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Predicting modular functions and neural coding of behavior from a synaptic wiring diagramPreprint

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Repurposing citizen science games as software tools for professional scientists

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Zebrafish as a Model for Revealing the Neuronal Basis of Behavior

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Oculomotor plant and neural dynamics suggest gaze control requires integration on distributed timescales

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Nervous system-wide single-cell morphology atlas of excitatory and inhibitory neurons in larval zebrafishPreprint

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Correlative light and electron microscopy identifies circuit motifs underlying processing of noisy visual motion in larval zebrafishPreprint

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SRPK3 Is Essential for Cognitive and Ocular Development in Humans and Zebrafish, Explaining X‐Linked Intellectual Disability

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Multiplexed volumetric CLEM enabled by scFvs provides insights into the cytology of cerebellar cortex

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Robust neural circuit reconstruction from serial electron microscopy with convolutional recurrent networksPreprint

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Image Processing for Volume Electron Microscopy

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Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortexPreprint

Han, X., Lu, X., Li, P. H., Wang, S., Schalek, R. L., Meirovitch, Y., Lin, Z., Adhinarta, J. K., Berger, D. R., Wu, Y., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.20.540091 · Cited by 5 · see citing works

SynapseCLR: Uncovering features of synapses in primary visual cortex through contrastive representation learning

Wilson, A. M., & Babadi, M. (2023) · Patterns · doi:10.1016/j.patter.2023.100693 · Cited by 4 · see citing works

Studying zebrafish nervous system structure and function in health and disease with electron microscopy

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Clinical applications of control systems models: The neural integrators for eye movements

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RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations

Wu, J., Turner, N. L., Bae, J. A., Vishwanathan, A., & Seung, H. S. (2022) · Frontiers in Neuroinformatics · doi:10.3389/fninf.2022.828169 · Cited by 4 · see citing works

Finding Needles in a Haystack with Light: Resolving the Microcircuitry of the Brain with Fluorescence Microscopy

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Genetically encoded sensors for analysing neurotransmission among synaptically-connected neuronsPreprint

Shindo, Y., Ashida, K., Masamoto, K., Takuwa, H., Takahashi, M., Higuchi, M., Ide, R., Hotta, K., & Oka, K. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.03.486903 · Cited by 4 · see citing works

Quantitative synapse analysis for cell-type specific connectomicsPreprint

Kuljis, D. A., Zemoura, K., Telmer, C. A., Lee, J., Park, E., Ackerman, D. S., Xu, W., Watkins, S. C., Arnold, D. B., Bruchez, M. P., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/386912 · Cited by 3 · see citing works

Eye movement defects in KO zebrafish reveals SRPK3 as a causative gene for an X‐linked intellectual disability

Kim, C.-H., Lee, Y.-R., Thomas, M., Roychaudhury, A., Skinner, C., Maconachie, G., Crosier, M., Horak, H., Constantinescu, C., Choi, T.-I., et al. (2023) · doi:10.21203/rs.3.rs-2683050/v1 · Cited by 3 · see citing works

Networks of linked radial muscles could influence dynamic skin patterning of squid chromatophores

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Ramp-to-threshold dynamics in a hindbrain population controls the timing of spontaneous saccades

Ramirez, A. D., & Aksay, E. R. F. (2021) · RePEc: Research Papers in Economics · Cited by 2 · see citing works

Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor SubcircuitsPreprint

Ma, M., Ramirez, A. D., Wang, T., Roberts, R. L., Harmon, K. E., Schoppik, D., Sharma, A., Kuang, C., Goei, S. L., Gagnon, J. A., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/658161 · Cited by 2 · see citing works

Attractor-like circuits improve visual decoding and behavior in zebrafishPreprint

Privat, M., Hansen, E. C. A., Pietri, T., Marachlian, E., Uribe‐Arias, A., Duchemin, A., Candat, V., Nourin, S., & Sumbre, G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.03.578596 · Cited by 2 · see citing works

A theory and recipe to construct general and biologically plausible integrating continuous attractor neural networksPreprint

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Progress in brain neural connectomics

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Ramp-to-Threshold Dynamics in a Hindbrain Population Controls the Timing of Spontaneous SaccadesPreprint

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Learning temporal integration from internal feedbackPreprint

Nygren, E., Ramirez, A. D., McMahan, B., Aksay, E. R. F., & Senn, W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.29.890509 · Cited by 1 · see citing works

Corrigendum to “Progress and remaining challenges in high-throughput volume electron microscopy” [Curr Opin Neurobiol 50 (June 2018) 261-267]

Kornfeld, J. M. R., & Denk, W. T. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.05.003

Uncovering features of synapses in primary visual cortex through contrastive representation learningPreprint

Wilson, A. M., & Babadi, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.07.495207

Split-Type Genetically Encoded Neurotransmitter Sensors for Reconstitution Between Synaptic PartnersPreprint

Shindo, Y., Ashida, K., Masamoto, K., Takuwa, H., Takahashi, M., Higuchi, M., Ide, R., Hotta, K., & Oka, K. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4119000

Wiring of a low-dimensional integrator network

Hu, B., & Friedrich, R. W. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01702-7

A theory and recipe to construct general and biologically plausible integrating continuous attractor neural networksPreprint

Claudi, F., Chandra, S., & Fiete, I. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.07.652608

A theory and recipe to construct general and biologically plausible integrating continuous attractor neural networksPreprint

Claudi, F., Chandra, S., & Fiete, I. (2025) · eLife · doi:10.7554/elife.107224

Ocular Motor Neural Integrator: Mechanistic and Structural Underpinnings and Consequences of Its Lesions

Ravat, P., Biswas, A., & Shaikh, A. G. (2026) · Contemporary clinical neuroscience · doi:10.1007/978-3-032-07539-0_29

Advances in brain connectomics: integrating light and electron microscopy for multiscale neural mapping

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Monosynaptic excitation of trochlear motoneurons following electrical stimulation of the prepositus hypoglossi nucleus

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A Structural and Genotypic Scaffold Underlying Temporal Integration

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Correlated Discharge among Cell Pairs within the Oculomotor Horizontal Velocity-to-Position Integrator

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Functional architecture underlying binocular coordination of eye position and velocity in the larval zebrafish hindbrain

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Behavioral/Systems/Cognitive Correlated Discharge among Cell Pairs within the

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