Michael Hawrylycz, Ph.D.
Investigator
Mike Hawrylycz joined the Allen Institute in 2003. He is responsible for the direction of the data analysis and annotation effort. Hawrylycz has worked in a variety of applied mathematics and computer science areas, addressing challenges in consumer and investment finance, electrical engineering and image processing, and computational biology and genomics. Hawrylycz received his Ph.D. in applied mathematics at the Massachusetts Institute of Technology. He subsequently was a post-doctoral researcher in the Computer Research and Applications Group at the Los Alamos National Laboratory.
Selected Publications View Publications
eLife
September 2, 2021
Bakken TE, van Velthoven CT, Menon V, Hodge RD, Yao Z, Nguyen TN, Graybuck LT, Horwitz GD, Bertagnolli D, Goldy J, Yanny AM, Garren E, Parry S, Casper T, Shehata SI, Barkan ER, Szafer A, Levi BP, Dee N, Smith KA, Sunkin SM, Bernard A, Phillips J, Hawrylycz MJ, Koch C, Murphy GJ, Lein E, Zeng H, Tasic B
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Cell
May 17, 2021
Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H.
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
Morphological diversity of single neurons in molecularly defined cell types
Nature
October 6, 2021
Peng H, Xie P, Liu L, Kuang X, Wang Y, Qu L, Gong H, Jiang S, Li A, Ruan Z, Ding L, Yao Z, Chen C, Chen M, Daigle TL, Dalley R, Ding Z, Duan Y, Feiner A, He P, Hill C, Hirokawa KE, Hong G, Huang L, Kebede S, Kuo HC, Larsen R, Lesnar P, Li L, Li Q, Li X, Li Y, Li Y, Liu A, Lu D, Mok S, Ng L, Nguyen TN, Ouyang Q, Pan J, Shen E, Song Y, Sunkin SM, Tasic B, Veldman MB, Wakeman W, Wan W, Wang P, Wang Q, Wang T, Wang Y, Xiong F, Xiong W, Xu W, Ye M, Yin L, Yu Y, Yuan J, Yuan J, Yun Z, Zeng S, Zhang S, Zhao S, Zhao Z, Zhou Z, Huang ZJ, Esposito L, Hawrylycz MJ, Sorensen SA, Yang XW, Zheng Y, Gu Z, Xie W, Koch C, Luo Q, Harris JA, Wang Y, Zeng H
Cellular anatomy of the mouse primary motor cortex
Nature
October 6, 2021
Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW
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
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
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
Nature
October 6, 2021
Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, Casper T, Colantuoni C, Crabtree J, Creasy H, Crichton K, Crow M, Dee N, Dougherty EL, Doyle WI, Dudoit S, Fang R, Felix V, Fong O, Giglio M, Goldy J, Hawrylycz M, Herb BR, Hertzano R, Hou X, Hu Q, Kancherla J, Kroll M, Lathia K, Li YE, Lucero JD, Luo C, Mahurkar A, McMillen D, Nadaf NM, Nery JR, Nguyen TN, Niu SY, Ntranos V, Orvis J, Osteen JK, Pham T, Pinto-Duarte A, Poirion O, Preissl S, Purdom E, Rimorin C, Risso D, Rivkin AC, Smith K, Street K, Sulc J, Svensson V, Tieu M, Torkelson A, Tung H, Vaishnav ED, Vanderburg CR, van Velthoven C, Wang X, White OR, Huang ZJ, Kharchenko PV, Pachter L, Ngai J, Regev A, Tasic B, Welch JD, Gillis J, Macosko EZ, Ren B, Ecker JR, Zeng H, Mukamel EA
A multimodal cell census and atlas of the mammalian primary motor cortex
Nature
October 6, 2021
BRAIN Initiative Cell Census Network (BICCN)
A community-based transcriptomics classification and nomenclature of neocortical cell types
Nature Neuroscience
August 24, 2020
Yuste R, Hawrylycz M, Aalling N, Aguilar-Valles A, Arendt D, Arnedillo RA, Ascoli GA, Bielza C, Bokharaie V, Bergmann TB, Bystron I, Capogna M, Chang Y, Clemens A, de Kock CPJ, DeFelipe J, Dos Santos SE, Dunville K, Feldmeyer D, Fiáth R, Fishell GJ, Foggetti A, Gao X, Ghaderi P, Goriounova NA, Güntürkün O, Hagihara K, Hall VJ, Helmstaedter M, Herculano S, Hilscher MM, Hirase H, Hjerling-Leffler J, Hodge R, Huang J, Huda R, Khodosevich K, Kiehn O, Koch H, Kuebler ES, Kühnemund M, Larrañaga P, Lelieveldt B, Louth EL, Lui JH, Mansvelder HD, Marin O, Martinez-Trujillo J, Moradi Chameh H, Nath A, Nedergaard M, Němec P, Ofer N, Pfisterer UG, Pontes S, Redmond W, Rossier J, Sanes JR, Scheuermann R, Serrano-Saiz E, Steiger JF, Somogyi P, Tamás G, Tolias AS, Tosches MA, García MT, Vieira HM, Wozny C, Wuttke TV, Yong L, Yuan J, Zeng H, Lein E
New light on cortical neuropeptides and synaptic network plasticity
Current Opinion in Neurobiology
August 2020
Smith SJ, Hawrylycz M, Rossier J, Sümbül U
The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas
Cell
May 14, 2020
Wang Q, Ding SL, Li Y, Royall J, Feng D, Lesnar P, Graddis N, Naeemi M, Facer B, Ho A, Dolbeare T, Blanchard B, Dee N, Wakeman W, Hirokawa KE, Szafer A, Sunkin SM, Oh SW, Bernard A, Phillips JW, Hawrylycz M, Koch C, Zeng H, Harris JA, Ng L
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.
Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells
Cell
November 12, 2020
Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H
PLoS One
September 4, 2019
Weed N, Bakken T, Graddis N, Gouwens N, Millman D, Hawrylycz M, Waters J
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
Classification of electrophysiological and morphological neuron types in mouse visual cortex
Nature Neuroscience
June 17, 2019
Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin S, Feng D, Anastassiou C, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle T, Dalley R, Dee N, Desta T, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris J, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina C, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips J, Zeng H, Koch C
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
Translational Psychiatry
May 29, 2018
Kumar VJ, Grissom NM, McKee SE, Schoch H, Bowman N, Havekes R, Kumar M, Pickup S, Poptani H, Reyes TM, Hawrylycz M, Abel T, Nickl-Jockschat T
An anatomic transcriptional atlas of human glioblastoma
Science
May 11, 2018
Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Amy Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD
Systematic generation of biophysically detailed models for diverse cortical neuron types
Nature Communications
February 19, 2018
Gouwens NW, Berg J, Feng D, Sorensen SA, Zeng H, Hawrylycz MJ, Koch C, and Arkhipov A
Generalized leaky integrate-and-fire models classify multiple neuron types
Nature Communications
February 19, 2018
Teeter C, Iyer R, Menon V, Gouwens N, Feng D, Berg J, Szafer A, Cain N, Zeng H, Hawrylycz M, Koch C, Mihalas S
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
From Maxwell's equations to the theory of current-source density analysis
European Journal of Neuroscience
February 8, 2017
Gratiy SL, Halnes G, Denman D, Hawrylycz MJ, Koch C, Einevoll GT, Anastassiou CA
Altered gene expression in the dorsolateral prefrontal cortex of individuals with schizophrenia
Molecular Psychiatry
March 26, 2013
Guillozet-Bongaarts AL, Hyde TM, Dalley RA, Hawrylycz MJ, Henry A, Hof PR, Hohmann J, Jones AR, Kuan CL, Royall J, Shen E, Swanson B, Zeng H, Kleinmann JE
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.
Allen Brain Atlas: an integrated spatiotemporal portal for exploring the central nervous system
Nucleic Acids Research
November 28, 2012
Sunkin SM, Ng L, Lau C, Dolbeare T, Gilbert TL, Thompson CL, Hawrylycz M, Dang C
Large-scale neuroinformatics for in situ hybridization data in the mouse brain
International Review of Neurobiology
2012
Ng LL, Sunkin SM, Feng DF, Lau C, Dang C, Hawrylycz MJ