Staff Profiles

Jennifer Whitesell, Ph.D.

Scientist II

Jennifer joined the Allen Institute in 2014 to work on an NIH-funded project mapping connectivity in mouse models of Alzheimer’s disease. She is also involved in studies using intersectional viral-mediated labeling with both retrograde and anterograde tracers to map brain-wide cell type projections defined by target connections. Her interests include understanding neural circuit architecture and how neuronal connections support information coding. As a postdoctoral fellow at Colorado State University, Jennifer studied mouse models of prion disease, primarily focusing on the behavioral and pathological changes that occur in the olfactory system during neurodegenerative disease. This work built on her graduate studies examining circuit mechanisms and coding in the olfactory bulb and piriform cortex. Jennifer received B.S. and M.S. degrees in Biochemistry from Colorado State University and a Ph.D. in Neuroscience from the University of Colorado Denver.


Research Interests

The mechanism by which the circuitry of the brain produces the experience of the mind is a fundamental and daunting question, even in a relatively simple organism such as the mouse. I am interested in learning how different types of neurons with different functional properties form interconnected circuits that can carry information, as well as how these connections break down in neurodegenerative diseases. The first goal of my research is to refine our understanding of cortical connectivity by mapping brain-wide projections from subtypes of cortical neurons defined by their target regions using paired retrograde and anterograde virus injections. The results of these experiments will lead to a more refined connectivity map that includes information about the diversity of cells within individual anatomical regions and the subsets of targets contacted by each class of cells. The second part of my work tests how neuronal connectivity is altered during the progression of Alzheimer’s disease. By mapping whole-brain connectivity patterns in an Alzheimer’s mouse model, we will determine how networks deteriorate as pathology progresses and test whether specific cell types and/or regions are more vulnerable to degeneration.


  • Systems neuroscience
  • Cell and molecular biology
  • Electrophysiology
  • Behavioral neuroscience

Research Programs

  • Connectivity in mouse models of Alzheimer’s disease

Selected Publications View Publications

Hierarchical organization of cortical and thalamic connectivity

October 30, 2019

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Choi H, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feiner A, Feng D, Gaudreault N, Gerfen CR, Graddis N, Groblewski PA, Henry AM, Ho A, Howard R, Knox JE, Kuan L, Kuang X, Lecoq J, Lesnar P, Li Y, Luviano J, McConoughey S, Mortrud MT, Naeemi M, Ng L, Oh SW, Ouellette B, Shen E, Sorensen SA, Wakeman W2, Wang Q2, Wang Y, Williford A, Phillips JW, Jones AR, Koch C, Zeng H

The organization of intracortical connections by layer and cell class in the mouse brain

April 18, 2018

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Knox J, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feng D, Gaudreault N, Gerfen C, Graddis N, Groblewski PA, Henry A, Ho A, Howard R, Kuan L, Lecoq J, Luviano J, McConoughey S, Mortrud M, Naeemi M, Ng L, Oh SW, Ouellette B, Sorensen SA, Wakeman W, Wang Q, Williford A, Phillips J, Jones A, Koch C, Zeng H

High resolution data-driven model of the mouse connectome

Network Neuroscience
April 1, 2018

Knox J, Harris KD, Graddis N, Whitesell JD, Zeng H, Harris JA, Shea-Brown E, Mihalas S

Nontoxic, double-deletion-mutant rabies viral vectors for retrograde targeting of projection neurons

Nature Neuroscience
March 5, 2018

Chatterjee S, Sullivan H, MacLennan BJ, Xu R, Hou Y, Lavin TK, Lea N, Michalski J, Babcock K, Dietrich S, Matthews GA, Beyeler A, Calhoon GG, Glober G, Whitesell J, Yao S, Cetin A, Harris J, Zeng H, Tye K, Reid RC, Wickersham IR

Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease

Journal of Comparative Neurology
October 12, 2018

Whitesell JD, Buckley AR, Knox JE, Kuan L, Graddis N, Pelos A, Mukora A, Wakeman W, Bohn P, Ho A, Hirokawa KE, Harris JA

Role of cortactin in dynamic actin remodeling events in gonadotrope cells

February 2014

Navratil AM, Dozier MG, Whitesell JD, Clay CM, Roberson MS

Metabotropic glutamate receptors promote disinhibition of olfactory bulb glomeruli that scales with input strength

Journal of Neurophysiology
December 31, 2014

Zak JD, Whitesell JD, Schoppa NE

Information for decision-making and stimulus identification is multiplexed in sensory cortex

Nature Neuroscience
August 2013

Gire DH, Whitesell JD, Doucette W, Restrepo D

Interglomerular lateral inhibition targeted on external tufted cells in the olfactory bulb

Journal of Neuroscience
January 23, 2013

Whitesell JD, Sorensen KA, Jarvie BC, Hentges ST, Schoppa NE

Mitral cells in the olfactory bulb are mainly excited through a multistep signaling path

Journal of Neuroscience
February 29, 2012

Gire DH, Franks KM, Zak JD, Tanaka KF, Whitesell JD, Mulligan AA, Hen R, Schoppa NE

Associative cortex features in the first olfactory brain relay station

March 24, 2011

Doucette W, Gire DH, Whitesell J, Carmean V, Lucero MT, Restrepo D