[[Full list also via Google Scholar or PubMed.]]
2025
Sager, G., Pfeiffer, P., Wu, H. Pallasdies, F., Gowers, R., Ravikumar, S., Wu, E., Colon-Ramos, D. A., Schreiber, S.*, Clark, D. A.* (2024) “Spatial and morphological organization of mitochondria in neurons across a connectome.” Science. (Co-corresponding authors.) [sneak peak]
Shomar, J.*, Wu, E.*, Au, B., Maier K., Zhou, B., Matos, N. C. B., Sager, G., Santana, G., Tanaka, R., Gish, C., Clark, D. A. (2025) “Visual circuitry for distance estimation in Drosophila.” Current Biology. (* Equal contributors.) [link]
Wu, N.*, Zhou, B.*, Agrochao, M., Clark, D. A. (2025) “Broken time reversal symmetry in visual motion detection.” Proceedings of the National Academy of Sciences 122(10): e2410768122. (* Equal contributors.) [link]
2024
Clark, D. A.* & Fitzgerald, J. E.* (2024) “Optimization in visual motion detection.” Annual Reviews in Vision Science 10: 2.1–2.24. (*Equal contributors.) [link]
Lei, W., Clark, D. A., Demb, J. B. (2024) “Compartmentalized pooling generates orientation selectivity in wide-field amacrine cells.” Proceedings of the National Academy of Sciences 121(49): e2411130121. [link]
Gou, T., Matulis, C. A., Clark, D. A. (2024) “Adaptation to visual sparsity enhances responses to isolated stimuli.” Current Biology 34(24): 5697-5713. [link]
2023
Tanaka, R., Zhou, B., Agrochao, M. A., Badwan, B. A., Au, B., Matos, N. C. B., Clark, D. A. (2023) “Neural mechanisms to incorporate visual counterevidence in self movement estimation.” Current Biology 33(22): 4960-4979.e7. [link]
Mano, O., Choi, M., Tanaka, R., Creamer, M. S., Matos, N.C.B., Shomar, J., Badwan, B. A., Clandinin, T. R., Clark, D. A. (2023) “Long timescale anti-directional rotation in Drosophila optomotor behavior.” eLife 12: e86076. [link]
Chen, J.*, Gish, C. M.*, Fransen, J. W., Salazar-Gatzimas, E., Clark, D. A.#, Borghuis, B. G.# (2023) “Direct comparison reveals algorithmic similarities in fly and mouse visual motion detection”, iScience 26: 107928. (* Equal contributors; # co-corresponding authors) [link]
2022
Kadakia, N., Demir, M., Michaelis, B. T., DeAngelis, B. D., Reidenbach, M. A., Clark, D. A.*, Emonet T.* (2022) “Odor motion sensing enhances navigation of complex plumes”, Nature. (* Co-corresponding authors.) [link] See also the accompanying News and Views about the result: link. And related article on olfactory navigation here: link.
Gonzalez-Suarez, A. D., Zavatone-Veth, J. A., Chen, J., Matulis, C. A., Badwan, B. A., and Clark, D. A. (2022) “Excitatory and inhibitory neural dynamics jointly tune motion detection.” Current Biology. [link]
Vashistha, H. & Clark, D. A. (2022) “Feature maps: how the insect visual system organizes information” (Dispatch), Current Biology 32(15): R847-R849. [link]
Tanaka, R. & Clark, D. A. (2022) “Neural mechanisms to exploit positional geometry for collision avoidance”, Current Biology. [link] See also the accompanying Dispatch: [link].
Tanaka, R. & Clark, D. A. (2022) “Identifying inputs to visual projection neurons in Drosophila lobula by analyzing connectomic data”, eNeuro 9(2): ENEURO.0053-22.2022. [link]
Zhou, B., Li, Z., Kim, S. S. Y., Lafferty, J.*, Clark, D. A.* (2022) “Shallow neural networks trained to detect collisions recover features of visual loom-selective neurons.” eLife e72076. (Equal contributors, co-corresponding authors.) [Link]
2021
Mano, O., Creamer, M. S., Badwan, B. A., Clark, D. A. (2021) “Predicting individual neural responses with anatomically constrained task optimization.” Current Biology 31: 1-14. [Link] See also an accompanying dispatch here: [Link].
2020
Agrochao, M.*, Tanaka, R.*, Salazar-Gatzimas, E., Clark, D. A. (2020) “Mechanism for analogous illusory motion perception in flies and humans”, Proceedings of the National Academy of Sciences, accepted. (* Equal contributions.) [Link] See also a story on this work in WIRED magazine: [Link], as well as mention of this work in National Geographic [Link].
Tanaka, R. & Clark, D. A. (2020) “Object-Displacement-Sensitive Visual Neurons Drive Freezing in Drosophila”, Current Biology 30(13): 2532-2550.e8. [Link] See also accompanying commentary here: [Link].
DeAngelis, B. D.*, Zavatone-Veth, J. A.*, Gonzalez-Suarez A. D., Clark, D. A. (2020) “Spatiotemporally precise optogenetic activation of sensory neurons in freely walking Drosophila”, eLife 9:e54183. (* Equal contributions.) [Link]
Matulis, C. A., Chen, J., Gonzalez-Saurez, A. D., Behnia, R., Clark, D. A. (2020) “Heterogeneous temporal contrast adaptation in Drosophila direction-selective circuits”, Current Biology 30: 222-236.e6. [Link] See also accompanying commentary here: [Link].
Zavatone-Veth, J. A., Badwan, B. A., Clark, D. A. (2020) “A minimal synaptic model for direction selective neurons in Drosophila”, Journal of Vision, 20(2), 1–22. [Link] Previous version of manuscript available at: https://www.biorxiv.org/content/10.1101/833970v1.
2019
Mano, O., Creamer, M. S., Matulis, C. A., Salazar-Gatzimas, E., Chen, J., Zavatone-Veth, J. A., Clark, D. A. (2019) “Using slow frame rate imaging to extract fast receptive fields”, Nature Communications 10: 4979. [Link]
Chen, J., Mandel, H. M., Fitzgerald, J. E.*, Clark, D. A.* (2019) “Asymmetric ON-OFF processing of visual motion cancels variability induced by the structure of natural scenes”, eLife 8:e47579. (* Corresponding authors) [Link]
Badwan, B. A., Creamer, M. S., Zavatone-Veth, J. A., Clark, D. A. (2019) “Dynamic nonlinearities enable direction opponency in Drosophila elementary motion detectors”, Nature Neuroscience 22: 1318–1326. [Link]
DeAngelis, B. D.*, Zavatone-Veth, J. A.*, Clark, D. A. (2019) “The manifold structure of limb coordination in walking Drosophila”, eLife 8:e46409. (* Equal contributions) [Link]
Creamer, M. S., Mano, O., Tanaka, R., Clark, D. A. (2019) “A flexible geometry for panoramic visual and optogenetic stimulation during behavior and physiology”, Journal of Neuroscience Methods 323: 48-55. [Link]
2018
Salazar-Gatzimas, E., Agrochao, M., Fitzgerald, J. E., Clark, D. A. (2018) “The neuronal basis of an illusory motion percept is explained by decorrelation of parallel motion pathways”, Current Biology 28: 3748-3760. [Link] [Short write-up on the paper here.]
Creamer, M. S., Mano, O., Clark, D. A. (2018) “Visual control of walking speed in Drosophila”, Neuron 100: 1460-1473. [Link]
Astigarraga, S., Douthit, J., Tarnogorska, D., Creamer, M. S., Mano, O., Clark, D. A., Meinertzhagen, I., Treisman, J. E. (2018) “Sidekick is required to establish the circuitry for visual motion detection in Drosophila”, Development: dev.158246. [Link]
2017
Gorur-Shandilya, S., Demir, M., Long, J., Clark, D. A., Emonet, T. (2017) “Olfactory receptor neurons use gain control and complementary kinetics to encode intermittent odorant stimuli”, eLife: e27670. [Link]
Mano, O., Clark, D. A. (2017) “Graphics Processing Unit-Accelerated Code for Computing Second-Order Wiener Kernels and Spike-Triggered Covariance”, PLOS ONE 12(1): e0169842. [Link]
2016
Clark, D. A., Demb J. B. (2016) “Parallel computations in insect and mammalian visual motion processing”, Current Biology 26: R1062–R1072. [Link]
Salazar-Gatzimas, E.*, Chen J. Y.*, Creamer, M. S.*, Mano, O., Mandel, H. B., Matulis, C. A., Pottackal, J., Clark, D. A. (2016) “Direct measurement of correlation responses in Drosophila elementary motion detectors reveals fast timescale tuning”, Neuron 92(1): 227-239. (*Equal contributions.) [Link]
2015
Fitzgerald, J.E., Clark, D. A. (2015) “Nonlinear circuits for naturalistic motion estimation”, eLife: e09123. [Link]
2014
Behnia, R., Clark, D. A., Carter, A. G., Clandinin, T. R., Desplan, C. (2014) “Processing properties of ON and OFF pathways for Drosophila motion detection”, Nature 512: 427-430. [Link]
Clark, D. A.*, Fitzgerald, J. E.*, Ales, J. M.*, Gohl, D. M., Silies, M. A., Norcia, A. M., Clandinin, T. R. (2014) “Flies and humans share a motion estimation strategy that exploits natural scene statistics”, Nature Neuroscience 17: 296-303. (*Equal contributions.) [Link]
(Media coverage: Reuters, Cnet, WiredUK.)
2013
Clark, D. A., Benichou, R., Meister, M., da Silveira, R. A. (2013) “Dynamical adaptation in photoreceptors”, PLoS Computational Biology 9(11): e1003289. [Link]
Clark, D. A., Freifeld, L., Clandinin, T. R. (2013) “Mapping and cracking sensorimotor circuits in genetic model organisms” (Perspective), Neuron 78: 583-595. [Link]
Freifeld, L., Clark, D. A., Schnitzer, M. J., Horowitz, M. A., Clandinin, T. R. (2013) “GABAergic lateral interactions tune the early stages of visual processing in Drosophila”, Neuron 78: 1075–1089. [Link]
Silies, M., Gohl, D. M., Fisher, Y. E., Freifeld, L., Clark, D. A., Clandinin, T. R. (2013) “Modular use of peripheral input channels tunes motion-detecting circuitry”, Neuron 79(1): 111-127. [Link]
Fly work before 2013
Clark, D. A., Burztyn, L., Horowitz, M., Schnitzer, M., Clandinin T. R. (2011) “Defining the computational structure of the motion detector in Drosophila”, Neuron 70(6): 1165-1177. [Link] (See also the accompanying Preview, “A genetic push to understand motion detection.” [Link])
Clark, D. A., de Vries, S. J., Clandinin T. R. (2010), “Watching the fly brain in action” (News and Views), Nature Methods 7: 505-506. [Link]