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Evolutionary Neural Coding Lab

Dragon eye cam
Photo from Mark(2)
CMOS MEA (24,600 channels) recordings
Eye brain preparation ex-vivo



Brains and the neuronal coding schemes therein are products of billions of years of evolution. Understanding neural systems thus requires taking an evolutionary perspective for revealing the blocks they are built on, and the constraints and principles that govern their "design".

We are exploring a key period in evolutionary history: the transition of vertebrates from aquatic to terrestrial environments. This period is particularly fascinating because of the changes in the brain's neural circuitry that accompanied it. Specifically, stem amniotes - the first clade to complete this transition - exhibited major modifications in their forebrain, including the emergence of a layered cerebral cortex and a claustrum as well as a massive increase in the sensory information it receives and processes. Understanding the function and processing schemes of these adapted brain areas, is key to exposing fundamental coding principles of vertebrate brains. To expose these schemes we study reptiles - the class closest to stem amniotes - and amphibians. We take a comparative approach by studying a diverse set of species allowing us to generalize and choose optimal species for different biological questions. 

We employ a wide set of techniques to study the hitherto under-explored reptilian brain: We use large-scale (thousands of electrodes) extra-cellular electrophysiology and intra-cellular electrophysiology to study circuits both ex-vivo and in-vivo. We develop data analysis approaches to deal with the overgrowing richness of our data sets. We couple our experiments with quantitative behavioral analysis and gaze estimation to place brain dynamics in context. We build computational models to test ideas and develop theories.





Journal publications

Eyal R, Shein-Idelson, M (2024). PreyTouch: An Automated System for Prey Capture Experiments Using a Touch Screen. BioRXiv, 📖

Jaeger et al (2024). Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians. BioRXiv,

Eisenberg T, Shein-Idelson M (2024). ReptiLearn: An automated home cage system for behavioral experiments in reptiles without human intervention. PLoS Biol. 22 (2): e3002411 📖

Orsher Y, Rom A, Perel R, Lahini Y, Blinder P, Shein-Idelson M (2023).  Sequentially activated discrete modules appear as traveling waves in neuronal measurements with limited spatiotemporal sampling. eLife. 📖 

Albeck N, Udi I D, Eyal R, Shvartsman A and Shein-Idelson M (2022). Temperature-robust rapid eye movement and slow wave sleep in the lizard Laudakia vulgaris. Comms Biol. 5, 1310 📖 

Yadav P and Shein-Idelson M (2021). Polarization vision in invertebrates: beyond the boundaries of navigation. Curr Opin Insect Sci. (48):50-56 📖 

Arieli E, Gerbi R, Shein-Idelson M, and Moran A (2020). Temporally-precise basolateral amygdala activation is required for the formation of taste memories in gustatory cortex. J Physiology. 598 (23):5505-5522. 📖

Hemberger M, Shein-Idelson M, Pammer L and Laurent G (2019). Reliable sequential activation of neural assemblies by single pyramidal cells in a three layered cortex. Neuron 104 (2):353-369. 📖 

Shein-Idelson M, Pammer L, Hemberger M and Laurent G (2017). Large-scale mapping of cortical synaptic projections with extracellular electrode arrays. Nature Methods 14(9):882-890. 📖

Shein-Idelson M*,Ondracek J M*, Liaw H, Reiter S, Laurent G (2016). Slow Waves, Sharp-waves, Ripples and REM in Sleeping Dragons. Science. 352 (6285), 590-595. 📖

Fournier J,  Mueller C M,  Shein-Idelson M, Hemberger M, Laurent G (2016). Consensus-Based Sorting of Neuronal Spike Waveforms. PLoS ONE 11(8): e0160494. 📖

Shein-Idelson M, Cohen G, Ben-Jacob E, Hanein Y (2016). Modularity induced gating and delays in neuronal networks. PLoS Computational Biolology 12(4): e1004883. 📖

Naumann R K, Ondracek J M, Reiter S, Shein-Idelson M, Tosches M A, Yamawaki T M, Laurent G (2015). The reptilian brain. Current Biology 25 (8), 317–321.  📖

Shein-Idelson M, Ben-Jacob E, Hanein Y (2011). Engineered neuronal circuits: A new platform for studying the role of modular topology. Frontiers in Neuroengineering 4:10. 📖

Herzog N, Shein-Idelson M, Hanein Y (2011). Optical validation of in vitro extra-cellular neuronal recordings. Journal of Neural Engineering 8(6),056008. 📖

Shein-Idelson M, Ben-Jacob E, Hanein Y (2010). Innate synchronous oscillations in freely-organized small neuronal circuits. PLoS One 5(12), e14443. 📖

Greenbaum A, Anava S, Ayali A, Shein M, David-Pur M, Ben-Jacob E, Hanein Y (2009). One-to-one neuron-electrode interfacing. Journal of Neuroscience Methods 182(2), 219-224. 📖

Shoval A, Adams C, David-Pur M, Shein M, Hanein Y, Sernagor E, (2009). Carbon nanotube electrodes for effective interfacing with retinal tissue. Frontiers in Neuroengineering 2, 4. 📖

Shein M, Greenbaum A, Gabay T, Sorkin R, David-Pur M, Ben-Jacob E, Hanein Y (2009). Engineered neuronal circuits shaped and interfaced with carbon nanotube microelectrode arrays. Biomedical Microdevices 11(2), 495-501. 📖

Shein M, Volman V, Raichman N, Hanein Y, Ben-Jacob E (2008). Management of synchronized network activity by highly active neurons. Physical Biology 5(3), 036008. 📖

Baruchi I, Volman V, Raichman N, Shein M, Ben-Jacob E (2008). The emergence and properties of mutual synchronization in in vitro coupled cortical networks. European Journal of Neuroscience 28(9), 1825-1835. 📖

Rubinsky L, Raichman N, Baruchi I, Shein M, Lavee J, Frenk H, Ben-Jacob E (2007). Study of hypothermia on cultured neuronal networks using multi-electrode arrays. Journal of Neuroscience Methods 160(2), 288-293. 📖

Baruchi I, Grossman D, Volman V, Shein M, Hunter J, Towle VL, Ben-Jacob E (2006). Functional holography analysis: simplifying the complexity of dynamical networks. Chaos 16(1), 015112. 📖

Book chapters:

Laurent G, Fournier G, Hemberger M, Mueller C, Naumann R, Ondracek J M, Pammer L, Reiter S, Shein-Idelson M, Tosches M A and Yamawaki T (2016). Cortical Evolution: Introduction to the Reptilian Cortex. In Buzsaki G, Christen Y (Eds.), Micro-, Meso- and Macro-Dynamics of the Brain.

Pur M, Shein M, Hanein Y (2010). Carbon Nanotube-Based Neurochips. In: Balasubramanian K, Burghard M (Eds.), Carbon Nanotubes: Methods and Protocols, pp. 171-177.

Raichman N, Rubinsky L, Shein M, Baruchi I, Volman V, Ben-Jacob E (2009). Cultured Neuronal Networks Express Complex Patterns of Activity and Morphological Memory. In: Boccaletti S, Latora V, Moreno Y (Eds.), World scientific lectures notes in complex systems, pp. 257-278.

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