
Amy Bernard, Ph.D.
Product Architect
Amy Bernard joined the Allen Institute in 2005 and has experience in both basic research and scientific administration capacities. With a background of over 25 years in molecular biology and neuroscience, she serves as part of the leadership team to provide strategic design and direction for the Allen Institute for Brain Science’s web products. Prior to joining the Allen Institute, Dr. Bernard was a research scientist at the University of Washington, where she studied gene regulatory patterns underlying vertebrate brain development. Dr. Bernard received a Bachelor’s degree in Natural Sciences and Mathematics from Bard College and a Ph.D. in Genetics and Biophysics from the University of Colorado, where she studied the regulation of receptor tyrosine kinases involved in signal transduction and control of cell growth. Her research interests include the use of cutting edge molecular and genetic approaches to explore the transcriptional basis of neuronal diversity and investigation of structure-function relationships in brain development. Dr. Bernard directed the Structured Science laboratory teams at the Allen Institute from 2009-2016, overseeing the delivery of petabytes of data for large-scale open science products, all made available to the public on brain-map.org. She has authored over 40 publications, with expertise in developmental neuroscience, molecular genetics, cell biology, biochemistry, high throughput laboratory system management, and technology solutions that foster open data sharing.

Selected Publications View on PUBMED
An anatomic transcriptional atlas of human glioblastoma
Science
May 11, 2018
Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Amy Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD
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
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
Highly Multiplexed Subcellular RNA Sequencing in Situ
Science
February 27, 2014
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM
Convergent transcriptional specializations in the brains of humans and song-learning birds
Science
December 12, 2014
Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED
Control of stress-induced persistent anxiety by an extra-amygdala septohypothalamic circuit
Cell
January 14, 2014
Anthony TE, Dee N, Bernard A, Lerchner W, Heintz N, Anderson DJ
A 0.5 cm3 four-channel 1.1 mW wireless biosignal interface with >20 m range
IEEE Transactions on Biomedical Circuits and Systems
June 19, 2013
Morrison T, Nagaraju M, Winslow B, Bernard A, Otis BP
Human Molecular Genetics
May 31, 2013
Stottmann RW, Donlin M, Hafner A, Bernard A, Sinclair DA, Beier DR
PLoS ONE
March 8, 2013
Kawano Y, Higgins C, Yamamoto Y, Nyhus J, Bernard A, Dong HW, Karten HJ, Schilling T
Shifting the paradigm: New approaches for characterizing and classifying neurons
Current Opinion in Neurobiology
October 2009
Bernard A, Sorensen S, Lein E