Shang, C#, Wang, Y#, Zhao, M#, Fan Q, Zhao S, Qian Y, Mu, Y.,* Hao, J.* , Du, J.* Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics.(2024) Nat. Neurosci.

Tao, R., Wang, K., Chen T., Zhang X., Cao, J., Zhao W., Du, J., Mu, Y.* (2023) A genetically encoded ratiometric indicator for tryptophan. Cell Discovery 9 (1), 106

Wang, S., Wang, Y., Mu, Y.* (2022). Locus Coeruleus in Non-Mammalian Vertebrates. Brain Sci. 12,124

Zhao, S., Qian, Y., Mu, Y.* (2021). Tracking single-cells in zebrafish brain. J Neurosci Methods 109086.

Mu, Y.*, Narayan, S., Mensh, B., Ahrens, M. (2020). Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish. Curr Opin Neurobiol. 2020, 64:151–160 [pdf]

Mu, Y.*^#, Bennett, D. V. ^#, Rubinov, M. ^#, Narayan, S., Yang, C., Tanimoto, M., Mensh, B., Looger, L.L., and Ahrens, M.* (2019). Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior. Cell 178, 27-43.e19. ( * corresponding author, # co-first author) (Highlighted in Current Biology 29, R847-R850; and Faculty of 1000). [pdf]

Chen, X. ^#, Mu, Y. ^#, Hu, Y. ^#, Kuan, A. ^#, Nikitchenko, M., Randlett, O., Chen, A.B., Gavornik, J., Sompolinsky, H., Engert, F., and Ahrens, M. (2018). Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish. Neuron 100, 876-890.e5. (# co-first author) [pdf]

Dunn, T.^#, Mu, Y. ^#, Narayan, S., Randlett, O., Naumann, E., Yang, C.T., Schier, A., Freeman, J., Engert, F., and Ahrens, M. (2016). Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion. Elife 5.  [[pdf]]

Mu, Y.*, Li, X. (2012). Hearing what your eyes see - visual modulation of auditory function. Chin Bull Life Sci. 24, 1380-1383.

Mu, Y. ^#, Li, X. ^#, Zhang, B., and Du, J. (2012). Visual Input Modulates Audiomotor Function via Hypothalamic Dopaminergic Neurons through a Cooperative Mechanism. Neuron 75, 688–699. (Nominated as one of 30 candidates for Top 10 Scientific Advancements of China in 2012)[[pdf]]

(* corresponding author, ^# co-first author)

Shang, C#, Wang, Y#, Zhao, M#, Fan Q, Zhao S, Qian Y, Mu, Y.,* Hao, J.* , Du, J.* Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics. (2024) Nat. Neurosci. .

Chai, Y., Qi, K., Wu, Y., Li, D., Tan, G., Guo, Y., Chu, J., Mu, Y., Shen, C., Wen, Q., (2024) All-optical interrogation of brain-wide activity in freely swimming larval zebrafish. iScience 27(1).

Wang, K., Chen T., Zhang X., Cao, J., Zhao W., Du, J.* , Mu, Y.* , Tao, R.* (2024) Unveiling Tryptophan Dynamics and Functions Across Model Organisms via Quantitative ImagingK. bioRxiv. 12.580012 .

Gu, W., Chen, JH., Zhang Y., Wang Z., Li, J., Wang S., Zhang H., Jiang A., Zhong Z., Zhang, J., Xi, C., Hou, T., Gill, D., Li, D., Mu, Y.*, Wang, S.*, Tang, A. *, Wang, Y. *, (2024) Highly Dynamic and Sensitive NEMOer Calcium Indicators for Imaging ER Calcium Signals in Excitable Cells. bioRxiv. 08.583332

Zhao, J., Xue, L., Mu, Y. , P Ji, P.* (2024)From animal biology to simulated models and back. Physics of life reviews 49, 17-18

Deng,P., Liu, X., Zhao, Y., Zhang, X., Kong, Y., Liu, L., Xiao, Y., Yang, S., Hu, J., Su, J., Xuan, A., Xu, J., Li, H., Su, X.,Wu, J., Jiang, Y., Mu, Y. , Shao, Z., Kong, C., Li, B., (2024) Long-working-distance high-collection-efficiency three-photon microscopy for in vivo long-term imaging of zebrafish and organoids. iScience 27, 8, 110554

Tao, R., Wang, K., Chen T., Zhang X., Cao, J., Zhao W., Du, J., Mu, Y.* (2023) A genetically encoded ratiometric indicator for tryptophan. Cell Discovery 9 (1), 106

Li, D., Mu, Y.* (2023) Neuromodulatory system in network science. Physics of Life Reviews 46, 155-157

Ji, P., Ye, J., Mu, Y., Lin, W., Tian, Y., Hens, C., Perc, M., Tang, Y., Sun, J., Kurths, J. (2023) Signal propagation in complex networks. Physics Reports, 1017, 1-96

Nanda, A., Johnson, G., Mu, Y., Ahrens, M., Chang, C., Englot, D., Breakspear, M., Rubinov, M. (2023) Time-resolved correlation of distributed brain activity tracks EI balance and accounts for diverse scale-free phenomena. Cell Rep., 41, 112254

Jiao, Z., Zhou, Z., Chen, Z., Xie, J., Mu, Y., Du, J., Fu, L. (2023) Simultaneous multi-plane imaging light-sheet fluorescence microscopy for simultaneously acquiring neuronal activity at varying depths. Optica, 10, 239-247

Koh, T., Bishop, W., Kawashima, T., Jeon, B., Srinivasan, R., Mu, Y., Wei, Z., Kuhlman, S., Ahrens, M., Chase, S., Yu, B., (2023) Dimensionality reduction of calcium-imaged neuronal population activity. Nat. Comp. Sci. 3,71-85

Wang, S., Wang, Y., Mu, Y.* (2022). Locus Coeruleus in Non-Mammalian Vertebrates. Brain Sci. 12,124

Zhao, S., Qian, Y., Mu, Y.* (2021). Tracking single-cells in zebrafish brain. J Neurosci Methods 2021, 109086.

Mu, Y.*, Narayan, S., Mensh, B., Ahrens, M.* (2020). Brain-wide, scale-wide physiology underlying behavioral flexibility in zebrafish. Curr Opin Neurobiol. 2020, 64:151–160 [pdf]

Mu, Y.*#, Bennett, D. V. ^#, Rubinov, M. ^#, Narayan, S., Yang, C., Tanimoto, M., Mensh, B., Looger, L.L., and Ahrens, M.* (2019). Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior. Cell 178, 27-43.e19. (Highlighted in Current Biology 29, R847-R850; and Faculty of 1000). 

Fleishman, G.M., Zhang, M., Tustison, N.J., Espinosa-Medina, I., Mu, Y., Khairy, K., and Ahrens, M. (2019). Deformable Registration of Whole Brain Zebrafish Microscopy Using an Implementation of the Flash Algorithm Within Ants. In 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), (IEEE), pp. 213–217. 

Chen, X. ^#, Mu, Y. ^#, Hu, Y. ^#, Kuan, A. ^#, Nikitchenko, M., Randlett, O., Chen, A.B., Gavornik, J., Sompolinsky, H., Engert, F., and Ahrens, M. (2018). Brain-wide Organization of Neuronal Activity and Convergent Sensorimotor Transformations in Larval Zebrafish. Neuron 100, 876-890.e5.

Vladimirov, N., Wang, C., Höckendorf, B., Pujala, A., Tanimoto, M., Mu, Y., Yang, C., Wittenbach, J., Freeman, J., Preibisch, S., Koyama, M., Keller, P., Ahrens, M. (2018). Brain-wide circuit interrogation at the cellular level guided by online analysis of neuronal function. Nat. Methods 15, 1117–1125. 

Friedrich, J., Yang, W., Soudry, D., Mu, Y., Ahrens, M.B., Yuste, R., Peterka, D.S., and Paninski, L. (2017). Multi-scale approaches for high-speed imaging and analysis of large neural populations. PLoS Comput. Biol. 13, e1005685. 

Dunn, T.^#, Mu, Y. ^#, Narayan, S., Randlett, O., Naumann, E., Yang, C.T., Schier, A., Freeman, J., Engert, F., and Ahrens, M. (2016). Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion. Elife 5.

Pnevmatikakis, E., Soudry, D., Gao, Y., Machado, T.A., Merel, J., Pfau, D., Reardon, T.,** Mu, Y.,** Lacefield, C., Yang, W., Ahrens, M., Bruno, R., Jessell, T., Peterka, D., Yuste, R., Paninski, L. (2016). Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data. Neuron 89, 285–299. 

Friedrich, J., Soudry, D., Mu, Y., Freeman, J., Ahrens, M., and Paninski, L. (2015). Fast Constrained Non-negative Matrix Factorization for Whole-Brain Calcium Imaging Data. NIPS workshop on statistical methods for understanding neural systems. 1–5. 

Shang, C., Mu, Y., and Du, J. (2015). Zebrafish Swimming into Neuroscience Research: A Visible Mind in A Transparent Brain. Science in China. 45(3):223-236. 

Shang, C., Mu, Y., and Du, J. (2014). Progress in the application of zebrafish in neuroscience research. Annual Review of New Biology. 3:141-170. 

Vladimirov, N., Mu, Y., Kawashima, T., Bennett, D. V, Yang, C., Looger, L., Keller, P., Freeman, J., and Ahrens, M. (2014). Light-sheet functional imaging in fictively behaving zebrafish. Nat. Methods 883–884.

Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N., Bennett, D., Rosen, J., Yang, C., Looger, L., and Ahrens, M. (2014). Mapping brain activity at scale with cluster computing. Nat. Methods 11, 941–950. 

Mu, Y.*, Li, X. (2012). Hearing what your eyes see - visual modulation of auditory function. Chin Bull Life Sci. 24, 1380-1383.

Mu, Y.^#, Li, X. ^#, Zhang, B., and Du, J. (2012). Visual Input Modulates Audiomotor Function via Hypothalamic Dopaminergic Neurons through a Cooperative Mechanism. Neuron 75, 688–699.  (Nominated as one of 30 candidates for Top 10 Scientific Advancements of China in 2012)

Han, Y., Mu, Y., Li, X., Xu, P., Tong, J., Liu, Z., Ma, T., Zeng, G., Yang, S., Du, J., Meng, A. (2011). Grhl2 deficiency impairs otic development and hearing ability in a zebrafish model of the progressive dominant hearing loss DFNA28. Hum. Mol. Genet. 20, 3213–3226. 

Feng, Y., Yan, T., Zheng, J., Ge, X., Mu, Y., Zhang, Y., Wu, D., Du, J., and Zhai, Q. (2010).Overexpression of Wld s or Nmnat2 in mauthner cells by single-cell electroporation delays axon degeneration in live zebrafish. J. Neurosci. Res. 88, 3319–3327. 

Liu, C., Mu, Y., and Du, J. (2007). Application of the zebrafish in the research of life sciences. Chin Bull Life Sci. 19, 382–386.

(* corresponding author, ^# co-first author)