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
- Background
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Education, Training, & Certifications
- Ph.D., Harvard University 2015
- Recognition
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In the News
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JAN 20, 2023 Bass Connections -
OCT 26, 2021 Pratt School of Engineering -
JUN 22, 2021 Duke Engineering News -
APR 23, 2021 Duke AI Health -
APR 19, 2021 Duke Forge -
NOV 8, 2016 Harvard MCB News -
FEB 3, 2016 Harvard MCB News
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Awards & Honors
- Technological Innovations in Neuroscience Award. McKnight Foundation. 2021
- 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
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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
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Global Scholarship
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Teaching
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- Research
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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
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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
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External Relationships
- Higgs Boson Health
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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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.Full Text
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text
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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.Full Text
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text Link to Item
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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.Full Text
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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.Full Text Link to Item
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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.
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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.Full Text Link to Item
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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.Full Text
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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.Full Text
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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.Full Text Link to Item
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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
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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.Full Text Link to Item
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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.Full Text
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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.Full Text
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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.Full Text
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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.Full Text
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Book Sections
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Dunn, T. W., D. L. Fortin, and R. H. Kramer. “Engineering light-regulated ion channels.” In Imaging in Neuroscience A Laboratory Manual, 2011.
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Conference Papers
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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.
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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.Full Text
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Theses and Dissertations
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Exhibitions, Screenings, & Performances
- Teaching & Mentoring
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Recent Courses
- BME 493: Projects in Biomedical Engineering (GE) 2023
- BME 791: Graduate Independent Study 2023
- BME 792: Continuation of Graduate Independent Study 2023
- BME 590: Special Topics in Biomedical Engineering 2022
- BME 791: Graduate Independent Study 2022
- BME 792: Continuation of Graduate Independent Study 2022
- AIPI 591: Special Readings in AI for Product Innovation 2021
- Scholarly, Clinical, & Service Activities
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Outreach & Engaged Scholarship
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Service to the Profession
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Service to Duke
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