Staff Profiles

Carol L. Thompson, Ph.D.

Senior Technical Program Manager

Carol Thompson has provided scientific leadership and management at the Allen Institute for Brain Science for the past 15 years. In the early days, as a follow-on to the Allen Mouse Brain Atlas, she oversaw from concept to execution, the Allen Developing Mouse Brain Atlas, a resource characterizing gene expression from the embryonic brain to the adult, and the Sleep Study, a resource that explores the many dynamic changes in gene expression induced by sleep deprivation. Beyond that, Carol has managed the build of integrated pipelines for high throughput generation of biological datasets, including hardware and software integration for neurophysiology, including calcium imaging and Neuropixels silicon probes, as well as for transcriptomics profiling and stem cell engineering, culminating in freely available community resources for neuroscience.  As the Program and Project Manager, she has supported the creation of the Allen Brain Observatory, a data resource for cellular physiological responses to visual input, and its sister project, OpenScope, which generates datasets based on proposals from the community.

Carol is interested in the power of projects that lie at the intersection of big data, biology and computation. She is currently coordinating community-generated data for the Brain Cell Data Center as part of the BRAIN Initiative Cell Census Network (BICCN) and she hopes to serve as a point of harmonization between BCDC data and other consortium data projects and standards efforts. Carol holds a BS in Biology from the University of Richmond and a PhD in Biochemistry from the University of North Carolina at Chapel Hill, where she studied cryptochromes under the guidance of Nobel laureate Aziz Sancar, MD, PhD.  


Research Interests

Research Interests From a broad perspective, I am interested in the power of projects that lie at the intersection of big biology and computation.  Specifically, advances in high throughput and high resolution transcriptomic technologies enable us to interrogate neuron development and diversity in new ways. The in vitro Human Cell Types program leverages advances in human stem cell technology, single cell profiling and genome engineering to study the molecular and genetic networks that govern brain development and neuropsychiatric disease.  


  • Gene Expression Profiling
  • Neuroanatomy
  • Developmental Neurobiology
  • Sleep and circadian rhythms
  • Stem Cell Biology

Research Programs

  • In vitro Human Cell Types, Human Cell Types

Selected Publications View on PUBMED

Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

PLoS One
May 1, 2019

Waters J, Lee E, Gaudreault N, Griffin F, Lecoq J, Slaughterbeck C, Sullivan D, Farrell C, Perkins J, Reid D, Feng D, Graddis N, Garrett M, Li Y, Long F, Mochizuki C, Roll K, Zhuang J, Thompson C

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Nature Neuroscience
December 16, 2019

de Vries S, Lecoq J, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng F, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon S, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin J, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten D, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, R Reid C, Koch C

Allen Brain Atlas: an integrated spatiotemporal portal for exploring the central nervous system

Nucleic Acids Research
November 28, 2012

Sunkin SM, Ng L, Lau C, Dolbeare T, Gilbert TL, Thompson CL, Hawrylycz M, Dang C

Cell-type-specific consequences of reelin deficiency in the mouse neocortex, hippocampus, and amygdala

Journal of Comparative Neurology
June 22, 2011

Boyle MP, Bernard A, Thompson CL, Ng L, Boe A, Mortrud M, Hawrylycz MJ, Jones AR, Hevner RF, Lein ES

Molecular and anatomical signatures of sleep deprivation in the mouse brain

Frontiers in Neuroscience
October 21, 2010

Thompson CL, Wisor JP, Lee C, Pathak SD, Gerashchenko D, Smith KA, Fischer SR, Kuan CL, Sunkin SM, Ng LL, Lau C, Hawrylycz M, Jones AR, Kilduff T, Lein ES

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

BMC Bioinformatics
March 18, 2008

Lau C, Ng L, Thompson C, Pathak S, Kuan L, Jones A, Hawrylycz M

Genomic anatomy of the hippocampus

December 26, 2008

Thompson CL, Pathak SD, Jeromin A, Ng LL, MacPherson CR, Mortrud MT, Cusick A, Riley ZL, Sunkin SM, Bernard A, Puchalski RB, Gage FH, Jones AR, Bajic VB, Hawrylycz MJ, Lein ES