Team

Staff Profiles

Julie Harris, Ph.D.

Associate Director, Neuroanatomy

julieha@alleninstitute.org

Julie Harris joined the Allen Institute in 2011 to help establish the Allen Mouse Brain Connectivity Atlas. She currently leads scientific efforts to generate a comprehensive map of neural projections between brain areas and from specific cell types within those regions throughout the adult mouse brain. Her research interests include understanding the relationship between anatomical and functional large-scale neural circuits in normal and disease states. As a postdoctoral fellow at the Gladstone Institute for Neurological Disease, she worked with mouse models to understand how Alzheimer's disease can propagate through vulnerable neuronal networks. Harris received a B.S. in zoology from Michigan State University and a Ph.D. in neurobiology and behavior from the University of Washington.

Research

Research Interests

Research Interests To understand how the brain functions in health and disease, we need to understand better its structure – what are the essential components, how many cell types exist, and how are they interconnected with each other in local circuits and across long distances? We recently generated the first whole brain structural connectome of the normal young adult mouse brain, an open access resource enabling new research efforts into defining structure/function relationships at the inter-areal network level. Now, we are pursuing two new areas of focus. First, we use the mouse visual system to explore the relationships between inter-areal anatomical connectivity and the computations that underlie visual perception and behavior in cognitively normal mice. Second, we aim to understand the effects of Alzheimer’s disease (AD), which causes cognitive deficits, on large scale network connectivity patterns, with a specific focus on vulnerable brain regions and cell types. For both research goals, in order to map brain wide cell type-specific connections, we primarily use or develop new genetic tools, for example, labeling neurons with recombinant viral vectors in combination with Cre driver transgenic mouse lines or mouse models of AD. Whole brain axonal projections and inputs are imaged with advanced 2P microscopy systems, and resulting data is analyzed in collaboration with computational scientists.

Expertise

  • Neuroanatomy
  • Neural circuits
  • Viral vectors
  • Neurodegenerative disease

Research Programs

  • Cell types
  • Atlasing
  • Connectivity in mouse models of Alzheimer’s disease

Selected Publications View on PUBMED

Classification of electrophysiological and morphological types in mouse visual cortex

bioRxiv
July 17, 2018

Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin S, Feng D, Anastassiou C, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle T, Dalley R, Dee N, Desta T, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris J, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina C, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips J, Zeng H, Koch C

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

Cell
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

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

bioRxiv
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

bioRxiv
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

Shared and distinct transcriptomic cell types across neocortical areas

Nature
October 31, 2018

Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H

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

Connectional architecture of a mouse hypothalamic circuit node controlling social behavior

bioRxiv
October 16, 2016

Lo L, Kim D, Yao S, Cetin A, Harris JA, Zeng H, Anderson DJ, Weissbourd B

A mesoscale connectome of the mouse brain

Nature
April 2, 2014

Oh SW, Harris JA, Ng L, Winslow B, Cain N, Mihalas S, Wang Q, Lau C, Kuan L, Henry AM, Mortrud MT, Ouellette B, Nguyen TN, Sorensen SA, Slaughterbeck CR, Wakeman W, Li Y, Feng D, Ho A, Nicholas E, Hirokawa KE, Bohn P, Joines KM, Peng H, Hawrylycz MJ, Phillips JW, Hohmann JG, Wohnoutka P, Gerfen CR, Koch C, Bernard A, Dang C, Jones AR, Zeng H

Systematic comparison of adeno-associated virus and biotinylated dextran amine reveals equivalent sensitivity between tracers and novel projection targets in the mouse brain

Journal of Comparative Neurology
February 22, 2014

Wang Q, Henry AM, Harris JA, Oh SW, Joines KM, Nyhus J, Hirokawa KE, Dee N, Mortrud M, Parry S, Ouellette B, Caldejon S, Bernard A, Jones AR, Zeng H, Hohmann JG

Reversing EphB2 depletion rescues cognitive functions in Alzheimer model

Nature
July 2011

Cisse, M, Halabisky B, Harris JA, Devidze N, Dubal D, Lotz G, Kim DH, Hamto P, Ho K, Yu G, Mucke L

Transsynaptic progression of amyloid-ß-induced neuronal dysfunction within the entorhinal-hippocampal networkTranssynaptic progression of amyloid-ß-induced neuronal dysfunction within the entorhinal-hippocampal network

Neuron
November 2010

Harris JA, Devidze N, Verret L, Halabisky B, Thwin MT, Ho K, Thwin MT, Kim D, Hamto P, Lo I, Yu G, Palop JJ, Masliah E, Mucke L