Team

Staff Profiles

Shawn Olsen, Ph.D.

Associate Investigator

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

Research Interests

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.

Research Interests

  • Behavior
  • Cognition
  • Cortical dynamics
  • Object recognition
  • Attention
  • Learning​

​Contact Information

  • shawno@alleninstitute.org

Selected Publications

Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

eLife
July 16, 2021

Siegle JH, Ledochowitsch P, Jia X, Millman DJ, Ocker GK, Caldejon S, Casal L, Cho A, Denman DJ, Durand S, Groblewski PA, Heller G, Kato I, Kivikas S, Lecoq J, Nayan C, Ngo K, Nicovich PR, North K, Ramirez TK, Swapp J, Waughman X, Williford A, Olsen SR, Koch C, Buice MA, de Vries SE.

Survey of spiking in the mouse visual system reveals functional hierarchy

Nature
January 20, 2021

Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries S., Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo D, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C

Characterization of Learning, Motivation, and Visual Perception in Five Transgenic Mouse Lines Expressing GCaMP in Distinct Cell Populations

Frontiers in Behavioral Neuroscience
June 23, 2020

Groblewski PA, Ollerenshaw DR, Kiggins JT, Garrett ME, Mochizuki C, Casal L, Cross S, Mace K, Swapp J, Manavi S, Williams D, Mihalas S, Olsen SR

Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex

Neuron
March 5, 2020

Billeh YN, Cai B, Gratiy SL, Dai K, Iyer R, Gouwens NW, Abbasi-Asl R, Jia X, Siegle JH, Olsen SR, Koch C, Mihalas S, Arkhipov A

Experience shapes activity dynamics and stimulus coding of VIP inhibitory and excitatory cells

eLife
February 26, 2020

Garrett M, Manavi S, Roll K, Ollerenshaw D, Groblewski P, Kiggins J, Jia X, Casal L, Mace K, Williford A, Leon A, Mihalas S, Olsen SR

High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification

Journal of Neurophysiology
March 6, 2019

Jia X, Siegle JH, Bennett C, Gale SD, Denman DJ, Koch C, Olsen SR

Higher-order thalamic circuits channel parallel streams of visual information in mice

Neuron
February 27, 2019

Bennett C, Gale SD, Garrett ME, Newton ML, Callaway EM, Murphy GJ, Olsen SR

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Nature Neuroscience
December 16, 2019

de Vries S, Lecoq J, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng F, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon S, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin J, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten D, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, R Reid C, Koch C

First spikes in visual cortex enable perceptual discrimination

eLife
April 16, 2018

Resulaj A, Olsen SR, Scanziani M. Elife

Visual physiology of the Layer 4 cortical circuit in silico

PLoS Computational Biology
November 12, 2018

Arkhipov A, Gouwens NW, Billeh YN, Gratiy S, Iyer R, Wei Z, Xu Z, Berg J, Buice M, Cain N, da Costa N, de Vries S, Denman D, Durand S, Feng D, Jarsky T, Lecoq J, Lee B, Li L, Mihalas S, Ocker GK, Olsen SR, Reid RC, Soler-LLavina G, Sorensen SA, Wang Q, Waters J, Scanziani M, Koch C