Staff Profiles

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

Science
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

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

A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing

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.

Anatomical structures, cell types and biomarkers of the Human Reference Atlas

Nature Cell Biology
November 23, 2021

Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G.

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

Parallel RNA and DNA analysis after deep sequencing (PRDD-seq) reveals cell type-specific lineage patterns in human brain

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.

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test

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

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, 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