Our Published Work

Updated on 3/15/2022.


Sanabria, B.D., Baskar, S.S., Lee, C.R., Margolis, D.J. Differential innervation of striatal microcircuitry by primary somatosensory and primary motor cortex. In prep.

Jeong, Y.Y., Han, S., Jia, N., Zhang, M., Sheshadri, P., Tammineni, P., Cheung, J., Nissenbaum, M., Baskar, S.S., Kwan, K., Margolis, D.J., Jiang, P., Kusnecov, A., Cai, Q. Broad mitophagy activation induces synaptic mitochondrial deficits in early tauopathy. Brain, 2022, awab243.


Liu, X., Bibineyshvili, Y., Robles, D.A., Boreland, A.J., Margolis, D.J., Shreiber, D.I., Zahn, J.D. Fabrication of multilayer implantable cortical microelectrode probe to improve recording potential. Journal of Microelectromechanical Systems, 30(4): 569-581.

Han, S., Zhang, M., Jeong, Y.Y., Margolis, D.J., Cai, Q. The role of mitophagy in the regulation of mitochondrial energetic status in neurons. Autophagy, 1-20.


Salsabilian, S., Zhu, L., Lee, C.R., Margolis, D.J., Najafizadeh, L. Identifying Task-Related Brain Functional States Via Cortical Networks. 2020 IEEE International Symposium on Circuits and Systems (ISCAS), 1-4.

Lee, C.R., Najafizadeh, L., Margolis, D.J. Investigating learning-related neural circuitry with chronic in vivo optical imaging. Brain Structure and Function, 225: 467-480.


Salsabilian, S., Bibineyshvili, Y., Margolis, D.J., Najafizadeh, L. Quantifying Changes in Brain Function Following Injury via Network Measures. 2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 5217-5220.

Yonk, A.J., Margolis, D.J. Traces of learning in thalamocortical circuits. Neuron, 103(2): 175-176.

Shvedov, N., Margolis, D.J. An optical expose of cortical function. Trends in Neuroscience, 42(8): 511-513.

Lee, C.R., Yonk, A.J., Wiskerke, J., Paradiso, K.G., Tepper, J.M., Margolis, D.J. Opposing influence of sensory and motor cortical input on striatal circuitry and choice behavior. Current Biology, 29(8): 1313-1323, e5.

Vajtay, T.J., Bandi, A., Upadhyay, A., Swerdel, M.R., Hart, R.P., Lee, C.R., Margolis, D.J. Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad. Journal of Neurophysiology, 121(4): 1491-1500.


Zhu, L., Lee, C.R., Margolis, D.J., Najafizadeh, L. Decoding cortical brain states from widefield calcium imaging data using visibility graph. Biomedical Optics Express, 9(7): 3017-3036.

Eyo, U.B., Mo, M., Yi, M.H., Murugan, M., Liu, J., Yarlagadda, R., Margolis, D.J., Xu, P., Wu, L. P2Y12R-dependent translocation mechanisms gate the changing microglial landscape. Cell Reports, 23(4): 959-966.

Salsabillan, S., Lee, C.R., Margolis, D.J., Najafizadeh, L. Using connectivity to infer behavior from cortical activity recorded through widefield transcranial imaging. Optics and the Brain, BTu2C, 4.

Bandi, A., Vajtay, T.J., Upadhyay, A., Yiatnsos, S.O., Lee, C.R., Margolis, D.J. Optogenetic probing of nerve and muscle function after facial nerve lesion in the mouse whisker system. Optogenetics and Optical Manipulation, 2018 10482, 104820C.


Zhu, L., Lee, C.R., Margolis, D.J., Najafizadeh, L. Probing the dynamics of spontaneous cortical activities via widefield Ca2+ imaging in GCaMP6 transgenic mice. Wavelets and Sparsity XVII, 10394, 103940C.

Steinmetz, N., [...], Lee, C.R., [...], Margolis, D.J., [...]. Aberrant cortical activity in multiple GCaMP6-expressing transgenic mouse lines. eNeuro.

Zhu, L., Lee, C.R., Margolis, D.J., Najafizadeh, L. Predicting behavior from cortical activity recorded through widefield transcranial imaging. 2017 Conference on Lasers and Electro-Optics (CLEO), 1-2.

Ye, X., Feng, T., Tammineni, P., Chang, Q., Jeong, Y.Y., Margolis, D.J., Cai, H., Kusnecov, A., Cai, Q. Regulation of synaptic amyloid-beta generation through BACE1 retrograde transport in a mouse model of Alzheimer's disease. Journal of Neuroscience, 37(10): 2639-2655.


Eyo, U.B., Peng, J., Murugan, M,. Mo, M., Lalani, A., Xie, P., Xu, P., Margolis, D.J., Wu, L. Regulation of physical microglia-neuron interactions by fractalkine signaling after status epilepticus. eNeuro, 3(6).

Lee, C.R., Margolis, D.J. Pupil dynamics reflect behavioral choice and learning in a go/nogo tactile decision-making task in mice. Frontiers in Behavioral Neuroscience, 10, 200.

Park, S., Bandi, A., Lee, C.R., Margolis, D.J. Peripheral optogenetic stimulation induces whisker movement and sensory perception in head-fixed mice. eLife, 5, e14140.


Chen, J.L., Margolis, D.J., Stankov, A., Sumanovski, L.T., Schneider, B.L., Helmchen, F. Pathway-specific reorganization of projection neurons in somatosensory cortex during learning. Nature Neuroscience, 18(8): 1101-1108.


Margolis, D.J., Lütcke, H., Helmchen, F. Microcircuit dynamics of map plasticity in barrel cortex. Current Opinion in Neurobiology, 24, 76-81.

Margolis, D.J., Gartland, A.J., Singer, J.H., Detwiler, P.B. Network oscillations drive correlated spiking of ON and OFF ganglion cells in the rd1 mouse model of retinal degeneration. PLoS One, 9(1): e86253.

Margolis, D.J., Lütcke, H., Helmchen, F., Weber, B., Haiss, F. Chronic two-photon imaging of neural activity in the anesthetized and awake behaving rodent. Optical Imaging of Neocortical Dynamics, 151-173.


Chen, J.L., Pfaffli, O.A., Voigt, F.F., Margolis, D.J., Helmchen, F. Online correction of licking-induced brain motion during two-photon imaging with a tunable lens. Journal of Physiology, 591(19): 4689-4698.

Lütcke, H., Margolis, D.J., Helmchen, F. Steady of changing? Long-term monitoring of neuronal population activity. Trends in Neuroscience, 36(7): 375-384.


Margolis, D.J., Lütcke, H., Schulz, K., Haiss, F., Weber, B., Kügler, S., Hasan, M.T., Helmchen, F. Reorganization of cortical population activity imaged through long-term sensory deprivation. Nature Neuroscience, 15(11): 1539-1546.

Minderer, M., Liu, W., Sumanovski, L.T., Kügler, S., Helmchen, F., Margolis, D.J. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator. Journal of Physiology, 590(1): 99-107.


Margolis, D.J., Detwiler, P.B. Cellular origin of spontaneous ganglion cell spike activity in animal models of retinitis pigmentosa. Journal of Opthamology.


Margolis, D.J., Gartland, A.J., Euler, T., Detwiler, P.B. Dendritic calcium signaling in ON and OFF mouse retinal ganglion cells. Journal of Neuroscience, 30(21): 7127-7138.

Lütcke, H., Murayama, M., Hahn, T., Margolis, D.J., [...], Hasan, M.T. Optical recording of neuronal activity with a genetically-encoded calcium indicator in anestheized and freely moving mice. Frontiers in Neural Circuits, 4.


Euler, T., Hausselt, S.E., Margolis, D.J., Breuninger, T., Castell, X., Detwiler, P.B. Denk, W. Eyecup scope -- optical recordings of light stimulus-evoked fluorescence signals in the retina. Pflugers Archiv - European Journal of Physiology, 457: 1393-1414.


Margolis, D.J. Increased bursting in layer 2/3 neurones of awake neocortex. Journal of Physiology, 586(Pt 18): 4341-4342.

Margolis, D.J., Newkirk, G., Euler, T., Detwiler, P.B. Functional stability of retinal ganglion cells after degeneration-induced changes in synaptic input. Journal of Neuroscience, 28(25): 6526-6536.


Margolis, D.J., Detwiler, P.B. Different mechanisms generate maintained activity in ON and OFF retinal ganglion cells. Journal of Neuroscience, 27(22): 5994-6005.