Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., Harvard University 2015
• Recognition
• 

  In the News

  • APR 23, 2021

    Duke AI Health

    Learning to DANNCE

  • NOV 8, 2016

    Harvard MCB News

    Neural Circuits at the Brain Scale

  • FEB 3, 2016

    Harvard MCB News

    Calculating Time to Collision
• 

  Awards & Honors

  • Peer Recognition Honor. Duke, Pratt School of Engineering. 2020
  • AI Watson XPrize Finalist (with team DataKind). IBM. 2017
  • Certificate of Distinction in Teaching. Harvard University . 2017
  • Certificate of Excellence in Teaching. Harvard University. 2017
  • Certificate of Distinction in Teaching. Harvard University . 2013
  • Graduate Research Fellowship. National Science Foundation . 2010
  • I.L. Chaikoff Award for Undergraduate Research. UC Berkeley . 2008
  • MCB Department Citation (Best in Class). UC Berkeley. 2008
• Expertise
• 

  Subject Headings

  • Animal behavior
  • Artificial Intelligence
  • Artificial intelligence--Biological applications
  • Artificial intelligence--Medical applications
  • Behavior
  • Brain--Research
  • Computational neuroscience
  • Computer vision
  • Data Science
  • Decision Making, Computer-Assisted
  • Global health
  • Machine learning
  • Neural circuitry
  • Neural networks (Computer science)
  • Neural networks (Neurobiology)
  • Neurobiology
  • Neurosciences
  • Neuroscientists
  • Optical measurements
  • Quantitative research
  • Statistics
  • Traumatic Brain Injury
  • Zebrafish
• 

  Global Scholarship

  • Teaching

    • Japan (Country) 
    • Singapore (Country) 
• Research
• 

  Selected Grants

  • A system for long-term high-resolution 3D tracking of movement kinematics in freely behaving animals awarded by  Harvard University 2021 - 2024
  • High-Resolution, Parallelized Imaging of Freely Swimming Zebrafish with a Gigapixel Microscope awarded by Ramona Optics, Inc. 2018 - 2020
• 

  Fellowships, Supported Research, & Other Grants

  • DGHI Pilot Grant awarded by Duke Global Health Institute 2020
  • DIHI Innovation Project Grant awarded by Duke Institute for Health Innovation 2020
  • Nvidia GPU Grant awarded by Nvidia 2017
  • A2 Fellowship awarded by Japan National Institute of Genetics 2015
  • Graduate Research Opportunities Worldwide Fellowship awarded by National Science Foundation 2013
  • Graduate Research Fellowship awarded by National Science Foundation 2010 - 2013
  • Nathan and Violet David Scholarship awarded by UC Berkeley, Nathan and Violet David Foundation 2007
  • Regents and Chancellor's Scholarship (full undergraduate tuition) awarded by UC Berkeley 2004 - 2008
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Dunn, Timothy W., Jesse D. Marshall, Kyle S. Severson, Diego E. Aldarondo, David G. C. Hildebrand, Selmaan N. Chettih, William L. Wang, et al. “Geometric deep learning enables 3D kinematic profiling across species and environments.” Nat Methods 18, no. 5 (May 2021): 564–73. https://doi.org/10.1038/s41592-021-01106-6.
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    • Adil, Syed M., Cyrus Elahi, Robert Gramer, Charis A. Spears, Anthony T. Fuller, Michael M. Haglund, and Timothy W. Dunn. “Predicting the Individual Treatment Effect of Neurosurgery for Patients with Traumatic Brain Injury in the Low-Resource Setting: A Machine Learning Approach in Uganda.” J Neurotrauma 38, no. 7 (April 1, 2021): 928–39. https://doi.org/10.1089/neu.2020.7262.
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    • Spears, Charis A., Syed M. Adil, Brad J. Kolls, Michael E. Muhumza, Michael M. Haglund, Anthony T. Fuller, and Timothy W. Dunn. “Surgical intervention and patient factors associated with poor outcomes in patients with traumatic brain injury at a tertiary care hospital in Uganda.” J Neurosurg, March 26, 2021, 1–10. https://doi.org/10.3171/2020.9.JNS201828.
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    • Marshall, Jesse D., Diego E. Aldarondo, Timothy W. Dunn, William L. Wang, Gordon J. Berman, and Bence P. Ölveczky. “Continuous Whole-Body 3D Kinematic Recordings across the Rodent Behavioral Repertoire.” Neuron 109, no. 3 (February 3, 2021): 420-437.e8. https://doi.org/10.1016/j.neuron.2020.11.016.
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    • Koltai, Deborah C., Timothy W. Dunn, Patrick J. Smith, Drishti D. Sinha, Samuel Bobholz, Mark Kaddumukasa, Angelina Kakooza-Mwesige, et al. “Sociocultural determinants and patterns of healthcare utilization for epilepsy care in Uganda.” Epilepsy Behav 114, no. Pt B (January 2021): 107304. https://doi.org/10.1016/j.yebeh.2020.107304.
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    • Elahi, Cyrus, Charis A. Spears, Sarah Williams, Timothy W. Dunn, Josephine N. Najjuma, Catherine A. Staton, João Ricardo Nickenig Vissoci, Anthony Fuller, David Kitya, and Michael M. Haglund. “An Attitude Survey and Assessment of the Feasibility, Acceptability, and Usability of a Traumatic Brain Injury Decision Support Tool in Uganda.” World Neurosurg 139 (July 2020): 495–504. https://doi.org/10.1016/j.wneu.2020.04.193.
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    • Dunn, Timothy W., and James E. Fitzgerald. “Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience.” Elife 9 (March 24, 2020). https://doi.org/10.7554/eLife.53684.
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    • Naumann, Eva A., James E. Fitzgerald, Timothy W. Dunn, Jason Rihel, Haim Sompolinsky, and Florian Engert. “From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response.” Cell 167, no. 4 (November 3, 2016): 947-960.e20. https://doi.org/10.1016/j.cell.2016.10.019.
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    • Dunn, Timothy W., Yu Mu, Sujatha Narayan, Owen Randlett, Eva A. Naumann, Chao-Tsung Yang, Alexander F. Schier, Jeremy Freeman, Florian Engert, and Misha B. Ahrens. “Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion.” Elife 5 (March 22, 2016): e12741. https://doi.org/10.7554/eLife.12741.
       Full Text  Open Access Copy  Link to Item
    • Dunn, Timothy W., Christoph Gebhardt, Eva A. Naumann, Clemens Riegler, Misha B. Ahrens, Florian Engert, and Filippo Del Bene. “Neural Circuits Underlying Visually Evoked Escapes in Larval Zebrafish.” Neuron 89, no. 3 (February 3, 2016): 613–28. https://doi.org/10.1016/j.neuron.2015.12.021.
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    • Huang, Kuo-Hua, Misha B. Ahrens, Timothy W. Dunn, and Florian Engert. “Spinal projection neurons control turning behaviors in zebrafish.” Curr Biol 23, no. 16 (August 19, 2013): 1566–73. https://doi.org/10.1016/j.cub.2013.06.044.
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    • Kokel, David, Timothy W. Dunn, Misha B. Ahrens, Rüdiger Alshut, Chung Yan J. Cheung, Louis Saint-Amant, Giancarlo Bruni, et al. “Identification of nonvisual photomotor response cells in the vertebrate hindbrain.” J Neurosci 33, no. 9 (February 27, 2013): 3834–43. https://doi.org/10.1523/JNEUROSCI.3689-12.2013.
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    • Fortin, Doris L., Timothy W. Dunn, Alexis Fedorchak, Duane Allen, Rachel Montpetit, Matthew R. Banghart, Dirk Trauner, John P. Adelman, and Richard H. Kramer. “Optogenetic photochemical control of designer K+ channels in mammalian neurons.” J Neurophysiol 106, no. 1 (July 2011): 488–96. https://doi.org/10.1152/jn.00251.2011.
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    • Fortin, Doris L., Matthew R. Banghart, Timothy W. Dunn, Katharine Borges, Daniel A. Wagenaar, Quentin Gaudry, Movses H. Karakossian, et al. “Photochemical control of endogenous ion channels and cellular excitability.” Nat Methods 5, no. 4 (April 2008): 331–38. https://doi.org/10.1038/nmeth.1187.
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    • Dunn, Timothy W., and Peter K. Koo. “Inferring Functional Neural Connectivity with Deep Residual Convolutional Networks,” n.d. https://doi.org/10.1101/141010.
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  • Book Sections

    • Fortin, D. L., T. W. Dunn, and R. H. Kramer. “Engineering light-regulated ion Channels,” 6:579–85, 2011. https://doi.org/10.1101/pdb.top112.
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  • Conference Papers

    • Zhang, Libby, Timothy Dunn, Jesse D. Marshall, Bence P. Ölveczky, and Scott Linderman. “Animal pose estimation from video data with a hierarchical von Mises-Fisher-Gaussian model,” 2021.
    • Harfouche, M., T. W. Dunn, E. A. Naumann, and R. Horstmeyer. “Imaging the behavior and neural activity of freely moving organisms with a gigapixel microscope.” In Optics Infobase Conference Papers, Vol. Part F169-BRAIN 2019, 2019. https://doi.org/10.1364/BRAIN.2019.BT3A.3.
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  • Theses and Dissertations

    • Dunn, Timothy. “Brain-Wide Neural Dynamics Underlying Looming-Evoked Escapes and Spontaneous Exploration,” n.d.
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  Exhibitions, Screenings, & Performances

  • Perceptron: An interactive video installation visualizing motion perception | Perceptron at Massachusetts Institute of Technology 2013
• Teaching & Mentoring
• 

  Teaching Activities

  • Coursera
    Lecturer. Introduction to Machine Learning
    
    Duke University
    Lecturer. EGR 190.06: AI for Everyone 2020
    Lecturer. Duke +DS 2018, 2019, 2020
    Lecturer. Duke Machine Learning Summer School 2018, 2019
    Lecturer. Duke Machine Learning Winter School 2018
    Lecturer. Duke School of Medicine Machine Learning School 2018
    
    Harvard University
    Lecturer. MCB 111: Mathematics in Biology 2017
    Guest Lecturer. NEURO 109A: Precision Neuroscience 2017
    Lecturer. MCB 112: Biological Data Analysis 2016
    Guest Lecturer. OEB 105: Neurobiology of Motor Control 2015
    Co-Director. Imaging and Behavioral Analysis Workshop 2013
    Teaching Fellow. MCB 105: Systems Neuroscience 2011, 2012, 2013
    
    Japan National Institute of Genetics
    Course Instructor. Zebrafish Imaging and Transgenesis 2015
• Scholarly, Clinical, & Service Activities
• 

  Service to the Profession

  • Reviewer. Thirty-Fifth AAAI Conference on Artificial Intelligence. AAAI. 2020  2020
  • Review Editor. Frontiers in Neuroscience. 2017  2017
• 

  Service to Duke

  • Organizer and Content Creator. Center for Computational Thinking. 2020  2020

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