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Shawn Olsen

Investigator, Neural Circuits and Behavior

teams /
Allenite

Shawn Olsen joined the Allen Institute in 2013 as an assistant investigator in the Neural Coding group. His team studies the neural basis of behavior and cognition using the mouse as a model system. Prior to joining the Allen Institute he was postdoctoral fellow at UCSD where he studied the cortical mechanisms of visual processing. He received a B.S. in biochemistry from the University of Utah and a Ph.D. in Neuroscience from Harvard University.

research focus

We are investigating the neural mechanisms underlying object recognition, attention, and learning. We seek to understand these phenomena at multiple levels organization and use genetic tools in the mouse to probe the detailed cellular and network mechanisms. Mice are trained to perform behavioral tasks and we map the underlying neural circuit dynamics across brain areas. We measure neural activity using both optical and electrophysiological approaches, and we use optogenetics to perform perturbation experiments in order to constrain causal models of neural operation. Transgenic mice provide cell type specificity to our mechanistic interrogations. Our experiments are guided by theory, modeling, and computational analysis. We conceptualize perception as an inferential process and are developing models of hierarchical processing that include both feedforward and feedback mechanisms. We are also developing more abstract models of behavior to explain foraging and decision-making phenomena.

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Summer Workshop on the Dynamic Brain: Ten years of collaboration and community
A two-week summer camp for neuroscience students building bridges, surfacing insights, and teaching cutting-edge computational methods
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Delving into the science of a mystifying optical illusion: visual masking
A new study sheds light on how our brains perceive - or fail to perceive - what we see
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From 300,000 mouse neurons, scientists hope to glean how the brain drives behavior
New public dataset captures billions of electrical spikes from brains of animals trained to identify ‘oddball’ photos

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featured publications

publication / 2025
Integrating multimodal data to understand cortical circuit architecture and function
Nature Neuroscience
publication / 2024
Behavioral strategy shapes activation of the Vip-Sst disinhibitory circuit in visual cortex
Neuron
publication / 2023
Gaussian Partial Information Decomposition: Bias Correction and Application to High-dimensional Data
Advances in Neural Information Processing Systems
preprint / 2023
Recurrent pattern completion drives the neocortical representation of sensory inference
publication / 2023
Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex
Nature Communications
publication / 2023
A survey of neurophysiological differentiation across mouse visual brain areas and timescales
Frontiers in Computational Neuroscience
publication / 2022
The geometry of representational drift in natural and artificial neural networks
PLoS computational biology
publication / 2022
Multi-regional module-based signal transmission in mouse visual cortex
Neuron
publication / 2020
A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex
Nature Neuroscience
publication / 2017
Aberrant Cortical Activity in Multiple GCaMP6-Expressing Transgenic Mouse Lines
eNeuro
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
publication / 2016
Characterization of Channelrhodopsin and Archaerhodopsin in Cholinergic Neurons of Cre-Lox Transgenic Mice
PloS One
publication / 2015
Optogenetics in Mice Performing a Visual Discrimination Task: Measurement and Suppression of Retinal Activation and the Resulting Behavioral Artifact
PloS One
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