Staff Profiles

Christopher Baker, Ph.D.

Scientist II

At the Allen Institute, Christopher Baker is tasked with establishing a platform for high-throughput interrogation of neural circuitry at single-cell resolution, which will eventually allow us to determine the prevalence and strength of connections between all the neuronal cell types that have been identified by efforts of other teams within the Institute. These efforts rely on techniques of two-photon excitation of engineered novel optogenetic molecules restricted to the neuronal cell body with simultaneous imaging of neuronal activity, developed during his studies of the neurobiology of autism at the Max Planck Florida Institute for Neuroscience. Earlier, he completed postdoctoral studies with Charles Weissmann at the Scripps Florida Research Institute, investigating the relationship between gene expression profiles of neuronal subtypes and their susceptibility to protein aggregation and neurodegeneration. He received his PhD in Neuroscience from Yale University, where he studied the neuroimmunology of prion disorders such as Mad Cow Disease and Creutzfeldt-Jakob Disease.


Research Interests

We ultimately seek to determine how changes in DNA sequence and in the messenger RNAs that a neuron expresses affect neuronal circuitry and, eventually, behavior of an organism. To achieve this, we identify neuronal subtypes with transcriptomic technology and integrate those data with connectivity maps produced by electrophysiological probing of neuronal activity. Once we complete such mapping experiments in a single species with a known genome, we can investigate how genetic changes, including those associated with different behavioral syndromes in humans, impact these neuronal maps.


  • Two-photon imaging
  • Electrophysiology
  • Transcriptomics
  • Neuroanatomy

Research Programs

  • Cell Types
  • Structured Science

Selected Publications

Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex

September 26, 2018

Seeman SC, Campagnola L, Davoudian PA, Hoggarth A, Hage TA, Bosma-Moody A, Baker CA, Lee, JH, Mihalas S, Teeter C, Ko AL, Ojemann JG, Gwinn RP, Silbergeld DL, Cobbs C, Phillips J, Lein E, Murphy G, Koch C, Zeng H, Jarsky T

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

July 12, 2018

Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ2, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H

Prion strain discrimination in cell culture: the cell panel assay

December 26, 2007

Mahal SP, Baker CA, Demczyk CA, Smith EW, Julius C, Weissmann C