Understanding normal and pathological brain computations

We are providing our brain mapping, control, and dynamical recording tools to the biology community, aiming to democratize the advanced analysis and repair of the brain and other biological systems. We also use these tools within our lab, to analyze how specific brain mechanisms (molecular, cellular, and circuit-level) give rise to behaviors and pathological states, or to the remedy thereof. One hope is to understand how the detailed molecular and circuit structures of brains give rise to brain circuit dynamics and signaling, which in turn yield complex emergent outputs such as behaviors; our work has touched upon topics including detailed patterns of synaptic activity, nonhuman primate cognition, emotional states, and decision making. These studies, often done in interdisciplinary collaborations, may yield fundamental insights into how best to go about treating brain disorders; our work has touched upon topics ranging from anesthesia to Alzheimer’s disease. To complement such studies, we develop accessory tools such as robots that can perform brain surgical techniques. We also seek to apply our toolsets to entire C. elegans and zebrafish brains, with the goal of understanding entire small brains and how their building blocks work together as an emergent whole. These neuroscience goals also motivate us to design and develop new tools, which we then deploy throughout the biology community. We also collaboratively apply our technologies to lots of other problems in biology and medicine, including in fields such as developmental biology, cancer, microbiology, virology, immunology, and aging.

Publications

A marmoset brain cell census reveals regional specialization of cellular identities

Science Advances | 2023

Krienen FM, Levandowski KM, Zaniewski H, Del Rosario RCH, Schroeder ME, Goldman M, Wienisch M, Lutservitz A, Beja-Glasser VF, Chen C, Zhang Q, Chan KY, Li KX, Sharma J, McCormack D, Shin TW, Harrahill A, Nyase E, Mudhar G, Mauermann A, Wysoker A, Nemesh J, Kashin S, Vergara J, Chelini G, Dimidschstein J, Berretta S, Deverman BE, Boyden E, McCarroll SA, Feng G (2023) A marmoset brain cell census reveals regional specialization of cellular identities, Science Advances 9(41):eadk3986.

Autism genes converge on asynchronous development of shared neuron classes

Nature | 2022

Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P (2022) Autism genes converge on asynchronous development of shared neuron classes, Nature 602(7896):268-273.

Voices in methods development

Nature Methods | 2019

Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X (2019) Voices in methods development, Nature Methods 16(10):945-951.

Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates

Scientific Reports | 2018

Senova S, Poupon C, Dauguet J, Stewart HJ, Dugué GP, Jan C, Hosomi K, Ralph GS, Barnes L, Drouot X, Pouzat C, Mangin JF, Pain F, Doignon I, Aron-Badin R, Brouillet E, Boyden ES, Mitrophanous KA, Hantraye P, Palfi S (2018) Optogenetic Tractography for anatomo-functional characterization of cortico-subcortical neural circuits in non-human primates, Scientific Reports 8(1):3362.

Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain

Journal of Neurophysiology | 2017

Annabelle C. Singer*, Giovanni Talei Franzesi*, Suhasa B. Kodandaramaiah, Francisco J. Flores, Jeremy D. Cohen, Albert K. Lee, Christoph Borgers, Craig R. Forest, Nancy J. Kopell, Edward S. Boyden (2017) Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain, Journal of Neurophysiology 118(2):1270-1291.

FEF inactivation with improved optogenetic methods

Proceedings of the National Academy of Sciences | 2016

Acker L, Pino EN, Boyden ES, Desimone R (2016) FEF inactivation with improved optogenetic methods, Proceedings of the National Academy of Sciences 113(46):E7297-E7306.

Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory

Molecular Psychiatry | 2015

Li P, Rial D, Canas PM, Yoo JH, Li W, Zhou X, Wang Y, van Westen GJ, Payen MP, Augusto E, Gonçalves N, Tomé AR, Li Z, Wu Z, Hou X, Zhou Y, PIJzerman A, Boyden ES, Cunha RA, Qu J, Chen JF (2015) Optogenetic activation of intracellular adenosine A2A receptor signaling in the hippocampus is sufficient to trigger CREB phosphorylation and impair memory, Molecular Psychiatry 20:1339–1349.

Hebbian and neuromodulatory mechanisms interact to trigger associative memory formation

Proceedings of the National Academy of Sciences | 2014

Johansen J.P., Diaz-Mataix L., Hamanaka H., Ozawa T., Ycu E., Koivumaa J., Kumar A., Hou M., Deisseroth K., Boyden E.S., LeDoux J.E. (2014) Hebbian and neuromodulatory mechanisms interact to trigger associative memory formation, Proceedings of the National Academy of Sciences 111(51):E5584–E5592.

Towards Optogenetic Sensory Replacement

Conference Proceedings of the IEEE Engineering in Medicine and Biology Society | 2011

Doroudchi, M. M., Greenberg, K. P., Zorzos, A. N., Hauswirth, W. W., Fonstad, C. G., Horsager, A., Boyden, E. S. (2011) Towards Optogenetic Sensory Replacement, Conference Proceedings of the IEEE Engineering in Medicine and Biology Society 2011:3139-41.

High-speed mapping of synaptic connectivity using photostimulation in channelrhodopsin-2 transgenic mice

Proceedings of the National Academy of Sciences | 2007

Wang, H., Peca, J., Matsusaki, M., Matsusaki, K., Noguchi, J., Qiu, L., Wang, D., Zhang, F., Boyden, E. S., Deisseroth, K., Kasai, H., Hall, W. C., Feng, G., Augustine, G. J. (2007) High-speed mapping of synaptic connectivity using photostimulation in channelrhodopsin-2 transgenic mice, Proceedings of the National Academy of Sciences 104(19):8143-848.