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

Assistant Investigator


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 Focus:

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.

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