Team

Staff Profiles

Jeremy Miller, Ph.D.

Senior Scientist

Jeremy Miller joined the Allen Institute in 2011 to help with computational data analysis of the Allen Human Brain Atlas project, and is currently extending his study to transcriptional atlases of the developing human and non-human primate brain. He is interested in using large-scale gene expression data to identify essential components (i.e., cell types) of the mammalian brain, as well as molecular pathways unique to human. Miller received a B.A. in mathematics and a B.S. in astronomy from the University of Maryland, and was subsequently a researcher at Los Alamos National Laboratory, where he used computer models to study the mammalian retina. Miller received his Ph.D. in neuroscience from UCLA, where he studied gene expression changes in the brain in Alzheimer's disease and normal aging.

Research

Research Interests

Research Interests The Allen Brain Atlas resources provide a wealth of information on gene expression patterns across brain regions, between species, and at many developmental time points in normal brain.  Future transcriptomics resources will focus on 1) identifying and characterizing distinct cell types in human cortex, 2) identifying genetic signatures of stem cell niches and anatomic components of glioblastoma, and 3) finding gene expression changes associated with the long term consequences of traumatic brain injury.  Through continued work on these large collaborative efforts, I hope to gain a better understanding of normal neurodevelopmental processes, to learn what happens when these processes fail, and to appreciate what makes the human brain different from other mammals.

Expertise

  • Transcriptomics
  • Bioinformatics

Research Programs

  • Human Cell Types

Selected Publications View on PUBMED

Epigenetic landscape and AAV targeting of human neocortical cell classes

bioRxiv
February 19, 2019

Mich JK, Hess EE, Graybuck LT, Somasundaram S, Miller JA, Ding Y, Shapovalova NV, Fong O, Yao S, Mortrud M, Chong P, Bertagnolli D, Goldy J, Casper T, Kroll M, Hodge RD, Bakken TE, Yao Z, Dee N, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Gradinaru V, Sunkin SM, Zeng H, Lein ES, Tasic B, Ting JT, Levi BP

A Microglial Signature Directing Human Aging and Neurodegeneration-Related Gene Networks

Frontiers in Neuroscience
January 24, 2019

Mukherjee S, Klaus C, Pricop-Jeckstadt M, Miller JA, Struebing FL

Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex

bioRxiv
January 13, 2019

Smith SJ, Sumbul U, Graybuck LT, Collman F, Sharmishtaa S, Gala R, Gliko O, Elabbady L, Miller J, Bakken T, Yao Z, Lein ES, Zeng H, Tasic B, Hawrylycz M

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

Cell type discovery using single-cell transcriptomics: implications for ontological representation

Human Molecular Genetics
May 1, 2018

Aevermann BD, Novotny M, Bakken T, Miller JA, Diehl AD, Osumi-Sutherland D, Lasken RS, Lein ES, Scheuermann RH

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

PLoS One
December 26, 2018

Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B

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

Neuron
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

Nature
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

Spatiotemporal dynamics of the postnatal developing primate brain transcriptome

Human Molecular Genetics
May 7, 2015

Bakken TE, Miller JA, Luo R, Bernard A, Bennett JL, Lee CK, Bertagnolli D, Parikshak NN, Smith KA, Sunkin SM, Amaral DG, Geschwind DH, Lein ES

Canonical genetic signatures of the adult human brain

Nature Neuroscience
December 2015

Hawrylycz M, Miller JA, Menon V, Feng D, Dolbeare T, Guillozet-Bongaarts AL, Jegga AG, Aronow BJ, Lee CK, Bernard A, Glasser MF, Dierker DL, Menche J, Szafer A, Collman F, Grange P, Berman KA, Mihalas S, Yao Z, Stewart L, Barabási AL, Schulkin J, Phillips J, Ng L, Dang C, Haynor DR, Jones A, Van Essen DC, Koch C, Lein E

JAKMIP1, a Novel Regulator of Neuronal Translation, Modulates Synaptic Function and Autistic-like Behaviors in Mouse

Neuron
November 25, 2015

Berg JM, Lee C, Chen L, Galvan L, Cepeda C, Chen JY, Peñagarikano O, Stein JL, Li A, Oguro-Ando A, Miller JA, Vashisht AA, Starks ME, Kite EP, Tam E, Gdalyahu A, Al-Sharif NB, Burkett ZD, White SA, Fears SC, Levine MS, Wohlschlegel JA, Geschwind DH

Transcriptional landscape of the prenatal human brain

Nature
April 2, 2014

Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slau

Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq

BMC Genomics
February 24, 2014

Miller JA, Menon V, Goldy J, Kaykas A, Lee CK, Smith KA, Shen EH, Phillips JW, Lein ES, Hawrylycz MJ

Genes and pathways underlying regional and cell type changes in Alzheimer's disease

Genome Medicine
May 25, 2013

Miller JA, Woltjer RL, Goodenbour JM, Horvath S, Geschwind DH

Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease

BMC Medical Genomics
February 13, 2013

Levine AJ, Miller JA, Shapshak P, Gelman B, Singer EJ, Hinkin CH, Commins D, Morgello S, Grant I, Horvath S

Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates

Development
November 15, 2013

Miller JA, Nathanson J, Dalley RA, Shapouri S, Smith KA, Sunkin SM, Bernard A, Bennett JL, Lee C, Hawrylycz MJ, Jones AR, Amaral DG, Gage FH, Lein ES

An anatomically comprehensive atlas of the adult human brain transcriptome

Nature
December 2012

Hawrylycz MJ, Lein ES, Guillozet-Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A, Riley ZL, Abajian C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, Cartagena PM, Chakravarty MM, Chapin M, Chong J, Dalley RA, Daly BD, Dang C, Datta S, Dee N, Dolbeare T, Faber V, Feng D, Fowler DR, Goldy J, Gregor BW, Haradon Z, Haynor DR, Hohmann JG, Horvath S, Howard RE, Jeromin A, Jochim JM, Kinnunen M, Lau C, Lazarz ET, Lee C, Lemon TA, Li L, Li Y, Morris JA, Overly CC, Parker PD, Parry SE, Reding M, Royall JJ, Schulkin J, Sequeria PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sun