Ying Shi

Ying Shi is a Senior Technical Specialist in the Simulation Neuroscience Division.

Ying is working on the 3D reconstruction of neurons, data collection and analysis, supporting the development of algorithms for neural morphologies, and the development of software for automated data processing and testing of neuronal information transmission.

Before joining Blue Brain, Ying spent 12 years working as a developer and researcher for the simulation and process control of Air Separation Units (ASU) at Nippon Sanso, Tokyo, Japan, where she was awarded three patents.

Ying began her studies in process control engineering at the East China University of Chemical Technology in Shanghai, China. She has a Masters in Mechanical Engineering from Sophia University, Tokyo, Japan.

In her free time, Ying is a keen table tennis player and enjoys hiking and reading.

Selected Publications


Michael W Reimann, Michael Gevaert, Ying Shi, Huanxiang Lu, Henry Markram, Eilif Muller.(2019) A null model of the mouse whole-neocortex micro-connectome. Nat Commun 10, 3903 (2019), 29 August 2019;  https://doi.org/10.1038/s41467-019-11630-x


Kanari L, Ramaswamy S, Shi Y, Morand S, Meystre J, Perin R, Abdellah M, Wang Y, Hess K and Markram H. Objective Morphological Classification of Neocortical Pyramidal Cells. Cerebral Cortex, April 2019;29: 1719–1735. https://doi: 10.1093/cercor/bhy339



Iavarone E, Yi J, Shi Y, Zandt B-J, O’Reilly C, Van Geit W, et al. (2019) Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons. PLoS Comput Biol 15(5): e1006753. https://doi.org/10.1371/journal.pcbi.1006753


Migliore R, Lupascu CA, Bologna LL, Romani A, Courcol J-D, Antonel S, Van Geit W, Thomson A, Mercer A, Lange S, Falck J, Rössert C, Shi Y, et al. (2018) The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow. PLoS Comput Biol 14(9): e1006423. https://doi.org/10.1371/journal.pcbi.1006423


Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Aguado Sanchez, C., et al. (2015). Reconstruction and simulation of neocortical microcircuitry. Cell 163, 456–492. http://dx.doi.org/10.1016/j.cell.2015.09.029