Jonathan J. Cannon, Ph.D.
Massachusetts Institute of Technology

Department of Brain and Cognitive Science

Bldg. 46-4077, 43 Vassar Street 02139, Cambridge, MA (USA)




2009 – 2014                Ph.D. & MA., Mathematics  Neural network modeling. Boston University

2004 – 2008                ScB., Mathematics/Computer Science. Brown University                        


Research Experience                        

2022 – present                 Assistant Prof. in Psychology, Neuroscience, and Behavior.
McMaster University.
                Affiliate: School of Computational Science and Engineering
Research questions: What are the computational, algorithmic, and neurophysiological underpinnings of our sense of rhythm, and how do they fit into the larger picture of brain and motor function?

Research activities:

2019 – 2022                 Postdoctoral Researcher in Neuroscience. MIT.
                Advisor: Prof. Pawan Sinha
Research question: How are temporal predictive abilities affected by autism?

Research activities:

2014 – 2016                 Postdoctoral Researcher in Neuroscience. Brandeis University.

                Advisor: Prof. Paul Miller
Research question: How can both synaptic and intrinsic homeostasic mechanisms cooperate to control neuronal firing rates in a network?

Research activities:


2009 – 2014                Graduate Researcher in Mathematical Neuroscience. Boston University.

                Advisor: Prof. Nancy Kopell

Research question: Do the physiological origins of gamma oscillations in the brain support their hypothesized role in facilitating communication between brain areas through phase coherence?

Research activities:

2008 – 2009                Research Assistant in Machine Learning. Brown University.
                Advisor: Elie Bienenstock.        Tree learning for natural language parsing.

Summers 2006, 2007        Research Assistant in Machine Learning. Washington University.
                Advisor: Robert Pless.                Manifold learning for CT scan reconstruction.



2022 – 2027                NSERC Discovery Grant.                                                $142,500
Exploring and Modeling Entrainment to Rhythm in the Motor System


Teaching and Advising

Classroom Teaching


2016 – 2019                 Teacher of Math and Science. Meridian Academy, Boston, MA.


2015                Instructor of Computational Neuroscience. Brandeis University.

                Received 4.67/5 overall rating and 4.69/5 instructor rating.

2013                Instructor of Introductory Quantitative Biology. Boston University.

2012                Teaching assistant: Calculus 1. Boston University.

2008–2009                Instructor: Vector Calculus Wheeler High School, Providence, RI.

Advising & Mentorship                

2022 – present        Graduate research supervisor. McMaster Unviersity.

        Matin Yousefabadi: PhD student in Psychology, Neuroscience, and Behaviour

        Yassaman Ommi: Masters student in Computational Science and Engineering

2022 – present        Graduate supervisory committee member. McMaster Unviersity.

        Emily Wood: PhD student in Psychology, Neuroscience, and Behaviour

2022 – present        Undergraduate research supervisor. McMaster University.

Arya Masoumi: Online experiment design in rhythm cognition, EEG analysis

Davina Premraj: EEG analysis

Jacob Duda: Whole-brain modeling

Lochana Kandimbige: Experiment design in rhythm cognition

Olivia Valentini: Literature review on time perception in Parkinson’s

2019 – 2022        Undergraduate research advisor. M.I.T.

Advised and guided three undergraduates in participation in research involving EEG analysis, behavioral data analysis, and online experiment design and programming.                        

2016 – 2019                High school research advisor. Meridian Academy, Boston, MA.

Advised three students in year-long research projects, including extensive literature review and creative synthesis of learning.

2016                Undergraduate mentor. Brandeis University

Advised Brandeis undergraduate in year-long project designing an experiment and a data analysis strategy to study neurofeedback in meditation.

2013 – 2014        Undergraduate mentor.
Remotely advised undergraduate student in thesis project on neural circuit modeling.

Outside Academia

2014 – 2016                Guest violin instructor.

Taught enrichment string orchestra workshops at elementary, middle, and high school levels at public schools in Waltham, Mansfield, and Rockport, MA.


2014 – 2015,                Private violin teacher.

2008 – 2009                Taught regular lessons to students of assorted ages and levels.                        




Professional Development

2022        Leadership and Professional Strategies and Skills (LEAPS) Training. MIT.

“Sharpen your professional strategies and skills”

Half-semester leadership training course for graduate students and postdocs

2022        CIFAR Neuroscience of Consciousness Winter School. Online.

        Three-day event where “tomorrow’s neuroscience leaders work closely with world-class                         researchers.”

2016 – 2017        New Teachers Collaborative. Francis Parker Charter School.

        Year-long bi-weekly course on progressive teaching methods.

2016        Summer School in Adaptive Neurotechnologies. Wadsworth Center.

NIH-funded intensive three-week course on technologies supporting real-time adaptive interaction with the nervous system.

        IMPACT program. MIT.

        NIH-funded six-month mentorship in science communication for real-world impact.

2010        Complex Systems Summer School. Santa Fe Institute.

Intensive four-week introduction to complex behavior in mathematical, physical, living, and social systems.        


Research Publications


Journal Articles

  1. Cinelytė, U., Cannon, J., Patel, A., & Mullensiefen, D. (2022). Testing beat perception without sensory cues to the beat: the Beat-Drop Alignment Test (BDAT). Attention, Perception, & Psychophysics, In Press

  2. Kaplan T, Cannon J, Jamone L, Pearce M (2022) Modeling enculturated bias in entrainment to rhythmic patterns. PLOS Computational Biology 18(9): e1010579.
  3. Cannon, J. (2021). Expectancy-based rhythmic entrainment as continuous Bayesian inference. PLOS Computational Biology, 17(6), e1009025.
  4. Cannon, J., O’Brien, A., Bungert, L., & Sinha, P.  (2021). Prediction in Autism Spectrum Disorder: A Systematic Review of Empirical Evidence. Autism Research, 14(4), 604–630.
  5. Cannon, J., & Patel, A. (2021). How beat perception co-opts motor neurophysiology. Trends in Cognitive Science, 25(2), 137–150.
  6. Miller, P., & Cannon, J. (2018). Combined mechanisms of neural firing rate homeostasis. Biological Cybernetics, 113(1), 47–59.
  7. Cannon, J. (2017b). Analytical calculation of mutual information between weakly coupled poisson-spiking neurons in models of dynamically gated communication. Neural Computation, 29(1), 118–145.
  8. Cannon, J., & Miller, P. (2017). Stable control of firing rate mean and variance by dual homeostatic mechanisms. Journal of Mathematical Neuroscience, 7(1), 1–38.
  9. Cannon, J., & Miller, P. (2016). Synaptic and intrinsic homeostasis cooperate to optimize single neuron response properties and tune integrator circuits. Journal of Neurophysiology, 116(5), 2004–2022.
  10. Cannon, J., & Kopell, N. (2015). The leaky oscillator: Properties of inhibition-based rhythms revealed through the singular phase response curve. SIAM J. on Applied Dynamical Systems, 14(4), 1930–1977.
  11. Cannon, J., Kopell, N., Gardner, T., & Markowitz, J. (2015). Neural sequence generation using spatiotemporal patterns of inhibition. PLOS Computational Biology, 11(11), e1004581.
  12. Cannon, J., McCarthy, M., Lee, S., Lee, J., Börgers, C., Whittington, M., & Kopell, N. (2014). Neurosystems: brain rhythms and cognitive processing. European Journal of Neuroscience, 39(5), 705–19.



  1. Cannon, J. (2014b). On the interaction of multiple gamma-rhythmic populations (Doctoral dissertation). Boston University.


Textbook Chapters


  1. Zinselmeyer, B., Dempster, J., Wokosin, D., Cannon, J., Pless, R., Parker, I., & Miller, M. (2009). Two-photon microscopy and multidimensional analysis of cell dynamics (T. Handel & D. Hamel, Eds.). In T. Handel & D. Hamel (Eds.), Methods in enzymology. Elsevier Science Publishing Co Inc.                        





Conference Presentations

  1. Cannon, J. (2021). A neurophysiological process theory of motor and covert beat-keeping. [16th International Conference on Music Perception and Cognition / 11th triennial conference of ESCOM, July 28, video online at]
  2. Cannon, J. (2021). A shared predictive framework for motor control and beat-based timing. [18th Rhythm Production and Perception Workshop, University of Oslo (virtual), June 22, video online at]
  3. Cannon, J. (2021). Expectancy-based rhythmic entrainment as continuous Bayesian inference. [Canadian Society for Brain, Behavior, and Cognitive Science (CSBBCS) meeting (virtual), June 18]
  4. Cannon, J. (2020). A Bayesian filtering framework for neural and sensorimotor entrainment [Neuromatch 3, October 27, video online at].
  5. Cannon, J. (2019). A neurocomputational model of beat-based temporal processing [Biennial Meeting of the Society for Music Perception and Cognition, NYU, New York, New York, Aug 6].
  6. Cannon, J. (2019). A neurocomputational model of beat-based temporal processing [17th Rhythm Production and Perception Workshop, Park Place Hotel and Conference Center, Traverse City, Michigan, Jun 18].
  7. Cannon, J. (2019). A neurocomputational model of beat-based temporal processing [New England Sequencing and Timing meeting, University of Connecticut, Storrs, CT, Apr 6].
  8. Cannon, J. (2017). Dual-mechanism firing rate homeostasis stabilizes multiple firing rate statistics [SIAM Conference on Applications of Dynamical Systems, Snowbird Resort, Snowbird, UT, May 25].
  9. Cannon, J. (2015). Stability analysis of dual activity-dependent homeostasis [Janelia Theoretical Neuroscience Workshop, Janelia Research Campus, Ashburn, VA, Nov 19].
  10. Cannon, J. (2015). Theoretical foundations and applications of dual activity-dependent homeostasis [Swartz Annual Meeting, Janelia Farm, Ashburn, VA, Aug 3].

Invited Talks

  1. Cannon, J. (2022). Rhythm Entrainment as Dynamic Bayesian Inference. [BRAMS-CRBLM Lecture Series Guest Speaker, Université de Montréal, Nov. 9]
  2. Cannon, J. (2022). Physiology and Theory of Motor and Covert Rhythm Entrainment. [Psychology, Neuroscience & Behaviour Graduate Research Day, Keynote Speaker, McMaster University, April 8]
  3. Cannon, J. (2022). Physiology and Theory of Motor and Covert Entrainment. [Human Neuroscience Journal Club Guest Speaker, University of Alabama at Birmingham, February 4]
  4. Cannon, J. (2021). Expectancy-based rhythmic entrainment as continuous Bayesian inference. [Guest Talk, Center for Music in the Brain, Aarhus University, December 3]
  5. Cannon, J. (2021). What do we “use” brain rhythms for? [Guest lecture, “Nonlinear Dynamics and Chaos,” Tufts University, November 4]
  6. Cannon, J. (2021). Following neural clues toward a shared predictive framework for motor control and beat-based timing. [Neuroscience and Music Lab virtual meeting, University of Western Ontario, May 4]
  7. Cannon, J. & O’Brien, A. (2021). Prediction in Autism Spectrum Disorder: What Does the Empirical Evidence Say? [Merav Ahissar lab virtual meeting, Hebrew University of Jerusalem, April 19]
  8. Cannon, J. (2021). The shared predictive roots of motor control and beat-based timing. [Centre for Systematic Musicology virtual weekly research seminar, University of Graz, Austria, April 13]
  9. Cannon, J. (2021). Auditory rhythm tracking as variational inference: Mathematical framework and neural substrates. [Theoretical Neurobiology Research Team virtual meeting (with PI Karl Friston),     University College London, April 6]
  10. Cannon, J. (2021). Neurophysiological And Cognitive Dynamics Of Rhythmic Time-Keeping [Department of Psychology, Neuroscience, and Behavior seminar, McMaster University, March 9]
  11. Cannon, J. & O’Brien, A. (2021). Prediction in Autism Spectrum Disorder: What Does the Empirical Evidence Say? [Centre for Autism meeting, University of Reading, March 3]
  12. Cannon, J. (2021). The shared predictive roots of motor control and beat-based timing [Timing Research Forum Journal Club, Feb 17, video online at].
  13. Cannon, J. (2021). Rhythmic Entrainment as Dynamic Inference [NJIT Mathematical Biology Seminar, Feb 2].
  14. Cannon, J. (2016). An information-theoretic framework for dynamic gating of neuronal communication [Applied Analysis and Computation Seminar, UMass Amherst, MA, Mar 30].
  15. Cannon, J. (2016). A mathematical framework for the transmission of oscillations and information among neuron populations [Physics Colloquium, UMass Boston MA, Apr 28].
  16. Cannon, J. (2015). A role for feedback inhibition and periodicity in sequence generation [NYU, Oct 2].
  17. Cannon, J. (2015). A role for feedback inhibition and periodicity in sequence generation [Cognitive Rhythms Collaborative retreat, Boston University, Boston, MA, Feb 23].
  18. Cannon, J. (2014a). A mathematical framework for the transmission of oscillations and information among neuronal populations [Brown/BU PDE Seminar, Boston University, Boston, MA, Dec 10].



  1. Cannon, J. (2021). A Bayesian framework for expectation-based rhythmic entrainment [Poster presented at Computational and Systems Neuroscience (COSYNE), Feb 26].
  2. Cannon, J. (2021). Prediction in Autism Spectrum Disorder: What Does the Empirical Evidence Say?  [Poster presented at Society for Neuroscience (SfN) Annual Meeting, Jan 12].
  3. Cannon, J. (2015a). Information theory of dynamic neural gating [Poster presented at Swartz Annual Meeting, Aug 2 - 5, Ashburn, VA].
  4. Cannon, J., & Miller, P. (2015). The dynamics and consequences of dual-mechanism homeostasis [Poster presented at Computational and Systems Neuroscience (COSYNE), Mar 5–8, Salt Lake City, Utah].
  5. Cannon, J., Markowitz, J., Kopell, N., & Gardner, T. (2014a). Sequence generation by spatio-temporal cycles of inhibition [Poster presented at Society for Neuroscience (SfN) Annual Meeting, Nov 15 - 19, Washington, DC].
  6. Cannon, J., Markowitz, J., Kopell, N., & Gardner, T. (2014b). Sequence generation by spatio-temporal cycles of inhibition [Poster presented at Computational and Systems Neuroscience (COSYNE), Feb 26 - Mar 2, Salt Lake City, Utah].
  7. Cannon, J., & Kopell, N. (2013). Gamma rhythms under periodic forcing [Poster presented at Rhythmic Dynamics and Cognition Conference, June 2013, Boston, MA].


Leadership & Service                                


2015 – present                Reviewer.

Science, Journal of Neural Computation, Journal of Chaos, Journal of Neurophysiology, European Journal of Neuroscience, Mathematical Intelligencer, e-Life, Current Biology, PLOS One, Timing & Time Perception, Frontiers in Psychology, Journal of Experimental Psychology, Cortex


2018 – 2021                Program committee chair, New England Folk Festival Association (NEFFA).

2014 – 2018                Member of board and program committee, New England Folk Festival Association.

2015 – 2017                Co-founder. “Eyes Up”.

                Vision research and rehabilitation project funded by Harvard Innovation Lab.

2014                Organizer. CV-Writing Professional Development Workshop.

                Supported by the Boston University Department of Mathematics and Statistics.

2011 – 2012                Co-Organizer and Recording Secretary. Alpha Rhythms Working Group.

Brought together researchers from BU, MIT, and Brown to discuss cognitive role of alpha rhythms, supported by the Cognitive Rhythms Collaborative (CRC).


                Founder and Organizer. Cognitive Rhythms Reading Group.

                Supported by the Cognitive Rhythms Collaborative (CRC).


Other Professional Experience


2015 – present                Co-founder, CFO, CTO, and CCO. “Flying Leap Games”.

Developed and launched storytelling card game “Wing It” now carried by over 200 retailers in the U.S., Canada, U.K., and Australia.


2013 – present                 Music Writer. Boston Herald “State of the Arts”,

Wrote and published online articles on traditional music, traditional dance, and music education


2010 – present                Semi-professional Fiddler and Guitarist. Assorted dance bands

                Played music for over 150 folk dances in eleven U.S. states.


2009 – present                Semi-professional Violinist. Ezekiel’s Wheels Klezmer Band

Released three studio albums, nominated for 2020 Boston Music Awards “International Artist of the Year,” awarded “Audience Choice Award” and “Best Klezmer Band” at 2012 International Jewish Music Festival in Amsterdam.


2008 – 2009                 Founder and Organizer. First annual Brown University Folk Festival.

                Wrote grant proposals, received over $4000 support



Technical Proficiency


Programming Languages

Proficient: Matlab, Python, Javascript, R

Some experience: C++, NetLogo, Scheme, LATEX

Machine Learning                Bayesian filtering, recurrent neural nets, hidden Markov models, Isomap,                         dimensionality reduction

Experiment Design                Analog audio/EEG integration, PsychoPy/PsychoJS development