Kok Hao CHEN

Group Leader,
Laboratory of Imagenomics




We are a group of researchers interested in developing and applying a new kind of 'in situ omics' technology for spatially resolved systems biology. We use state of the art microscopy, fluidics, and Next-gen Sequencing, combined with cutting edge computational tools to analyze genomics, transcriptomics, and other information of single cells from and within complex tissues. Such 'in situ omics' data can reveal molecularly defined cell types, gene networks, as well as cellular signaling events within their spatial context, all of which are critical for understanding tissue biology and disease mechanisms. For more information, visit our lab website

Currently, we have several opportunities for talented researchers to work on the design, execution, and analysis of single-cell spatial transcriptomics experiments involving healthy and pathological tissues. If you are interested, contact us (

Selected Publications

  • Li, H., Courtois, E. T., Sengupta, D., Tan, Y., Chen, K. H., Goh, J. J. L., et al. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nature Genetics (49), 708–718 Abstract
  • Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P. & Zhuang, X. High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc. Natl. Acad. Sci. 113 (39), 11046-11051 Abstract
  • Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015). Abstract
  • Chen, K. H., Hobley, J., Foo, Y. L. & Su, X. Wide-field single metal nanoparticle spectroscopy for high throughput localized surface plasmon resonance sensing. Lab Chip 11, 1895–1901 Abstract
  • Dempsey, G. T., Vaughan, J. C., Chen, K. H., Bates, M. & Zhuang, X. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nature Methods 8, 1027–1036 Abstract