Retroviruses and Opportunistic Infections; 2018 Mar 4-7; Boston, MA.
- Jervis, E.*, McLaughlin, A., Hukezalie, K., Woodside, S., Thomas, T.E., Eaves, A.C., & Louis, S. Expansion of human pluripotent stem cells as aggregates in suspension cultures. Poster presentation at International Society for Stem Cell Research; 2016 Jun 22-25; San Francisco, CA.
- Jervis, E.*, McLaughlin, A., Hukezalie, K., Woodside, S., Thomas, T.E., Eaves, A.C., & Louis, S. Expansion of hPSCs as aggregates in suspension bioreactors. Poster presentation at International Society for Stem Cell Research; 2015 Jun 24-27; Stockholm, Sweden.
Funding
- Scholarship, 11th IAS Conference on HIV Science, July 2021
- Frederick Banting and Charles Best Doctoral Award, CIHR, Sept 2020 – Aug 2023
- 2019 Novel Coronavirus (COVID-19) Rapid Research Funding team grant, CIHR, April 2020 – 2021
- Biodiversity Research Centre Collaboration Grant, Jan 2020
- CREATE Bioinformatics Graduate Training Program Grant, NSERC, Sept 2019 – Sept 2020
- Travel Award (to attend Canadian Conference on HIV/ AIDS Research), CIHR, May 2019
- New Investigator Scholarship, Conference on Retroviruses and Opportunistic Infections, Mar 2019
- Dr. Ken Benson Memorial Bursary, Health Officers Council of British Columbia, Oct 2018
- New Investigator Scholarship, Conference on Retroviruses and Opportunistic Infections, Mar 2018
- Young Investigator's Award, HIV Dynamics and Evolution, Apr 2018
- Dorothy Helmer Scholarship in Medicine, UBC Faculty of Medicine, Jan 2018
- Frederick Banting and Charles Best Canada Graduate Scholarship, CIHR, Sep 2017 – Sep 2018
- Go Global Scholarship, University of British Columbia, Jan 2011
- Dean's Honour List, University of British Columbia, Apr 2008 – Apr 2014
- UBC President's Entrance Scholarship, University of British Columbia, Sep 2008
Research Experience
Research Assistant, Molecular Epidemiology and Evolutionary Genetics
BC Centre for Excellence in HIV/AIDS, St. Paul’s Hospital, Vancouver, BC
May 2017 – present
- Study the genomic epidemiology of rapidly evolving viruses, HIV-1 and SARS-CoV-2.
- Write scripts in R, bash, and python to clean data, align and subsample sequences, infer phylogenetic trees, and build epidemiological models for large datasets.
- Master's thesis
- Mapped the spatiotemporal distribution of HIV phylogenetic diversification rates to predict geographic transmission patterns in British Columbia.
- Compared patient characteristics associated with transmission and clustering.
- Characterized birth-death model identifiability in collaboration with researchers from University of Oregon, University of Toronto, and University of British Columbia
Research Associate, Bioengineering
STEMCELL Technologies, Vancouver, BC, May 2014 – May 2017
- Collaborated with multiple teams to design, run, and analyze experiments to optimize media and protocols for the maintenance and differentiation of human stem cells in bioreactors.
- Contributed towards lab management, employee training, co-op mentorship, technology transfer, stability studies, technical writing, and inter-departmental education.
- Primary author of the mTeSR3D Technical Manual
Research Assistant, Dr. James Piret Laboratory
Michael Smith Laboratories, UBC, Vancouver, BC, July 2013 – May 2014
- Undergraduate thesis: “A scalable method of simulating fed-batch growth and productivity by resuspending CHO cultures in conditioned media”.
- Developed methods to culture and rank Chinese Hamster Ovary (CHO) clones for the production of recombinant antibodies in microfluidic devices.
Intern/Researcher, Cell Line Development
Bayer HealthCare Pharmaceuticals, Berkeley, CA, July 2012 – July 2013
- Transfected, cloned, scaled up, and ranked Chinese Hamster Ovaries (CHO) cell lines to produce recombinant biopharmaceutical antibodies.
- Collected, analyzed, and presented data to scientific and corporate audiences.
Volunteer Experience
Canadian Red Cross Emergency Response Team,
Vancouver, BC, Dec 2020 - present
- Contribute to emergency response by assisting victims to meet their immediate needs.
Dr. Peter Centre
Vancouver, BC, May 2018 – Jan 2020
- Engaged with HIV+ community and helped with therapy activities within the Day Health Program.
Physical Activity Research Centre, ICORD
Vancouver, BC, Nov 2014 - July 2015
- Assisted research participants with spinal cord injuries with their rehabilitative exercises.
Vancouver Folk Music Festival
Vancouver, BC, July 2014 – July 2019
- As a Shift Coordinator, managed 30 volunteers per shift to run beer garden with capacity for 1500 festival attendees.
Vancouver Adaptive Snow Sports
Vancouver, BC, Jan 2014 – Mar 2019
- Taught adaptive snowboarding at Grouse Mountain for people with physical and cognitive disabilities.