UC San Diego School of Biological Sciences
Department of Neurobiology

 

Blumenstock, S., Arakelyan, D., del Grosso, N., Schneider, S., Shao, Y., Gjoni, E., Klein, R., Dudanova, I., and Komiyama, T. (2026)
Restoring cortical disinhibition improves Huntington’s disease phenotypes (PDF)
Nature https://www.nature.com/articles/s41586-026-10671-9

Zhang, Y. E., Danskin, B. P., Zhou, M., Uppalapati, E., Medina, A., Lin, C.-Y., and Komiyama, T. (2026)
Adaptive reorganization of history encoding in the retrosplenial cortex supports flexible decision-making strategies (PDF)
Neuron https://www.cell.com/neuron/fulltext/S0896-6273(26)00335-1

Wright, W. J., Chen, E. C.-Y., Zhou, B., Wang, J., Liu, Z., Morales, B. C., and Komiyama, T. (2026)
Local plasticity underlies the reorganization of cortical circuit dynamics during motor learning (PDF)
Current Biology https://www.sciencedirect.com/science/article/pii/S0960982226005877

Gjoni, E., Sristi, R. D., Liu, H., Dror, S., Lin, X., O’Neil, K., Arroyo, O. M., Hong, S. W., Kim, H., Liu, J., Blumenstock, S., Lim, B., Mishne, G., and Komiyama, T. (2026)
“Complementary cortical and thalamic contributions to cell type–specific striatal activity dynamics during movement” (PDF)
Science Advances https://www.science.org/doi/10.1126/sciadv.aea3935

Yu, B., Yue, Y., Ren, C., Yun, R., Lim, B., and Komiyama, T. (2025)
“Cholinergic feedback for context-specific modulation of sensory representations” (PDF)
Science https://www.science.org/doi/10.1126/science.ads9152

Ramot, A., Taschbach, F. H., Yang, Y. C., Hu, Y., Chen, Q., Morales, B. C., Wang, X. C., Wu, A., Tye, K. M., Benna, M. K., and Komiyama, T. (2025)
“Motor learning refines thalamic influence on motor cortex.” (PDF)
Nature https://www.nature.com/articles/s41586-025-08962-8

Wright, W.J.#, Hedrick, N.G., and Komiyama, T.# (2025)
“Distinct synaptic plasticity rules operate across dendritic compartments in vivo during learning.” (PDF)
Science https://www.science.org/doi/10.1126/science.ads4706

Blumenstock, S., Arakelyan, D., del Grosso, N., Schneider, S., Shao, Y., Gjoni, E., Klein, R., Dudanova, I., and Komiyama, T. (2025)
“Optogenetic restoration of neuron subtype-specific cortical activity ameliorates motor deficits in Huntington’s Disease mice” (PDF)
bioRxiv https://www.biorxiv.org/content/10.1101/2025.02.07.637155v1

Wu, A., Chen, Q., Yu, B., Chae, S., Tan, Z., Ramot, A., and Komiyama, T. (2025)
“Targeted stimulation of motor cortex neural ensembles drives learned movements” (PDF)
bioRxiv https://www.biorxiv.org/content/10.1101/2025.01.06.631504v1

Economo, M., Komiyama, T.*, Kubota, Y.*, and Shiller, J.* (2024)
“Learning and control in motor cortex across cell types and scales.” (Review) (PDF)
Journal of Neuroscience https://www.jneurosci.org/content/44/40/e1233242024

Hedrick, N.G., Wright, J. William., and Komiyama, T. (2024)

“Local and global predictors of synapse elimination during motor learning.” (PDF)
Science Advances https://www.science.org/doi/epdf/10.1126/sciadv.adk0540.

Dunton, K.L.*, Hedrick, N.G.*, Meamardoost, S., Ren, C., Howe, J.R., Wang, J., Root, C.M., Gunawan, R., Komiyama, T.#, Zhang, Y.#, Hwang, E.J.# (2024)
“Divergent learning-related transcriptional states of cortical glutamatergic neurons.” (PDF)
Journal of Neuroscience https://doi.org/10.1523/JNEUROSCI.0302-23.2023.

Ramezani, M., Kim, JH., Liu, X, Ren, C, Alothman, A., De-Eknamkul, C., Wilson, M.N., Cubukcu, E., Gilja, V., Komiyama, T., and Kuzum, D. (2024)
“High-density transparent graphene arrays for predicting cellular calcium activity at depth from surface potential recordings.” (PDF)
Nature Nanotechnology https://doi.org/10.1038/s41565-023-01576-z.

Danskin, B.P., Hattori, R., Zhang, Y.E., Babic, Z., Aoi, M. , and Komiyama, T. (2023)

“Exponential history integration with diverse temporal scales in retrosplenial cortex supports hyperbolic behavior.” (PDF)
Science Advances https://www.science.org/doi/10.1126/sciadv.adj4897

Hattori, R., Hedrick, N.G., Jain, A., Chen, S., You, H., Hattori, M., Choi, J.H., Lim, B.K., Yasuda, R., and Komiyama, T. (2023)
“Meta-reinforcement learning via orbitofrontal cortex.” (PDF)
Nature Neuroscience https://www.nature.com/articles/s41593-023-01485-3

Komiyama, T. (2023)
“Diversity of primate brain cells unraveled” (Introduction to the special issue) (PDF)
Science Advances https://www.science.org/doi/10.1126/sciadv.adl0650

Meamardoost, S., Bhattacharya, M., Hwang, E.J., Ren, C., Wang, L., Mewes, C., Zhang, Y., Komiyama, T., and Gunawan, R. (2023),
“Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning.” (PDF)
Data Science in Science https://www.tandfonline.com/doi/full/10.1080/26941899.2023.2260431#abstract

Ramezani, M., Liu, X., Ren, C., Komiyama, T., Kuzum, D. (2023)
“Processing multimodal neural data and decoding neural dynamics using cross-modality inference.” (PDF)
11th International IEEE/EMBS Conference on Neural Engineering (NER) https://ieeexplore.ieee.org/document/10123822

Sarangi, P., Hattori, R., Komiyama, T., and Pal, P. (2023)
“Super-resolution with Binary Priors: Theory and Algorithms.” (PDF)
IEEE Transactions on Signal Processing https://ieeexplore.ieee.org/document/10078298

Chen, Z., Zhang, R., Fang, H.S., Zhang, Y. E., Bal, A., Zhou, H., Rock, R.R., Padilla-Coreano, N., Keyes, L., Zhu, H., Li, Y.L., Komiyama, T., Tye, K.M., and Lu, C. (2023)
“AlphaTracker: A Multi-Animal Tracking and Behavioral Analysis Tool.” (PDF)
Frontiers in Behavioral Neuroscience https://www.frontiersin.org/journals/behavioral-neuroscience/articles/10.3389/fnbeh.2023.1111908/full

Sarangi, P., Hattori, R., Komiyama, T., and Pal, P. (2023)
“Super-resolution with Binary Priors: Theory and Algorithms.” (PDF)
IEEE Transactions on Signal Processing, Preprint at https://arxiv.org/pdf/2301.01724.pdf

Meamardoost, S., Bhattacharya, M., Hwang, E.J., Ren, C., Wang, L., Mewes, C., Zhang, Y., Komiyama, T., and Gunawan, R. (2022)
“Rewiring Dynamics of Functional Connectome in Motor Cortex during Motor Skill Learning.”
Data Science in Science https://www.tandfonline.com/doi/full/10.1080/26941899.2023.2260431

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 https://iopscience.iop.org/article/10.1088/1741-2552/ac8fb5

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 https://www.nature.com/articles/s41593-022-01086-6

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 https://www.cell.com/neuron/fulltext/S0896-6273(24)00358-1

Hattori, R. and Komiyama, T. (2022)
“Longitudinal two-photon calcium imaging with ultra-large cranial window for head-fixed mice” (PDF)
STAR Protocols https://www.sciencedirect.com/science/article/pii/S2666166722002234

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 Methods https://www.sciencedirect.com/science/article/pii/S2667237522000637

Hattori, R. and Komiyama, T. (2022)
“Context-dependent persistency as a coding mechanism for robust and widely distributed value coding.” (PDF)
Neuron https://www.sciencedirect.com/science/article/pii/S0896627321008916?via%3Dihub

Ren, C. and Komiyama, T. (2021)
“Wide-field calcium imaging of cortex-wide activity in awake, head-fixed mice.” (PDF)
STAR Protocols https://www.sciencedirect.com/science/article/pii/S2666166721006791?via%3Dihub

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 https://www.mdpi.com/2076-3425/11/12/1556

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 https://iopscience.iop.org/article/10.1088/1741-2552/ac33e7

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 Neuroscience https://www.jneurosci.org/content/41/33/7029

Ren, C. and Komiyama, T. (2021)
“Characterizing cortex-wide dynamics with wide-field calcium imaging.” (Review) (PDF)
Journal of Neuroscience https://www.jneurosci.org/content/41/19/4160

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 https://www.nature.com/articles/s41593-021-00841-5

Bathe, M.*, Hernandez, R.*, Komiyama, T.*, Machiraju, R.*, and Neogi S.* (*: co-first authors) (2021)
“Autonomous Computing Materials.” (Perspective)  (PDF)
ACS Nano https://pubs.acs.org/doi/10.1021/acsnano.0c09556

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 https://www.science.org/doi/10.1126/sciadv.abc8319

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 https://journals.physiology.org/doi/full/10.1152/jn.00061.2020

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 https://ieeexplore.ieee.org/document/9039710

Wu. A., Yu. B., and Komiyama, T. (2020)
“Plasticity in olfactory bulb circuits.” (Review) (PDF)
Current Opinion in Neurobiology https://www.sciencedirect.com/science/article/pii/S0959438820300088?via%3Dihub

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 https://pubmed.ncbi.nlm.nih.gov/31706697/

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 https://www.science.org/doi/10.1126/sciadv.aay0001

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 https://www.sciencedirect.com/science/article/pii/S0092867419304465?via%3Dihub


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

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 https://advanced.onlinelibrary.wiley.com/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 https://elifesciences.org/articles/33006

Mitani, A., Dong, M. and Komiyama, T. (2018)
“Brain-computer interface with inhibitory neurons reveals subtype-specific strategies.” (PDF)
Current Biology https://www.sciencedirect.com/science/article/pii/S0960982217315178?via%3Dihub

Liu, X., Lu, Y., Iseri, E., Ren, C., Liu, H., Komiyama, T., and Kuzum, D. (2017).
“Transparent artifact-free graphene electrodes for compact closed-loop optogenetics systems.” (PDF)
Electron Devices Meeting (IEDM) https://ieeexplore.ieee.org/document/8268461

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 https://www.nature.com/articles/s41467-017-01356-z

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 https://www.eneuro.org/content/4/5/ENEURO.0287-17.2017

Hattori, R.*, Kuchibhotla, K.*, Froemke, R.#, and Komiyama, T.#(2017)
“Functions and dysfunctions of neocortical inhibitory neuron subtypes.” (Review) (PDF)
Nature Neuroscience https://www.nature.com/articles/nn.4619

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 https://www.nature.com/articles/nn.4596

 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 https://www.sciencedirect.com/science/article/pii/S0896627317303410?via%3Dihub

 

Peters, A.J., Liu, H. and Komiyama, T. (2017)
“Learning in the rodent motor cortex.” (Review) (PDF)
Annual Review of Neuroscience https://www.annualreviews.org/content/journals/10.1146/annurev-neuro-072116-031407

McIntyre, J.C., Thiebaud, N., McGann, J.P., Komiyama, T. and Rothermel, M. (2017)
“Neuromodulation in chemosensory systems.” (Review) (PDF)
Chemical Senses https://academic.oup.com/chemse/article/42/5/375/3100451

Makino, H., Hwang, E.J., Hedrick, N. and Komiyama, T. (2016)
“Circuit mechanisms of sensorimotor learning.” (Review) (PDF)
Neuron https://www.sciencedirect.com/science/article/pii/S0896627316307796?via%3Dihub

Chu, M.W., Li, W.L. and Komiyama, T. (2016)
“Balancing the robustness and efficiency of odor representations during learning.” (PDF)
Neuron https://www.sciencedirect.com/science/article/pii/S0896627316305633?via%3Dihub

Makino, H. and Komiyama, T. (2015)
“Learning Enhances the Relative Impact of Top-down Processing in Visual Cortex.” (PDF)
Nature Neuroscience https://www.nature.com/articles/nn.4061

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 https://www.nature.com/articles/nn.4049

 

Boyd, A.M., Kato, H.K., Komiyama, T., Isaacson, J.S. (2015)
“Broadcasting of Cortical Activity to the Olfactory Bulb.” (PDF)
Cell Reports https://www.sciencedirect.com/science/article/pii/S2211124715000728?via%3Dihub

  • 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 https://www.nature.com/articles/nature13235

  • 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 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088678

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 https://www.sciencedirect.com/science/article/pii/S0896627313007952?via%3Dihub

 

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 https://www.sciencedirect.com/science/article/pii/S0896627312008963?via%3Dihub

  • 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 https://www.sciencedirect.com/science/article/pii/S0896627311008774?via%3Dihub

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 https://www.nature.com/articles/nature08897

  • 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 https://www.jneurosci.org/content/30/5/1947

    Before 2010 (Selected)

    Komiyama, T. and Luo, L. (2007)
    “Intrinsic control of precise dendritic targeting by an ensemble of transcription factors.” (PDF)
    Current Biology https://www.sciencedirect.com/science/article/pii/S0960982206025887?via%3Dihub

    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     https://www.sciencedirect.com/science/article/pii/S0092867407000426?via%3Dihub

    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     https://www.sciencedirect.com/science/article/pii/S0896627306009421?via%3Dihub (*: equal contribution)

    Komiyama, T. and Liqun Luo (2006)
    “Development of wiring specificity of the olfactory system.” (PDF)
    Current Opinion in Neurobiology https://www.sciencedirect.com/science/article/pii/S0959438805001844?via%3Dihub

    Komiyama, T., Carlson, J.R. and Luo, L. (2004)
    “Olfactory receptor neuron axon targeting: Intrinsic transcriptional control and hierarchical interactions.” (PDF)
    Nature Neuroscience https://www.nature.com/articles/nn1284

    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 https://www.sciencedirect.com/science/article/pii/S0092867403000308 (*: equal contribution)