Jeremy Miller, Ph.D.
Senior Scientist
Jeremy joined the Allen Institute in 2011 to help with computational data analysis of the Allen Human Brain Atlas project. He is first author on several major manuscripts describing the Allen Institute’s large-scale transcriptomic resources on the adult and developing human and non-human primate brain, including the Aging, Dementia, and Traumatic Brain Injury Study. 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
The Allen Brain Atlas resources provide a wealth of information on gene expression patterns in different cell types, across brain regions, between species, and at many developmental time points in normal brain. Ongoing work aims to expand on the identification and characterization of distinct cell types in different human and mouse brain areas, and to match cell types defined by transcriptomics with those defined by morphology, electorphysiology, and other features. Through continued work on these large collaborative efforts, I hope to gain a better understanding of normal cell types, to learn how features of these cell types change with disease, and to appreciate what makes the human brain different from other mammals.
Expertise
- Transcriptomics
- Bioinformatics
Research Programs
- Human Cell Types
Selected Publications View Publications
Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
eLife
August 13, 2021
Lee BR, Budzillo A, Hadley K, Miller JA, Jarsky T, Baker K, Hill D, Kim L, Mann R, Ng L, Oldre A, Rajanbabu R, Trinh J, Vargas S, Braun T, Dalley RA, Gouwens NW, Kalmbach BE, Kim TK, Smith KA, Soler-Llavina G, Sorensen S, Tasic B, Ting JT, Lein E, Zeng H, Murphy GJ, Berg J
Genome Research
June 4, 2021
Aevermann BD, Zhang Y, Novotny M, Keshk M, Bakken TE, Miller JA, Hodge RD, Lelieveldt B, Lein ES, Scheuermann RH.
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex
Cell Reports
March 30, 2021
Mich JK, Graybuck LT, Hess EE, Mahoney JT, Kojima Y, Ding Y, Somasundaram S, Miller JA, Kalmbach BE, Radaelli C, Gore BB, Weed N, Omstead V, Bishaw Y, Shapovalova NV, Martinez RA, Fong O, Yao S, Mortrud M, Chong P, Loftus L, Bertagnolli D, Goldy J, Casper T, Dee N, Opitz-Araya X, Cetin A, Smith KA, Gwinn RP, Cobbs C, Ko AL, Ojemann JG, Keene CD, Silbergeld DL, Sunkin SM, Gradinaru V, Horwitz GD, Zeng H, Tasic B, Lein ES, Ting JT, Levi BP
Consistent cross-modal identification of cortical neurons with coupled autoencoders
Nature Computational Science
February 22, 2021
Gala R, Budzillo A, Baftizadeh F, Miller J, Gouwens N, Arkhipov A, Murphy G, Tasic B, Zeng H, Hawrylycz M, Sumbul U
Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
Science
January 29, 2021
Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A; IMAXT Consortium, Church GM, Marblestone AH, Boyden ES.
Comparative cellular analysis of motor cortex in human, marmoset and mouse
Nature
October 6, 2021
Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, Zeng H, Zhang K, Feng G, Ecker JR, Linnarsson S, Lein ES
Human neocortical expansion involves glutamatergic neuron diversification
Nature
October 6, 2021
Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES
Proceedings of the National Academy of Sciences
June 10, 2020
Huang AY, Li P, Rodin RE, Kim SN, Dou Y, Kenny CJ, Akula SK, Hodge RD, Bakken TE, Miller JA, Lein ES, Park PJ, Lee EA, Walsh CA
Common cell type nomenclature for the mammalian brain
eLife
December 29, 2020
Miller JA, Gouwens NW, Tasic B, Collman F, van Velthoven CT, Bakken TE, Hawrylycz MJ, Zeng H, Lein ES, Bernard A.
Briefings in Bioinformatics
November 30, 2020
Zhang Y, Aevermann BD, Bakken TE, Miller JA, Hodge RD, Lein ES, Scheuermann RH.
Conserved cell types with divergent features in human versus mouse cortex
Nature
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
An Inflammatory Landscape for Preoperative Neurologic Deficits in Glioblastoma
Frontiers in Genetics
June 4, 2019
Katrib A, Jeong HH, Fransen NL, Henzel KS, Miller JA
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
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks.
eLife
November 11, 2019
Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, 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
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
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
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
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
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, David Daly B, Dang C, Datta S, Dee N, Dolbeare TA, 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, Sequeira PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sunkin SM, Swanson BE, Vawter MP, Williams D, Wohnoutka P, Zielke HR, Geschwind DH, Hof PR, Smith SM, Koch C, Grant SGN, Jones AR.
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways
PNAS
July 13, 2010
Miller JA, Horvath S, Geschwind DH