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RESEARCH

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 https://khchenlab.github.io/.

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 (email:chenkh@gis.a-star.edu.sg).

Selected Publications

• Zhou, X.*, Seow, W. Y.*, Ha, N., Cheng, T. H., Lingfan, J., Boonruangkan, J., Goh, J. J. L., Prabhakar, S., Chou, N.#, & Chen, K. H.# (2024). Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nature Communications, 15, 2342.
• Singhal, V.*, Chou, N.*, Lee, J., Yue, Y., Liu, J., Chock, W. K., Lin, L., Chang, Y.-C., Teo, E., Aow, J., Lee, H. K., Chen, K. H.#, & Prabhakar, S.# (2024). BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis. Nature Genetics, 56, 431-441.
• Goh, J. J. L.*, Chou, N.*, Seow, W. Y., Ha, N., Cheng, C. P. P., Chang, Y.-C., Zhao, Z. W., & Chen, K. H. (2020). Highly specific multiplexed RNA imaging in tissues with split-FISH. Nature Methods, 17(7), 689–693.
• Li, H., Courtois, E. T., Sengupta, D., Tan, Y., Chen, K. H., Goh, J. J. L., Kong, S. L., Chua, C., Hon, L. K., Tan, W. S., Wong, M., Choi, P. J., Wee, L. J. K., Hillmer, A. M., Tan, I. B., Robson, P., & Prabhakar, S. (2017). Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nature Genetics, 49(5), 708–718.
• Moffitt, J. R., Hao, J., Wang, G., Chen, K. H., Babcock, H. P., & Zhuang, X. (2016). High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proceedings of the National Academy of Sciences, 113(39), 201612826.
• Chen, K. H.*, Boettiger, A. N.*, Moffitt, J. R.*, Wang, S., & Zhuang, X. (2015). Spatially resolved, highly multiplexed RNA profiling in single cells. Science, 348(6233), aaa6090–aaa6090.
• Bates, M., Dempsey, G. T., Chen, K. H., & Zhuang, X. (2012). Multicolor super-resolution fluorescence imaging via multi-parameter fluorophore detection. ChemPhysChem, 13(1), 99–107.
• Cha, T. G., Baker, B. A., Salgado, J., Bates, C. J., Chen, K. H., Chang, A. C., Akatay, M. C., Han, J. H., Strano, M. S., & Choi, J. H. (2012). Understanding oligonucleotide-templated nanocrystals: Growth mechanisms and surface properties. ACS Nano, 6(9), 8136–8143.
• Chen, K. H., Hobley, J., Foo, Y. L., & Su, X. (2011). Wide-field single metal nanoparticle spectroscopy for high throughput localized surface plasmon resonance sensing. Lab on a Chip, 11(11), 1895–1901.
• Dempsey, G. T.*, Vaughan, J. C.*, Chen, K. H.*, Bates, M., & Zhuang, X. (2011). Evaluation of fluorophores for optimal performance in localization- based super-resolution imaging. Nature Methods, 8(12), 1–44.
• Ishitsuka, Y., Okumus, B., Arslan, S., Chen, K. H., & Ha, T. (2010). Temperature-independent porous nanocontainers for single-molecule fluorescence studies. Analytical Chemistry, 82(23), 9694–9701.
• Choi, J. H., Chen, K. H., Han, J., Chaffee, A. M. & Strano, M. S. (2009). DNA Aptamer-Passivated Nanocrystal Synthesis: A Facile Approach for Nanoparticle-Based Cancer Cell Growth Inhibition. Small, 5(6), 672-675.
• Mateo-Alonso, A., Ehli, C., Chen, K. H., Guldi, D.M., Prato, M. (2007). Dispersion of single-walled carbon nanotubes with an extended diazapentacene derivative. The Journal of Physical Chemistry A, 111(49), 12669-12673.
• Choi, J. H., Chen, K. H., & Strano, M. S. (2006). Aptamer-capped nanocrystal quantum dots: A new method for label-free protein detection. Journal of the American Chemical Society, 128(49), 15584–15585.