Staff Profiles

Changkyu (CK) Lee, Ph.D.

Senior Bioinformatics Scientist

Changkyu (CK) Lee did his undergraduate studies in Electrical Engineering at Seoul National University in Korea, and then moved to the United States. He studied computer vision and pattern recognition and received his M.S. and Ph.D. in Electrical Engineering from the University of Washington. He joined Neopath as an algorithm designer where he worked on image segmentation and classifier design on microscopic cell images. He moved to Rosetta Inpharmatics as a data analyst where he learned gene expression data analysis using microarray data. Since joining the Allen Institute as a senior analyst in 2006, he has worked on ISH and microarray probe design, data QC for all microarray projects, and performed gene expression analyses for the Allen Human Brain Atlas and the Allen Developing Mouse Brain Atlas. Currently CK is working on molecular cell type identification using single cell RNAseq data and the design and development of a spike sorting algorithm applicable for high density electrode arrays.


Research Interests

My general interest is to apply machine learning algorithms to extract relevant information out of Big Data from various modalities. Specifically, I would like to contribute to identifying cell types from single cell RNAseq data and finding the determining factors of different cell types along the differentiation process.


  • Image Processing
  • Statistical Pattern Recognition

Research Programs

  • Molecular Cell Types
  • Neural Coding
  • MAT

Selected Publications

Comprehensive Analysis of Long-Range Connectivity from and to the Posterior Parietal Cortex of the Mouse

Cerebral Cortex
September 9, 2020

Oh SW, Son SJ, Morris JA, Choi JH, Lee C, Rah JC

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells

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