Staff Profiles

Trygve Bakken, M.D., Ph.D.

Senior Scientist

Trygve Bakken joined the Allen Institute in 2013 to develop computational tools to study gene expression dynamics during primate cortical development. He currently co-leads an effort to define the cellular components of adult human brain circuits using high-throughput, single nucleus RNA-sequencing and to compare these cell types across human individuals and other species. Previously, he completed an M.D. and a Ph.D. in Neuroscience at the University of California, San Diego where he identified genomic variation shaping human brain morphology and a developmental scaling rule optimizing conduction velocities in the fish visual system under the co-mentorship of Charles Stevens and Nicholas Schork. Prior to that, he completed an M.Sc. in Philosophy and History of Science at the London School of Economics and a B.A. in Physics and Philosophy at Yale University.


Research Interests

The human brain is a complex circuit composed of over 170 billion neuronal and non-neuronal cells that have diverse molecular profiles, connectivity, and firing properties. I co-lead a team to characterize cellular diversity in human brain using high-throughput, unbiased single nucleus RNA-sequencing. This technology provides a global snapshot of transcribed genes that collectively shape the identity of a cell. I am interested in developing robust computational tools to group cells based on shared identity and to compare these cell types across brain regions, human individuals, and species. We are investigating whether there is a canonical neocortical circuit with shared cellular components and the relationship between the mature identity and developmental origin of cell types. We are examining how cell types vary in the human population due to many variables, including genomic variation and disease state. We are testing whether cell type function can be predicted from the expression of well-characterized gene families, such as voltage-gated ion channels and neurotransmitter receptors. Finally, we are quantifying the conservation of human and mouse brain circuits and comparing expression of homologous cell types to better understand the limitations of the rodent as a model system for probing human brain function. In the future, profiling cellular diversity in a much broader range of species will refine the core transcriptomic identity of conserved cell types and will enable comparisons between species traits and the emergence of novel cell types and divergent expression.


  • Molecular Neuroscience
  • Genomics
  • Comparative Biology
  • Informatics

Research Programs

  • Human Cell Types

Selected Publications View on PUBMED

Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type

Nature Neuroscience
August 27, 2018

Boldog E, Bakken TE, Hodge RD, Novotny M, Aevermann BD, Baka J, Bordé S, Jennie L. Close, Diez-Fuertes F, Ding SL, Faragó N, Kocsis AK, Kovács B, Maltzer Z, McCorrison JM, Miller JA, Molnár G, Oláh G, Ozsvár A, Rózsa M, Shehata SI, Smith KA, Sunkin SM, Tran DN, Venepally P, Wall A, Puskás LG, Barzó P, Steemers FJ, Schork NJ, Scheuermann RH, Lasken RS, Lein ES, Tamás G

Genetic identification of brain cell types underlying schizophrenia

Nature Genetics
May 21, 2018

Skene NG, Bryois J, Bakken TE, Breen G, Crowley JJ, Gaspar HA, Giusti-Rodriguez P, Hodge RD, Miller JA, Muñoz-Manchado A, O'Donovan MC, Owen MJ, Pardiñas AF, Ryge J, Walters JTR, Linnarsson S, Lein ES, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sullivan PS, Hjerling-Leffler J

h-Channels Contribute to Divergent Intrinsic Membrane Properties of Supragranular Pyramidal Neurons in Human versus Mouse Cerebral Cortex

November 1, 2018

Kalmbach BE, Buchin A, Long B, Close J, Nandi A, Miller JA, Bakken TE, Hodge RD, Chong P, de Frates R, Dai K, Maltzer Z, Nicovich PR, Keene CD, Silbergeld DL, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Koch C, Anastassiou CA, Lein ES, Ting JT

Shared and distinct transcriptomic cell types across neocortical areas

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

A comprehensive transcriptional map of primate brain development

July 13, 2016

Bakken TE, Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Dalley RA, Royall JJ, Lemon T, Shapouri S, Aiona K, Arnold J, Bennett JL, Bertagnolli D, Bickley K, Boe A, Brouner K, Butler S, Byrnes E, Caldejon S, Carey A, Cate S, Chapin M, Chen J, Dee N, Desta T, Dolbeare TA, Dotson N, Ebbert A, Fulfs E, Gee G, Gilbert TL, Goldy J, Gourley L, Gregor B, Gu G, Hall J, Haradon Z, Haynor DR, Hejazinia N, Hoerder-Suabedissen A, Howard R, Jochim J, Kinnunen M, Kriedberg A, Kuan CL, Lau C, Lee CK, Lee F, Luong L, Mastan N, May R, Melchor J, Mosqueda N, Mott E, Ngo K, Nyhus J, Oldre A, Olson E, P

The complete genome sequence of a Neanderthal from the Altai Mountains

January 2, 2014

Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelsho J, Pääbo S

Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans

March 2012

Bakken TE, Roddey JC, Djurovic S, Akshoomoff N, Amaral DG, et al

Visual system scaling in teleost fish

Journal of Comparative Neurology
January 2012

Bakken TE, Stevens CF

Association of genetic variants on 15q12 with cortical thickness and cognition in schizophrenia

Archives of General Psychiatry
August 2011

Bakken TE, Bloss CS, Roddey JC, Joyner AH, Rimol LM, et al