Staff Profiles

Carol L. Thompson, Ph.D.

Senior Scientific Program Manager

Carol Thompson is the Scientific Program Manager for the in vitro Human Cell Types Program. Since joining the Allen Institute in 2004, she has provided scientific leadership and project oversight for 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.  Thompson has contributed to a variety of different fields. As a postdoctoral fellow, Thompson defined discrete proximodistal and septotemporal domains of hippocampal field CA3 on the basis of molecular identity and connectivity. As a graduate student, she earned a UNC Lineberger Fellow Award for her research establishing a role for cryptochromes in mediating nonvisual responses to light, such as circadian clock resetting and acute suppression of locomotor activity by light.  She holds a B.S. in Biology from the University of Richmond and a Ph.D. in Biochemistry from the University of North Carolina at Chapel Hill. 


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

September 12, 2018

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

June 29, 2018

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