From the perspective of complex systems science, analyzing multi-dimensional information such as structure, function, and molecules at the whole-brain scale with cellular resolution is a crucial strategy for elucidating the principles of brain function. Our group uses zebrafish as a model organism and has developed various new technologies for whole-brain scale studies, conducting a series of studies on the sensorimotor system. The research has been published in journals such as Cell, Nature Neuroscience, Neuron, and eLife. Specifically, the group has designed and constructed optical microscopes capable of observing the entire brain, developed fluorescent probes for live imaging, and established behavioral paradigms in virtual reality to explore object recognition and behavioral decision-making experiments along with whole-brain modeling.

Further integrating the complex systems science approach, which considers both local and global aspects, and leveraging the features of whole-brain scale research with a focus on visual-motor transduction: structurally, using information from whole-brain neural connectivity maps to analyze the underlying architecture of brain networks; functionally, dissecting the whole-brain dynamics of decision-making and recognition in visual-motor transduction and its information processing mechanisms; and intellectually, explaining the flexibility and robustness of visual-motor transduction emergent from whole-brain neural connectivity structures and dynamics. Thus, the project aims to reveal the fundamental principles of visual-motor transduction on a whole-brain scale, promoting a shift from local to holistic research paradigms in brain science.

2006.9 – 2013.6     Ph.D. Candidate, Neuroscience, Institute of Neuroscience, Chinese Academy of Sciences

2011.6 - 2011.7      Neural Systems & Behavior Course, MBL, Woods Hole, MA

2002.9 - 2006.8      B.S., Biology, Nanjing University

Publications

1.      * Shang, C^#, Wang, Y^#, Zhao, M^#, Fan Q, Zhao S, Qian Y, Mu, Y.*, Hao, J.*, Du, J.* (2024) Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics. Nat. Neurosci. 1-5. ( *corresponding author)

2.      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).

3.      * 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 . ( *corresponding author)

4.      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 ( *corresponding author)

5.      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

6.      * 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 ( *corresponding author)

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

8.       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

9.       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

10.    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

11.    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

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

13.    Ye, H., Xu, X., Wang, J., Wang, J., He, Y., Mu, Y., Shi, G. (2022) Polarization effects on the fluorescence emission of zebrafish neurons using light-sheet microscopy. Biomed. Opt. Express 12, 6733-6744

14.  Zhao, S., Qian, Y., Mu, Y. * (2021). Tracking single-cells in zebrafish brain. J Neurosci Methods. 353, 109086 ( *corresponding author)

15.  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 (*corresponding author)

16.  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)

17.  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 (IEEE), 213–217.

18.  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)

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

20.  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.

21.  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. (# co-first author)

22.  Pnevmatikakis, E., Soudry, D., Gao, Y., Machado, T.A., Merel, J., Pfau, D., Reardon, T., Mu, Y., Lacefield, C., Yang, W., et al. (2016). Simultaneous Denoising, Deconvolution, and Demixing of Calcium Imaging Data. Neuron 89, 285–299.

23.  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.

24.  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.

25.  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.

26.  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.

27.  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.

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

29.  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. (# co-first author)

30.  Han, Y., Mu, Y., Li, X., Xu, P., Tong, J., Liu, Z., Ma, T., Zeng, G., Yang, S., Du, J., et al. (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.

31.  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.

32.  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.

现指导学生

李丹阳  硕士研究生  071006-神经生物学  

王斯佳  硕士研究生  071006-神经生物学  

赵姗  硕士研究生  071006-神经生物学