Emerson Harkin 
Emerson Harkin
contact-739please-dont-spam-me@efharkin.com at efharkin.com
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Education
Ph.D. in neuroscience
- Center for Neural Dynamics, University of Ottawa
- Advisor: Richard Naud
- Thesis: Making sense of serotonin through spike frequency adaptation
2019 – 2023
- Research-intensive doctoral program located in the Faculty of Medicine, enabling close collaboration between experimental and computational neuroscientists.
- Introduced a computational model of the serotonin system that merges top-down ideas from reinforcement learning with bottom-up experimental insights into its signal processing features (Harkin, Grossman, et al., 2023; Harkin, Lynn, et al., 2023).
- Contributed to designing and implementing analysis of large-scale calcium imaging data as part of collaborative projects on reward coding in motor cortex (Lee, Harkin, et al., 2022) and visual coding (ongoing collaboration with Allen Institute for Brain Science, Charité University, and University of Melbourne).
- Developed Python frameworks for training spiking neural networks (Harkin, Shen, et al., 2022) and manipulating demultiplexed spiketrains (internal).
M.Sc. in neuroscience
- Center for Neural Dynamics, University of Ottawa
- Advisors: Jean-Claude Béïque and Richard Naud
- Thesis: A simplified serotonin neuron model
2016 – 2018
- Identified the dominant biophysical mechanisms governing the activation function of serotonin neurons (Harkin, 2018).
- Carried out patch-clamp electrophysiological experiments (advised by Jean-Claude Béïque) then developped and fitted a new class of semi-biophysical generalized leaky integrate-and-fire model (advised by Richard Naud; see Harkin, Béïque, and Naud, 2022).
- Created ez-ephys, a Python library for designing and simulating electrophysiological experiments.
- Completed coursework in cellular and molecular neuroscience, neurotransmission and neuromodulation, and computational neuroscience.
B.Sc. with honours in biomedical sciences, summa cum laude
- Faculty of Science, University of Ottawa
- Advisor: Paul Albert
- Thesis: Transcriptional regulation of the serotonin-1A receptor by lithium
2012 – 2016
- Coursework in neuroscience, physiology, pharmacology, applied physics, and statistics.
- Research internships in neuropharmacology (advised by Paul Albert), plant-derived medicine (advised by Cory Harris; see Mazhar, Harkin et al., 2016), and pesticide toxicity (advised by John Arnason).
Honours and awards
Queen Elizabeth II Graduate Scholarship in Science and Technology
- Government of Ontario
Jan 2023 – Dec 2023
Queen Elizabeth II Graduate Scholarship in Science and Technology
- Government of Ontario
Jan 2022 – Dec 2022
Doctoral Post-Graduate Scholarship (PGS-D)
- Natural Sciences and Engineering Research Council (NSERC)
Jan 2019 – Dec 2021
Frederick Banting and Charles Best Canada Graduate Scholarship (CGS-M)
- Canadian Institutes of Health Research (CIHR)
May 2017 – Apr 2018
Excellence Scholarship
- University of Ottawa
May 2017 – Dec 2023
Graduate Admission Scholarship
- University of Ottawa
Sep 2016 – Apr 2017
Undergraduate Student Research Award
- Natural Sciences and Engineering Research Council (NSERC)
May 2015 – Aug 2015
Dean's Honour List
- Faculty of Science, University of Ottawa
Sep 2012 – Apr 2016
Undergraduate Admission Scholarship
- University of Ottawa
Sep 2012 – Apr 2016
Research contributions
Collaborations
Publications
- Harkin EF, Nasrallah G, Le François B, and Albert PR. "Transcriptional regulation of the human 5-HT1A receptor gene by lithium: Role of Deaf1 and GSK3β." International Journal of Molecular Sciences, 24, 2023. doi: 10.3390/ijms242115620
- Harkin EF, Grossman CD, Cohen JY, Béïque J-C, and Naud R. "Serotonin predictively encodes value." bioRxiv, 2023. doi: 10.1101/2023.09.19.558526
- Harkin EF, Lynn MB, Payeur A, Boucher JF, Caya-Bissonnette L, Cyr D, Stewart C, Longtin A, Naud R*, and Béïque J-C*. "Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework." eLife, 12, 2023. doi: 10.7554/eLife.72951
- Lynn MB, Geddes S, Chahrour M, Maillé S, Harkin E, Harvey-Girard É, Haj-Dahmane S, Naud R, and Béïque J-C. "A slow 5-HT1AR-mediated recurrent inhibitory network in raphe computes contextual value through synaptic facilitation." bioRxiv, 2022. doi: 10.1101/2022.08.31.506056
- Harkin EF*, Shen PR*, Goel A, Richards BA*, and Naud R*. "Parallel and recurrent cascade models as a unifying force for understanding subcellular computation." Neuroscience, 489:200-215, 2022. doi: 10.1016/j.neuroscience.2021.07.026
- Lee C, Harkin E, Yin X, Naud R, and Chen S. "Cell-type-specific responses to associative learning in the primary motor cortex." eLife, 2022. doi: 10.7554/eLife.72549
- Mazhar H, Harkin E, Foster B, and Harris C. "Complementary and alternative medicine use in pediatric ADHD." Current Developmental Disorders Reports, 3(1):15-24, 2016.
Textbook chapters
- Harkin EF, Béïque J-C, and Naud R. "A user's guide to generalized integrate-and-fire models." Computational Modelling of the Brain, eds. Giugliano, Negrello, and Linaro, Springer, 69-89, 2022. doi: 10.1007/978-3-030-89439-9_3
Conference abstracts
- Harkin EF, Béïque J-C, and Naud R. "Serotonin predictively encodes value." Talk at Neuroscience, Washington, D.C., U.S.A., Nov 2023.
- Harkin EF, Payeur A, Lynn MB, Boucher J-F, Caya-Bissonnette L, Cyr D, Stewart C, Longtin A, Naud R*, and Béïque J-C*. "Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework." Poster presented at Neuroscience, San Diego, U.S.A., Nov 2022.
- Harkin EF, Payeur A, Lynn MB, Boucher J-F, Caya-Bissonnette L, Cyr D, Stewart C, Longtin A, Béïque J-C*, and Naud R*. "Temporal derivative computation in the dorsal raphe network revealed by an experimentally-driven augmented integrate-and-fire modeling framework." Poster presented at Bernstein Conference, virtual, Sep 2021. doi: 10.12751/nncn.bc2021.p083
- Lynn M, Geddes SD, Chahrour M, Maillé S, Harkin E, Harvey-Girard É, Haj-Dahmane S, Naud R, and Béïque. "Dynamic filtering of habenulo-raphe inputs by a serotonergic reccurent inhibitory network acting over behavioural timescales." Poster presented by M Lynn at Neuroscience, virtual, Sep 2021.
- Harkin E, Payeur A, Boucher J-F, Caya-Bissonnette L, Cyr D, Longtin A, Lynn M, Stewart C, Naud R*, and Béïque J-C*. "From single neurons to networks in the dorsal raphe nucleus." Poster presented at COSYNE, virtual, Feb 2021.
- Harkin E, Payeur A, Boucher J-F, Caya-Bissonnette L, Cyr D, Longtin A, Lynn M, Stewart C, Béïque J-C*, and Naud R*. "Multiple mechanisms of gain modulation in the serotonin system." Talk presented at Canadian Computational Neuroscience Spotlight, virtual, Jun 2020.
- Harkin E, Payeur A, Boucher J-F, Caya-Bissonnette L, Cyr D, Longtin A, Lynn M, Stewart C, Béïque J-C*, and Naud R*. "Multiple mechanisms of gain modulation in the serotonin system." Talk presented at Neuromatch 1.0, virtual, May 2020.
- Harkin E, Payeur A, Lynn M, Boucher J-F, Longtin A, Naud R*, and Béïque J-C*. "Multiple mechanisms of gain modulation in the serotonin system." Poster accepted to Canadian Association for Neuroscience 14th Annual Meeting, Montréal, Canada, May 2020.†
- Lynn M, Geddes S, Chahrour M, Maillé S, Harkin E, Haj-Dahmane S, Naud R, and Béïque J-C. "A recurrent network motif in the dorsal raphe nucleus supports an operational classification of habenula inputs." Poster accepted to Canadian Association for Neuroscience 14th Annual Meeting, Montréal, Canada, May 2020.†
- Lynn M, Geddes S, Chahrour M, Maillé S, Harkin E, Haj-Dahmane S, Naud R, and Béïque J-C. "A recurrent network motif in the dorsal raphe nucleus supports an operational classification of habenula inputs." Poster presented by M Lynn at Canadian Association for Neuroscience 13th Annual Meeting, Toronto, Canada, May 2019.
- Harkin E, Lynn M, Payeur A, Longtin A, Naud R, and Béïque J-C. "Non-uniform subthreshold dynamics and integrative features in dorsal raphe neurons." Poster presented at Canadian Association for Neuroscience 12th Annual Meeting, Vancouver, Canada, May 2018.
- Harkin E, Cardin V, and Albert P. "Transcriptional regulation of the serotonin 1A receptor by lithium: roles of glycogen synthase kinase 3β and Deaf-1." Poster presented at Ottawa-Carleton Institute of Biology Symposium, Ottawa, Canada, 2016.
- Equal contribution.
- Abstract accepted, but in-person conference cancelled due to COVID.
Mentorship
Undergraduate research rotation supervisor
2022
Advised École Polytechnique Fédérale de Lausanne engineering undergraduate on training spiking neural networks with Richard Naud during six-week research rotation leading to successful defence of model parameter optimization and software architecture improvement.
M.Eng. thesis supervisor
2021
Advised Université de Lyon master's student on robust analysis of large-scale calcium imaging data with Richard Naud during six-month remote research rotation leading to successful degree completion.
Undergraduate research rotation supervisor
2019
Advised University of Ottawa Faculty of Medicine undergraduate on simulation of generalized leaky integrate-and-fire neuron models with Richard Naud during six-week rotation leading to successful poster presentation.
Service
Student representative
- Canadian Association for Neuroscience Hill Day
- Theme: science outreach
2022
Met with Members of Parliament as part of a group of neuroscience researchers and students to advocate for increased public research investment in Canada.
Invited speaker
- University of Ottawa Brain Health Awareness Week
- Theme: science outreach
2019 – 2021
Presented highlights of my work on computational models of the serotonin system to >100 person public audience at yearly outreach event to increase community awareness of local neuroscience research.
Classroom workshop volunteer
- Let's Talk Science
- Theme: science outreach
2017 – 2018
Led hands-on elementary school classroom activities together with another volunteer to increase youth science engagement.
Mentorship circle volunteer
- Circles of Support and Accountability
- Theme: restorative justice
2016 – 2017
Offered social support while maintaining personal accountability of a recently-incarcerated person together with a circle of four other volunteers, helping the individual to reintegrate into society.
