Team

Staff Profiles

Amy Bernard, Ph.D.

Director, Science & Technology Strategy

Amy Bernard joined the Allen Institute in 2005. With over 30 years of expertise in bioscience and technology at academic and nonprofit research organizations, Dr. Bernard provides strategic guidance for the Allen Institute’s research portfolio.

Dr. Bernard led the Research & Development and Structured Science teams at the Allen Institute for Brain Science from 2009-2016, overseeing the generation of petabytes of data for large-scale open science initiatives such as the Allen Connectivity Atlas, Allen Developing Brain Atlas, and Allen Human Brain Atlas. She then served as Product Architect and led the technology product program to deliver open data and tools to the research community through the brain-map.org portal, until 2019.  She has authored over 50 publications, in developmental neuroscience, molecular genetics, cell biology, biochemistry, imaging, physiology and high throughput laboratory system management. 

Prior to joining the Allen Institute, Dr. Bernard’s research focused on gene regulatory patterns underlying vertebrate brain development at the University of Washington. She received a Ph.D. in Biophysics & Genetics from the University of Colorado,  where she studied receptor tyrosine kinase signaling in cell growth, and received a B.A. in Natural Sciences & Mathematics from Bard College. Her current interests include the use of cutting edge molecular and genetic approaches to explore the transcriptional basis of cellular diversity in health and disease, and structure-function relationships in brain development. Dr. Bernard is an advocate of open science, and serves on several advisory boards and review committees for the National Institutes of Health, and other organizations.

Selected Publications View Publications

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Cell
May 14, 2020

Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L

International Brain Initiative: An Innovative Framework for Coordinated Global Brain Research Efforts

Neuron
January 22, 2020

Adams A, Albin S, Amunts K, Asakawa T, Bernard A, Bjaalie JG, Chakli K, Deshler JO, De Koninck Y, Ebell CJ, Egan G, Hale ME, Häusser M, Jeong SJ, Illes J, Lanyon L, Li P, Li Y, Magistretti P, McMahon A, Montojo C, Ohtsuka T, Okabe S, Okano H, Pei G, Pouget A, Reindorp J, Richards LJ, Rommelfanger KS, Sajda P, Scobie KN, Suh PG, Tanaka K, Thiels E, Valdes-Sosa PA, Welchman AE, White S, Wilson G, Yuste R, Zhang X, Zheng J

Conserved cell types with divergent features in human versus mouse cortex

Nature
August 21, 2019

Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES

Hierarchical organization of cortical and thalamic connectivity

Nature
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

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

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

PLoS One
December 26, 2018

Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B

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

A mutation in Tubb2b, a human polymicrogyria gene, leads to lethality and abnormal cortical development in the mouse

Human Molecular Genetics
May 31, 2013

Stottmann RW, Donlin M, Hafner A, Bernard A, Sinclair DA, Beier DR

Dark field adapter for whole slide imaging: Adapting a darkfield internal reflection illumination system to extend WSI applications

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