Staff Profiles

Carol L. Thompson, Ph.D.

Associate Director, Data Management

Carol Thompson has provided scientific leadership and management at the Allen Institute for Brain Science for over 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 responsible for coordinating the data ecosystem for community-generated data as part of the BRAIN Initiative Cell Census Network (BICCN) and for BRAIN Initiative Cell Atlas Network (BICAN), and is also responsible for consortium administration. Carol holds a BS in Biology from the University of Richmond and a Ph.D. in Biochemistry from the University of North Carolina at Chapel Hill, where she studied cryptochromes under the guidance of Nobel laureate Aziz Sancar, M.D., Ph.D.  


Research Interests

Research Interests From a broad perspective, I am interested in the power of projects that lie at the intersection of big data, biology and computation. To make an impact, data must be useful, and this requires that we understand how to interpret data in the context of its provenance, the complexity of biology, and the limitations of our current knowledge and available assays.  I hope to support continuing integration of data from many sources to understand cell types and their function in the brain, and value interactions with efforts by the scientific community to harmonize efforts and extend the life and utility of the data to support deep understanding and continuing discoveries about the complex organ that makes us truly human: the brain.  


  • Program Management
  • Hardware and software integration projects
  • Project Lifecycle Management
  • Strategic and Tactical Planning
  • Gene Expression Profiling
  • Neuroanatomy
  • Developmental Neurobiology
  • Sleep and Circadian Rhythms
  • Stem Cell Biology
  • DNA Repair
  • Data Analysis

Selected Publications View Publications

Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia

Proceedings of the National Academy of Sciences
April 12, 2022

Su-Feher L, Rubin AN, Silberberg SN, Catta-Preta R, Lim KJ, Ypsilanti AR, Zdilar I, McGinnis CS, McKinsey GL, Rubino TE Jr, Hawrylycz MJ, Thompson C, Gartner ZJ, Puelles L, Zeng H, Rubenstein JLR, Nord AS

Transcriptional network orchestrating regional patterning of cortical progenitors

Proceedings of the National Academy of Sciences
December 21, 2021

Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL.

Survey of spiking in the mouse visual system reveals functional hierarchy

January 20, 2021

Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries S., Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo D, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C

A multimodal cell census and atlas of the mammalian primary motor cortex

October 6, 2021

BRAIN Initiative Cell Census Network (BICCN)

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