Team

Staff Profiles

Kimberly Smith

Senior Manager, Molecular Biology

kimberlys@alleninstitute.org

With 20 years’ experience overseeing large scale genomic and transcriptomic projects, Kim Smith has spent the last 14 of them at the Allen Institute influencing, producing, and managing many of the most well known Brain-map products. In particular, she has managed production groups, methods development, and data handling for six research atlases including the signature brain atlas and mouse spinal cord atlas. Kim currently serves as the manager of the Single Cell RNASeq Core, supporting the Cell Types Mouse and Human Projects.

Kim’s first experiences with large scale genomics project management was working on Chromosome 7 of the Human Genome Project, the Pseudomonas Genome Project, and the Rice Genome Project, all while at the University of Washington. She then went on to develop and manage the Center for Expression Arrays at the University of Washington, branching out into the new Microarray technology at the time. After a few years at a new biotechnology venture that did not succeed, Kim welcomed the opportunity to start at the ground floor of the Allen Institute for Brain Science, employing her experience both at the bench and at establishing new production pipelines.

Kim received a B.S. in Cell and Molecular Biology from the University of Washington.

Research

Research Interests

As the first bench scientist hired at Allen Institute for Brain Science, Kim has enjoyed being a part of the growth and development of the Institute over the last 14 years. She is passionate about generating high quality datasets that have high impact on scientific understanding of our world. She enjoys developing new processes and production pipelines as the backbone to generating these datasets.

Expertise

  • Large scale, high throughput, genomic and transcriptomic projects

Research Programs

  • Allen Brain Atlas
  • Allen Human Brain Atlas
  • Allen Developing Mouse Brain Atlas
  • BrainSpan Atlas of the Developing Human Brain
  • Non-Human Primate Atlas
  • Human Brain and BrainSpan LCM & Microarray projects
  • Ivy GAP (Glioblastoma)
  • TBI RNASeq Project
  • Allen Cell Types Database

Selected Publications

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

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

Cell
July 12, 2018

Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ2, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, 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

Distinct descending motor cortex pathways and their roles in movement

Nature
October 31, 2018

Economo MN, Viswanathan S, Tasic B, Bas E, Winnubst J, Menon V, Graybuck LT, Nguyen TN, Smith KA, Yao Z, Wang L, Gerfen CR, Chandrashekar J, Zeng H, Looger LL, Svoboda K

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

Team

As Senior Manager of Molecular Biology at Allen Institute, Kim leads three production teams. The Histology team is responsible for production tissue staining, ISH, and reagent preparation. The Genotyping team is responsible for providing end point genotyping results in support of our Transgenic Colony Management team. The Single Cell RNASeq Core, the largest of the teams, is responsible for all single cell and nucleus RNA Sequencing.