Staff Profiles

Jennie Close, Ph.D.

Senior Scientist

Jennie Close joined the Allen Institute in 2011. As part of the molecular networks program, she works closely with the cell biology and genome engineering teams to develop protocols to generate cortical inhibitory interneurons from human cells in vitro. Close is also developing methods to co-culture excitatory pyramidal neurons and interneurons in traditional two-dimensional, as well as more novel three-dimensional cultures, in order to generate more mature neuronal cell types. In her previous work, Close characterized the molecular and temporal aspects of GABAergic interneuron specification and differentiation as a postdoctoral fellow at New York University. She received a Ph.D. in 2005 in neurobiology and behavior from the University of Washington, where she discovered a role for TGF beta superfamily members in the proliferation of retinal progenitors and glia.


Research Interests

Research Interests In order to truly understand what makes the human brain unique, as well as what can go wrong in disease states, we need to develop methods for studying human neurons and neuronal progenitors in vitro. This will provide us with an invaluable tool by which we can recapitulate development, recreate circuits, and engineer models designed to illuminate the role played by each brain cell type. The brain is composed of a dazzling array of cell types, which interact with each other in a variety of ways. In recent years, the loss or malfunction of inhibitory interneurons has been shown to be involved in a number of disorders, including epilepsy, schizophrenia, and autism spectrum disorders. My ultimate goals are: 1) to provide a reliable source of inhibitory interneurons of all subtypes for systems biology experiments; 2) to further our understanding of the differentiation and functional role of interneurons through in vitro molecular characterization and 3) to recapitulate human cortical circuits in vitro for use in molecular, imaging and electrophysiological experiments. Building on my previous work in neuronal specification and differentiation, my role at the Allen Institute is to generate brain cell types found in the human brain from progenitor cells such as induced pluripotent stem cells (IPSCs). Once the protocols for generating the most important cell types in the brain are established, the molecular networks team will use these cells to assay the molecular events that characterize the differentiation of specific human neuronal populations. This information will be invaluable for comparison with neurons generated from IPSCs derived from individuals with neuropsychiatric disorders, yielding clues to the mechanisms and potential treatments for these disorders.


  • Developmental neuroscience
  • Molecular biology
  • Cell biology
  • Neuroscience

Research Programs

  • Molecular networks

Selected Publications View Publications

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

June 30, 2022

Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X

Spatially resolved transcriptomics in neuroscience

Nature Methods
January 18, 2021

Close JL, Long BR, Zeng H.

Conserved cell types with divergent features in human versus mouse cortex

August 21, 2019

Hodge RD, Bakken TE, Miller JA, Smith KA, Barkan ER, Graybuck LT, Close JL, Long B, Johansen N, Penn O, Yao Z, Eggermont J, Höllt T, Levi BP, Shehata SI, Aevermann B, Beller A, Bertagnolli D, Brouner K, Casper T, Cobbs C, Dalley R, Dee N, Ding SL, Ellenbogen RG, Fong O, Garren E, Goldy J, Gwinn RP, Hirschstein D, Keene CD, Keshk M, Ko AL, Lathia K, Mahfouz A, Maltzer Z, McGraw M, Nguyen TN, Nyhus J, Ojemann JG, Oldre A, Parry S, Reynolds S, Rimorin C, Shapovalova NV, Somasundaram S, Szafer A, Thomsen ER, Tieu M, Quon G, Scheuermann RH, Yuste R, Sunkin SM, Lelieveldt B, Feng D, Ng L, Bernard A, Hawrylycz M, Phillips JW, Tasic B, Zeng H, Jones AR, Koch C, Lein ES

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

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

Satb1 is an activity-modulated transcription factor required for the terminal differentiation and connectivity of medial ganglionic eminence-derived cortical interneurons

Journal of Neuroscience
December 2012

Close J, Xu H, De Marco García N, Batista-Brito R, Rossignol E, Rudy B, Fishell G

The distinct temporal origins of olfactory bulb interneuron subtypes

Journal of Neuroscience
April 2008

Batista-Brito R, Close J, Machold R, Fishell G

Retinal stem cells and regeneration

International Journal of Developmental Biology

Moshiri A, Close J, Reh TA

Targeted deletion of 5'HS1 and 5'HS4 of the beta-globin locus control region reveals additive activity of the DNaseI hypersensitive sites

October 2001

Bender MA, Roach JN, Halow J, Close J, Alami R, Bouhassira EE, Groudine M, Fiering SN