Timothy Dunn | Scholars@Duke

Timothy Dunn
Assistant Professor of Biomedical Engineering

Current Research Interests

Machine learning, computer vision, neurobiology, animal behavior, computational neuroscience, prognostic modeling, traumatic brain injury

Current Appointments & Affiliations

Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2021
Assistant Professor in Neurosurgery, Neurosurgery, Neurosurgery 2020

Contact Information

Background
Education, Training, & Certifications
- Ph.D., Harvard University 2015
Recognition
In the News
- JAN 20, 2023 Bass Connections
  
  Bass Connections Team Aims for Global Health Change
- OCT 26, 2021 Pratt School of Engineering
  
  Welcome the Pratt School New Faculty
- JUN 22, 2021 Duke Engineering News
  
  Timothy Dunn: Tracking Movement to Decipher Brain Activity
- APR 23, 2021 Duke AI Health
  
  Learning to DANNCE
- APR 19, 2021 Duke Forge
  
  Tim Dunn - The DANNCE Study
- NOV 8, 2016 Harvard MCB News
  
  Neural Circuits at the Brain Scale
- FEB 3, 2016 Harvard MCB News
  
  Calculating Time to Collision
Awards & Honors
Expertise
Subject Headings
Global Scholarship
- Teaching
  - Japan (Country)
  - Singapore (Country)
Research
Selected Grants
- Development of brain-scale neural circuits underlying vertebrate visuomotor transformations awarded by National Institutes of Health 2022 - 2027
- Building and implementing a TBI prognostic model featuring real-time analysis of brain CT images awarded by National Institutes of Health 2022 - 2027
- Functional connectivity of a brain-scale neural circuit for motion perception awarded by National Institutes of Health 2022 - 2025
- A system for long-term high-resolution 3D tracking of movement kinematics in freely behaving animals awarded by Harvard University 2021 - 2024
- Neurobiology Training Program awarded by National Institutes of Health 2019 - 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
External Relationships
- Higgs Boson Health
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Thomson, Eric, Mark Harfouche, Kanghyun Kim, Pavan Konda, Catherine W. Seitz, Colin Cooke, Shiqi Xu, et al. “Gigapixel imaging with a novel multi-camera array microscope.” Elife 11 (December 2022): e74988. https://doi.org/10.7554/elife.74988.
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  - Adil, Syed M., Cyrus Elahi, Dev N. Patel, Andreas Seas, Pranav I. Warman, Anthony T. Fuller, Michael M. Haglund, and Timothy W. Dunn. “Deep Learning to Predict Traumatic Brain Injury Outcomes in the Low-Resource Setting.” World Neurosurg 164 (August 2022): e8–16. https://doi.org/10.1016/j.wneu.2022.02.097.
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  - Adil, Syed M., Lefko T. Charalambous, Shashank Rajkumar, Andreas Seas, Pranav I. Warman, Kelly R. Murphy, Shervin Rahimpour, et al. “Machine Learning to Predict Successful Opioid Dose Reduction or Stabilization After Spinal Cord Stimulation.” Neurosurgery 91, no. 2 (August 1, 2022): 272–79. https://doi.org/10.1227/neu.0000000000001969.
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  - Kirsch, Elayna P., Alexander Suarez, Katherine E. McDaniel, Rajeev Dharmapurikar, Timothy Dunn, Shivanand P. Lad, and Michael M. Haglund. “Construct validity of the Surgical Autonomy Program for the training of neurosurgical residents.” Neurosurg Focus 53, no. 2 (August 2022): E8. https://doi.org/10.3171/2022.5.FOCUS22166.
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  - Satyadev, Nihal, Pranav I. Warman, Andreas Seas, Brad J. Kolls, Michael M. Haglund, Anthony T. Fuller, and Timothy W. Dunn. “Machine Learning for Predicting Discharge Disposition After Traumatic Brain Injury.” Neurosurgery 90, no. 6 (June 1, 2022): 768–74. https://doi.org/10.1227/neu.0000000000001911.
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  - Warman, Pranav I., Andreas Seas, Nihal Satyadev, Syed M. Adil, Brad J. Kolls, Michael M. Haglund, Timothy W. Dunn, and Anthony T. Fuller. “Machine Learning for Predicting In-Hospital Mortality After Traumatic Brain Injury in Both High-Income and Low- and Middle-Income Countries.” Neurosurgery 90, no. 5 (May 1, 2022): 605–12. https://doi.org/10.1227/neu.0000000000001898.
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  - Marshall, Jesse D., Tianqing Li, Joshua H. Wu, and Timothy W. Dunn. “Leaving flatland: Advances in 3D behavioral measurement.” Current Opinion in Neurobiology 73 (April 2022): 102522. https://doi.org/10.1016/j.conb.2022.02.002.
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  - Yao, Xing, Vinayak Pathak, Haoran Xi, Amey Chaware, Colin Cooke, Kanghyun Kim, Shiqi Xu, et al. “Increasing a microscope's effective field of view via overlapped imaging and machine learning.” Optics Express 30, no. 2 (January 2022): 1745–61. https://doi.org/10.1364/oe.445001.
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  - 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 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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  - Yao, X., H. Xi, K. C. Zhou, A. Chaware, C. Cooke, Y. Li, T. Dunn, P. C. Konda, and R. Horstmeyer. “Increasing a microscope’s effective field of view via overlapped imaging and machine learning.” Optics Infobase Conference Papers, January 1, 2021.
  - 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 2020): e53684. https://doi.org/10.7554/elife.53684.
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  - Dunn, T. W., and P. K. Koo. “Inferring Functional Neural Connectivity With Deep Residual Convolutional Neural Networks.” Biorxiv, May 25, 2017. https://doi.org/10.1101/141010.
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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.” Current Biology : Cb 23, no. 16 (August 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.” The Journal of Neuroscience : The Official Journal of the Society for Neuroscience 33, no. 9 (February 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.” Journal of Neurophysiology 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.” Nature Methods 5, no. 4 (April 2008): 331–38. https://doi.org/10.1038/nmeth.1187.
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- Book Sections
  - Dunn, T. W., D. L. Fortin, and R. H. Kramer. “Engineering light-regulated ion channels.” In Imaging in Neuroscience A Laboratory Manual, 2011.
- 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
Recent Courses
Scholarly, Clinical, & Service Activities
Outreach & Engaged Scholarship
- Bass Connections Team Leader. Building Sustainable Neurosurgical Systems in Developing Countries . 2022 - 2023 2022 - 2023
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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Education, Training, & Certifications

In the News

Awards & Honors

Subject Headings

Global Scholarship

Teaching

Selected Grants

Fellowships, Supported Research, & Other Grants

External Relationships

Selected Publications

Academic Articles

Book Sections

Conference Papers

Theses and Dissertations

Exhibitions, Screenings, & Performances

Recent Courses

Outreach & Engaged Scholarship

Service to the Profession

Service to Duke