Team

Staff Profiles

Wayne Wakeman

Manager, Software Project Management

Wayne leads a team that builds information systems to collect, process and serve petabytes of neuroscience data. He dives deep into each project to learn all the details and to understand how it relates to the overall organizational strategy. 

Prior to the Allen Institute, Wayne helped scientists use commercial software packages for the analysis of genomics data and biological sequences. He began his career as a molecular biologist, including a stint at a start-up that was to become an industry leader in the production of reagents for siRNA research.


Wayne earned a MBA degree with honors from the University of Washington, Foster School of Business. Outside of work, he spends time with family and races bicycles.

Selected Publications

Survey of spiking in the mouse visual system reveals functional hierarchy

Nature
January 20, 2021

Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries S., Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo D, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C

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

A multimodal cell census and atlas of the mammalian primary motor cortex

Nature
October 6, 2021

BRAIN Initiative Cell Census Network (BICCN)

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

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

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

Neuron
December 7, 2020

Whitesell JD, Liska A, Coletta L, Hirokawa KE, Bohn P, Williford A, Groblewski PA, Graddis N, Kuan L, Knox JE, Ho A, Wakeman W, Nicovich PR, Nguyen TN, van Velthoven CTJ, Garren E, Fong O, Naeemi M, Henry AM, Dee N, Smith KA, Levi B, Feng D, Ng L, Tasic B, Zeng H, Mihalas S, Gozzi A, Harris JA.

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

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

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Nature Neuroscience
December 16, 2019

de Vries S, Lecoq J, Buice MA, Groblewski PA, Ocker GK, Oliver M, Feng F, Cain N, Ledochowitsch P, Millman D, Roll K, Garrett M, Keenan T, Kuan L, Mihalas S, Olsen S, Thompson C, Wakeman W, Waters J, Williams D, Barber C, Berbesque N, Blanchard B, Bowles N, Caldejon S, Casal L, Cho A, Cross S, Dang C, Dolbeare T, Edwards M, Galbraith J, Gaudreault N, Griffin F, Hargrave P, Howard R, Huang L, Jewell S, Keller N, Knoblich U, Larkin J, Larsen R, Lau C, Lee E, Lee F, Leon A, Li L, Long F, Luviano J, Mace K, Nguyen T, Perkins J, Robertson M, Seid S, Shea-Brown E, Shi J, Sjoquist N, Slaughterbeck C, Sullivan D, Valenza R, White C, Williford A, Witten D, Zhuang J, Zeng H, Farrell C, Ng L, Bernard A, Phillips JW, R Reid C, Koch C

Hierarchical organization of cortical and thalamic connectivity

Nature
October 30, 2019

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Choi H, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feiner A, Feng D, Gaudreault N, Gerfen CR, Graddis N, Groblewski PA, Henry AM, Ho A, Howard R, Knox JE, Kuan L, Kuang X, Lecoq J, Lesnar P, Li Y, Luviano J, McConoughey S, Mortrud MT, Naeemi M, Ng L, Oh SW, Ouellette B, Shen E, Sorensen SA, Wakeman W2, Wang Q2, Wang Y, Williford A, Phillips JW, Jones AR, Koch C, Zeng H

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

The organization of intracortical connections by layer and cell class in the mouse brain

bioRxiv
April 18, 2018

Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Knox J, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feng D, Gaudreault N, Gerfen C, Graddis N, Groblewski PA, Henry A, Ho A, Howard R, Kuan L, Lecoq J, Luviano J, McConoughey S, Mortrud M, Naeemi M, Ng L, Oh SW, Ouellette B, Sorensen SA, Wakeman W, Wang Q, Williford A, Phillips J, Jones A, Koch C, Zeng H

Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease

Journal of Comparative Neurology
October 12, 2018

Whitesell JD, Buckley AR, Knox JE, Kuan L, Graddis N, Pelos A, Mukora A, Wakeman W, Bohn P, Ho A, Hirokawa KE, Harris JA