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people

Anton Arkhipov

Investigator, D3 Scientific

teams /
Allenite

Anton Arkhipov joined the Allen Institute in 2013 as an Assistant Investigator in the Modeling, Analysis, and Theory group. He is leading efforts to carry out biophysically detailed simulations of individual neurons as well as large-scale neuronal circuits from the mouse visual system. The main focus of his research is on integration of experimental anatomical and physiological data to build sophisticated, highly realistic computational models of cortical circuitry, with the aim of elucidating mechanisms underlying processing of visual information in the cortex. Before joining the Allen Institute he was a Postdoctoral Fellow at D. E. Shaw Research in New York City, where he used a specialized supercomputing architecture to perform computational studies of structure-function relationships in proteins, with the emphasis on cancer-associated cell-surface receptors. Arkhipov received his B.S. and M.S. in Physics from Moscow Institute of Physics and Technology and a Ph.D. in Physics from the University of Illinois at Urbana-Champaign.

research focus

Anton Arkhipov applies high-performance computing to simulate neuronal activity in the mouse visual system. Using experimentally observed neuronal morphologies, connectivity patterns, and electrophysiological properties, he constructs highly detailed, biophysically accurate models of neuronal circuits. The main aim is to build powerful models that, on the one hand, reproduce major features of in vivo experimental recordings from anesthetized and awake mice and, on the other, allow for testable predictions about mechanisms involved in processing of the visual information in the cortex.

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news
One of world’s most detailed virtual brain simulations is changing how we study the brain
Scientists use supercomputer that can process quadrillions of calculations per second to simulate mouse cortex for “virtual experiments”
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Mapping the whole human brain: Allen Institute to lead global collaboration
NIH BRAIN Initiative to fund primate brain atlases, maps of developing mouse brain, coordination and knowledge sharing, and brain function research

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featured publications

publication / 2025
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex
Nature Neuroscience
publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2024
Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations
PLoS computational biology
publication / 2024
Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex
Neuron
preprint / 2023
Coordinated changes in a cortical circuit sculpt effects of novelty on neural dynamics
publication / 2023
Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex
eLife
preprint / 2023
Stimulus novelty uncovers coding diversity in visual cortical circuits
publication / 2023
Influence of claustrum on cortex varies by area, layer, and cell type
Neuron
publication / 2023
A survey of neurophysiological differentiation across mouse visual brain areas and timescales
Frontiers in Computational Neuroscience
publication / 2022
Simulations of cortical networks using spatially extended conductance-based neuronal models
The Journal of Physiology
publication / 2022
Non-Separability of Physical Systems as a Foundation of Consciousness
Entropy (Basel, Switzerland)
publication / 2022
Local connectivity and synaptic dynamics in mouse and human neocortex
Science (New York, N.Y.)
publication / 2022
Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex
eNeuro
publication / 2021
Human neocortical expansion involves glutamatergic neuron diversification
Nature
publication / 2021
Survey of spiking in the mouse visual system reveals functional hierarchy
Nature
publication / 2021
Consistent cross-modal identification of cortical neurons with coupled autoencoders
Nature Computational Science
publication / 2020
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
publication / 2020
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
PLoS computational biology
publication / 2020
Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex
Neuron
publication / 2020
The SONATA data format for efficient description of large-scale network models
PLoS computational biology
publication / 2019
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Nature Neuroscience
publication / 2018
Visual physiology of the layer 4 cortical circuit in silico
PLoS computational biology
publication / 2018
Systematic generation of biophysically detailed models for diverse cortical neuron types
Nature Communications
publication / 2018
BioNet: A Python interface to NEURON for modeling large-scale networks
PloS One
publication / 2016
Inferring cortical function in the mouse visual system through large-scale systems neuroscience
Proceedings of the National Academy of Sciences of the United States of America
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