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Selected Publications

Du Y, Dylda E, Stibůrek M, Gomes AD, Turtaev S, Pakan JMP, Čižmár T. (2024) Advancing the path to in-vivo

         imaging in freely moving mice via multimode-multicore fiber based holographic endoscopy. 

         Neurophotonics. S11506.

Mocellin P, Barnstedt O, Luxem K, Kaneko H, Vieweg S, Henschke J, Dalügge D, Fuhrmann F, Karpova A, 

         Pakan JMP, Kreutz MR, Mikulovic S*, Remy S*. (2024) A septal-ventral tegmental area circuit drives

         exploratory behavior. Neuron. 112, 1-13.

Henschke JU and Pakan JMP (2023) Engaging distributed cortical and cerebellar networks through motor

         execution, observation, and imagery. Front. Syst. Neurosci. 17:1165307.

Li R, Huang J, Li L, Zhao Z, Liang S, Liang S, Wang M, Liao X, Lyu J, Zhou Z, Wang S, Jin W, Chen H, Holder D,

         Liu H, Zhang J, Li M, Tang Y, Remy S, Pakan JMP, Chen X, Jia H. (2023). Holistic Bursting Cells Store

         Long-term Memory in Auditory Cortex. Nature Communications. 14: 8090

Cangalaya C, Wegmann S, Sun W, Diez L, Gottfried A, Richter K, Stoyanov S, Pakan JMP, Fischer K-D &

         Dityatev A. (2023). Real-time mechanisms of exacerbated synaptic remodeling by microglia in acute

         models of systemic inflammation and tauopathy. Brain, Behavior, and Immunity 110: 245–259

Huang W, Wang Y, Qin J, He C, Li Y, Wang Y, Li M, Lyu J, Zhou Z, Jia H, Pakan JMP, Xie P & Zhang J. (2023).

         A corticostriatal projection for sound-evoked and anticipatory motor behavior following temporal

         expectation. Neuroreport 34: 1–8


Tang J, Xue R, Wang Y, Li M, Jia H, Pakan JMP, Li L, Chen X & Li X. (2022). Optical Fiber-Based Recording of

         Climbing Fiber Ca2+ Signals in Freely Behaving Mice. Biology 11: 907

Sun W*, Choi I*, Stoyanov S, Senkov O, Ponimaskin E, Winter Y, Pakan JMP & Dityatev A. (2021).

         Context Value Updating and Multidimensional Neuronal Encoding in the Retrosplenial Cortex.

         Nature Communications. 12: 1–17.


Dylda E, & Pakan JMP. (2021). Visual plasticity: Illuminating the role of the hippocampus in cortical

         sensory encoding. Current Biology 31: R1087–R1089.


Dacre J, Colligan M, Clarke T, Ammer JJ, Schiemann J, Chamosa-Pino V, Claudi F, Harston JA, Eleftheriou C,

         Pakan JMP, Huang C-C, Hantman AW, Rochefort NL & Duguid I. (2021). A cerebellar-thalamocortical

         pathway drives behavioral context-dependent movement initiation. Neuron 109: 1–13

Henschke JU, Price AT & Pakan JMP. (2021). Enhanced modulation of cell-type specific neuronal responses in

         mouse dorsal auditory field during locomotion. Cell Calcium 96: 102390

Henschke, JU & Pakan, JMP. (2020). Disynaptic cerebrocerebellar pathways originating from multiple 

         functionally distinct cortical areas. Elife 9: 1–27


Henschke JU*, Dylda E*, Katsanevaki D*, Dupuy N, Currie SP, Amvrosiadis T, Pakan JMP* & Rochefort NL*.                (2020). Reward Association Enhances Stimulus-Specific Representations in Primary Visual Cortex.                  Current Biology 30: 1866-1880.e5

Dylda E, Pakan JMP & Rochefort NL. (2018). Chronic Two-Photon Calcium Imaging in the Visual Cortex                      of Awake Behaving Mice. in Handbook of Behavioral Neuroscience 28: 235–251.


Turtaev S, Leite IT, Altwegg-Boussac T, Pakan JMP, Rochefort NL & Čižmár T. (2018). High-fidelity

          multimode fibre-based endoscopy for deep brain in vivo imaging. Light: Science and Applications 7: 92.

​Pakan JMP*, Currie S*, Fischer L*, Rochefort NL. (2018). The Impact of Visual Cues, Reward, and Motor

          Feedback on the Representation of Behaviorally Relevant Spatial Locations in Primary Visual Cortex. 

          Cell Reports. 24:2521–2528.

Lim L., Pakan J.M.P., Selten M.M., Marques-Smith A., Llorca A., Bae S.E., Rochefort N.L. and Marin O. (2018).              Optimization of interneuron function by direct coupling of cell migration and axonal targeting.                          Nature Neuroscience. DOI: 10.1038/s41593-018-0162-9.

Pakan J.M.P., Francioni V, Rochefort, NL. (2018). Action and learning shape the activity of neuronal circuits in

          the visual cortex. Current Opinion in Neurobiology 52: 88:97.

Long. R.M., Pakan, J.M.P., Graham, D.J. Hurd., P.L., Gutiérrez-Ibáñez, C. and Wylie, D.R. (2018). Modulation of

          complex spike activity differs between zebrin positive and negative Purkinje cells in the pigeon

          cerebellum. Journal of Neurophysiology DOI: 10.1152/jn.00797.2017.

Keemink S.W., Lowe S.C., Pakan J.M.P, Dylda E., van Rossum M., and Rochefort N.L. (2018). FISSA: A neuropil

         decontamination toolbox for calcium imaging signals. Scientific Reports. 8: 3493.

Howarth C., Sutherland B.A., Choi C.H., Martin C., Pakan J.M.P., Ellis-Davies G.C.R., Sibson N.R.,

Buchan A.M. and MacVicar B.A. (2017). Astrocyte contributions to neurovascular coupling and hypercapnia vasodilation: regulation by glutathione. Journal of Neuroscience. 37(9):2403-2414.

Pakan, J.M.P, Lowe S.C., Dylda E., Keemink S.W., Currie, S.P., Coutts C.A. and Rochefort N.L. (2016). 

Behavioural state modulation of inhibition is context-dependent and cell-type specific in mouse V1. Elife. 5: e14985.

Dmitriev R.I., Kondrashina A.V., Koren K., Klimant I., Zhdanov A.V., Pakan J.M.P., McDermott K.W.,

Papkovsky D.B. (2014). Small molecule phosphorescent probes for O2 imaging in 3D tissue models. Biomaterials Science. 46:76-9.

Pakan, J.M.P. and McDermott, K.W. (2014). A method to investigate radial glia cell behavior using two-photon

time-lapse microscopy in an ex vivo model of spinal cord development. Frontiers in Neuroanatomy. 8:22.

Barry D.S., Pakan J.M.P., O’Keeffe G.W., and McDermott K.W. (2013). The spatial and temporal

arrangement of the radial glial scaffold suggests a key role in axon tract formation in the developing spinal cord. Journal of Anatomy. 222(2):203-13.

Mathew A.*, Pakan J.M.P.*, Collin E., Wang W., McDermott K.W., Fitzgerald U., Reynolds R. and Pandit A.

(2013). An Ex-Vivo Multiple Sclerosis Model of Inflammatory Demyelination using Hyperbranched Polymers. Biomaterials. 34(23):5872-82.

Pakan J.M.P., Graham D.J. Gutiérrez-Ibáñez C. and Wylie D.R. (2011). Organization of the cerebellum:

Correlating zebrin immunochemistry with optic flow zones in the pigeon flocculus. Visual Neuroscience. 28(2):163-74.

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