Publications

Publications

Meamardoost, S., Bhattacharya, M., Hwang, E.J., Ren, C., Wang, L., Mewes, C., Zhang, Y., Komiyama, T., and Gunawan, R.
“Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning.”
Preprint at https://www.biorxiv.org/content/10.1101/2022.07.12.499746v1

Liu, F., Meamardoost, S., Gunawan, R., Komiyama, T., Mewes, C., Zhang, Y., Hwang, E.J.*, Wang, L.* (2022)
“Deep Learning for Neural Decoding in Motor Cortex.” (PDF)
Journal of Neural Engineering, 19(5), 056021.

Hedrick, N.G., Lu, Z., Bushong, E., Singhi, S., Nguyen, P., Magaña, Y., Jilani, S., Lim, B.K., Ellisman, M., and Komiyama, T. (2022)
“Learning binds new inputs into functional synaptic clusters via spinogenesis” (PDF)
Nature Neuroscience, 25, 726–737.

Ren, C., Peng, K., Yang, R., Liu, W., Liu, C., and Komiyama, T. (2022)
“Global and subtype-specific modulation of cortical inhibitory neurons regulated by acetylcholine during motor learning” (PDF)
Neuron, S0896-6273 (22), 00408-1.

Hattori, R. and Komiyama, T. (2022)
“Longitudinal two-photon calcium imaging with ultra-large cranial window for head-fixed mice” (PDF)
STAR Protocols, 3 (2), 101341.

Hattori, R. and Komiyama, T. (2022)
“PatchWarp: Corrections of non-uniform image distortions in two-photon calcium imaging data by patchwork affine transformations.” (PDF)
Cell Reports Methods100205.

Hattori, R. and Komiyama, T. (2022)
“Context-dependent persistency as a coding mechanism for robust and widely distributed value coding.” (PDF)
Neuron, S0896-6273 (21), 00891-6.

Ren, C. and Komiyama, T. (2021)
“Wide-field calcium imaging of cortex-wide activity in awake, head-fixed mice.” (PDF)
STAR Protocols, 2 (4), 100973.

Meamardoost, S., Bhattacharya, M., Hwang, E.J., Komiyama, T., Mewes, C., Wang, L., Zhang, Y., Gunawan, R. (2021)
“FARCI: Fast and Robust Connectome Inference.” (PDF)
Brain Sciences, 11(12), 1556.

Liu, X.*, Ren, C.*, Huang, Z., Wilson, M., Kim, J-H., Lu, Y., Ramezani, M., Komiyama, T., and Kuzum, D. (2021)
“Decoding of cortex-wide brain activity from local recordings of neural potentials.” (PDF)
Journal of Neural Engineering,18(6), 066009.

Hwang, E.J.*, Dahlen, J.E.*, Mukundan, M., and Komiyama, T. (2021)
“Disengagement of motor cortex during long-term learning tracks the performance level of learned movements.” (PDF)
Journal of Neuroscience41(33), 7029-7047.

Ren, C. and Komiyama, T. (2021)
“Characterizing cortex-wide dynamics with wide-field calcium imaging.” (Review) (PDF)
Journal of Neuroscience, 41(19), 4160-4168
Liu, X.*, Ren, C.*, Lu, Y.*, Liu, Y., Kim, J., Leutgeb, S., Komiyama, T.#, and Kuzum, D.# (#: co-correspondence) (2021)
“Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical–hippocampal interactions.” (PDF)
Nature Neuroscience (cover article) 24, 886-896
Bathe, M.*, Hernandez, R.*, Komiyama, T.*, Machiraju, R.*, and Neogi S.* (*: co-first authors) (2021)
“Autonomous Computing Materials.” (Perspective)  (PDF)
ACS Nano, 15, 3, 3586-3592.
Komiyama, T. (2020)
“Threat detection starts in the eyes.” (Preview) (PDF)
Part of ‘This week in Science’ in Science, 370:6519, pp. 926.
Wu, A.*, Yu, B.*, Chen, Q., Matthews, G.A., Lu, C., Campbell, E., Tye, K.M., and Komiyama, T. (2020)
“Context-dependent plasticity of adult-born neurons instructed by cortical feedback.” (PDF)
Science Advances, 6(42), eabc8319.
Ma, Z., Liu, H., Komiyama, T., and Wessel, R. (2020)
“Stability of layer-specific motor cortex network states during learning-associated neural reorganizations.” (PDF)
Journal of Neurophysiology, 124(5), 1327-42.
Ding, D., Lu, Y., Zhao, R., Liu, X., De-Eknamkul, C., Ren, C., Mehrsa, A., Komiyama, T., and Kuzum, D. (2020)
“Evaluation of Durability of Transparent Graphene Electrodes Fabricated on Different Flexible Substrates for Chronic in vivo Experiments.” (PDF)
IEEE Transactions on Biomedical Engineering, DOI:10.1109/TBME.2020.2979475.6(42), eabc8319
Wu. A., Yu. B., and Komiyama, T. (2020)
“Plasticity in olfactory bulb circuits.” (Review) (PDF)
Current Opinion in Neurobiology, 64:17-23.

Hwang, E.J., Link, T.D., Hu, Y.Y., Lu, S., Wang, E.H., Lilascharoen, V., Aronson, S., O’Neil, K., Lim, B.K., and Komiyama, T. (2019)
“Corticostriatal Flow of Action Selection Bias.” (PDF)
Neuron, 104(6): 1126-1140.

 

Hwang, E.J., Dahlen, J.E., Hu, Y.Y., Aguilar, K., Yu, B., Mukundan, M., Mitani, A., and Komiyama, T. (2019)
“Disengagement of motor cortex from movement control during long-term learning.” (PDF)
Science Advances, 5(10): eaay0001.

 

Hattori, R., Danskin, B., Babic, Z., Mlynaryk, N., and Komiyama, T. (2019)
“Area-Specificity and Plasticity of History-Dependent Value Coding During Learning.” (PDF)
Cell, 177(7):1858-1872.

Mitani, A. and Komiyama, T. (2018)
“Real-Time Processing of Two-Photon Calcium Imaging Data Including Lateral Motion Artifact Correction.” (PDF)
Frontiers in Neuroinformatics
, DOI:10.3389/fninf.2018.00098

Lu, Y., Liu, X., Hattori, R., Ren, C., Komiyama, T., and Kuzum, D. (2018)
“Ultra-low Impedance Graphene Microelectrodes with High Optical Transparency for Simultaneous Deep 2-photon Imaging in Transgenic Mice.” (PDF)
Advanced Functional Materials, DOI:10.1002/adfm.201800002.
Li, W.L., Chu, M., Wu, A., Suzuki, Y., Imayoshi, I., and Komiyama, T. (2018)
“Adult-born neurons facilitate olfactory bulb pattern separation during task engagement.” (PDF)
eLife, 2018;7:e33006.
Mitani, A., Dong, M. and Komiyama, T. (2018)
“Brain-computer interface with inhibitory neurons reveals subtype-specific strategies.” (PDF)
Current Biology, 28(1), 77-83.

X. Liu, Y. Lu, E. Iseri, C. Ren, H. Liu, T. Komiyama and D. Kuzum (2017).
“Transparent artifact-free graphene electrodes for compact closed-loop optogenetics systems.” (PDF)
Electron Devices Meeting (IEDM), 2017 IEEE International, 26.1.1-26.1.4.

Hwang, E.J.*, Dahlen, J.E.*, Mukundan, M. and Komiyama, T. (2017)
“History-based action selection bias in the posterior parietal cortex.” (PDF)
Nature Communications, 8, 1242.

Chu, M.W., Li, W.L. and Komiyama, T. (2017)
“Lack of pattern separation in sensory inputs to the olfactory bulb during perceptual learning.” (PDF)
eNeuro, 0287-17.201.

Hattori, R.*, Kuchibhotla, K.*, Froemke, R.#, and Komiyama, T.#(2017)
“Functions and dysfunctions of neocortical inhibitory neuron subtypes.” (Review) (PDF)
Nature Neuroscience, 20, 1199-1208.

Peters, A.J., Lee, J., Hedrick, N.G., O’Neil, K., and Komiyama, T. (2017)
“Reorganization of corticospinal output during motor learning.” (PDF)
Nature Neuroscience, 20, 1133-41.

 

Makino, H.*#, Ren, C.*, Liu, H.*, Kim, A.N., Kondapaneni, N., Liu, X., Kuzum, D. and Komiyama, T.#(2017)
“Transformation of cortex-wide emergent properties during motor learning.” (PDF)
Neuron, 94(4), 880-90.

  • Preview by Banerjee and Long, Neuron 94(4), 698-700.

Peters, A.J., Liu, H. and Komiyama, T. (2017)
“Learning in the rodent motor cortex.” (Review) (PDF)
Annual Review of Neuroscience, 40, 77-97.

McIntyre, J.C., Thiebaud, N., McGann, J.P., Komiyama, T. and Rothermel, M. (2017)
“Neuromodulation in chemosensory systems.” (Review) (PDF)
Chemical Senses, 42(5), 375-9.

Makino, H., Hwang, E.J., Hedrick, N. and Komiyama, T. (2016)
“Circuit mechanisms of sensorimotor learning.” (Review) (PDF)
Neuron, 92(4), 705-721.

Chu, M.W., Li, W.L. and Komiyama, T. (2016)
“Balancing the robustness and efficiency of odor representations during learning.” (PDF)
Neuron, 92(1), 174-186.

Makino, H. and Komiyama, T. (2015)
“Learning Enhances the Relative Impact of Top-down Processing in Visual Cortex.” (PDF)
Nature Neuroscience, 18(8), 1116-22.

Chen, S.X., Kim, A.N., Peters, A.J. and Komiyama, T. (2015)
“Subtype-specific Plasticity of Inhibitory Circuits During Motor Learning.” (PDF)
Nature Neuroscience, 18(8), 1109-15.

  • News and Views by Grillo, F.W., West, L. and De Paola, V., Nature Neuroscience 18(8), 1062-64.

Boyd, A.M., Kato, H.K., Komiyama, T., Isaacson, J.S. (2015)
“Broadcasting of Cortical Activity to the Olfactory Bulb.” (PDF)
Cell Reports, 10(7), 1032-9.

  • Rated by Faculty of 1000.

Peters, A.J., Chen, S.X. and Komiyama, T. (2014)
“Emergence of Reproducible Spatiotemporal Activity During Motor Learning.” (PDF)
Nature, 510(7504), 263-7.

  • Rated by Faculty of 1000.

Guo ZV, Hires SA, Li N, O’Connor DH, Komiyama T, Ophir E, Huber D, Bonardi C, Morandell K, Gutnisky D, Peron S, Xu NL, Cox J, Svoboda K. (2014)
“Procedures for behavioral experiments in head-fixed mice.” (PDF)
Plos ONE, 9(2):e88678.

Kato, H.K., Gillet, S.N, Peters, A.J., Isaacson, J.S. and Komiyama, T. (2013)
“Parvalbumin-Expressing Interneurons Linearly Control Olfactory Bulb Output.” (PDF)
Neuron, 80(5), 1218-31.

  • Preview by Uchida, N., Eshel, N. and Watabe-Uchida, M., Neuron 80, 1106-09.
  • Research Highlight’ by Yates, D., Nature Reviews Neuroscience 15, 4-5.
  • Rated by Faculty of 1000.

Kato, H.K.*, Chu, M.W.*, Isaacson, J.S. and Komiyama, T. (2012)
“Dynamic Sensory Representations in the Olfactory Bulb: Modulation by Wakefulness and Experience.” (PDF)
Neuron, 76(5), 962-975.

  • Rated by Faculty of 1000.

Sweeney LB, Chou YH, Wu Z, Joo W, Komiyama T, Potter CJ, Kolodkin AL, Garcia KC, Luo L. (2011)
“Secreted semaphorins from degenerating larval ORN axons direct adult projection neuron dendrite targeting.” (PDF)
Neuron, 72(5), 734-47.

Komiyama, T.*, Sato, T.R., O’Connor, D.H., Zhang, Y.X., Huber, D., Hooks, B.M., Gabbito, M. and Svoboda, K. (2010)
“Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice.” (PDF)
Nature, 464(7292), 1182-1186. (*: correspondence) Faculty of 1000 Article Factor: 15

  • Rated by Faculty of 1000.

O’Connor, D.H., Clack, N.G., Huber, D., Komiyama, T., Myers, E.W. and Svoboda, K. (2010)
“Vibrissa-based object localization in head-fixed mice.” (PDF)
J. Neuroscience, 30, 1947-1967

Before 2010 (Selected)

Komiyama, T. and Luo, L. (2007)
“Intrinsic control of precise dendritic targeting by an ensemble of transcription factors.” (PDF)
Current Biology 17, 278-285.

Komiyama, T., Sweeney, L.B., Schuldiner, O., Garcia, K.C. and Luo, L. (2007)
“Graded expression of Semaphorin-1a cell-autonomously directs dendritic targeting of olfactory projection neurons.” (PDF)
Cell
 128, 399-410.

Sweeney, L.B.*, Couto, A., Chou, Y-H., Berdnik, D., Dickson, B.J., Luo, L. and Komiyama, T.* (2007)
“Temporal target restriction of olfactory receptor neurons through Semaphorin-1a/PlexinA mediated axon-axon interactions.” (PDF)
Neuron
 53, 185-200. (*: equal contribution)

Komiyama, T. and Liqun Luo (2006)
“Development of wiring specificity of the olfactory system.” (PDF)
Current Opinion in Neurobiology 16(1), 67-73.

Komiyama, T., Carlson, J.R. and Luo, L. (2004)
“Olfactory receptor neuron axon targeting: Intrinsic transcriptional control and hierarchical interactions.” (PDF)
Nature Neuroscience 7, 819-825.

Komiyama, T.*, Johnson, W.A., Luo, L. and Jefferis, G.S.X.E.* (2003)
“From lineage to wiring specificity: POU domain transcription factors control precise connections of Drosophila olfactory projection neurons.” (PDF)
Cell 112, 157-167. (*: equal contribution)