Welcome to the Chen Lab at the
Genome Institute of Singapore

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.

BANKSY: A Spatial Omics Algorithm that Unifies Cell Type Clustering and Tissue Domain Segmentation

By constructing a product space of cell and neighbourhood transcriptomes, representing cell state and microenvironment, BANKSY improves cell type clustering and domain segmentation on spatial omics data. Software

Highly Specific RNA Imaging with Split-FISH

By using a split-probe design to achieve enhanced specificity, Split-FISH reduces off-target background fluorescence, decreases false positives, and enables accurate profiling in uncleared tissues. Read more.

People

Former Members

Jazlynn Tan, 2022. University of Toronto

Jeeranan Boonruangkan, 2018-2022. Biofourmis

Jie Lin Jolene Goh, 2016-2022. Veranome Biosystems

Mike Jin-An Huang, 2018-2021. 1910 Genetics

Paul Cheng, 2018-2021. Veranome Biosystems

Kaviya Selva Raju, 2018-2020. Research associate at Applied Materials

Siyi Chen, 2018. Senior scientist at Maiden Therapeutics

Christabelle Goh, 2018. Scientist II at Applied Materials

Ziqing, Winston Zhao, 2018-2019. Assistant professor at National University of Singapore

Teck Por Lim, 2018-2019.

Mei Lun Chow, 2018. Project officer at Nanyang Technological University

Publications

Goh, J. J. L.*, Chou, N.*, Seow, W. Y., Ha, N., Cheng, C. P. P., Chang, Y., Zhao, Z. W., Chen, K. H. Highly specific multiplexed RNA imaging in tissues with split-FISH. Nature Methods, (2020) https://doi.org/10.1038/s41592-020-0858-0.

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 (2017).

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. P.N.A.S. 113 (39), 11046-11051 (2016).

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).

Cha, T. G., Baker, B.A., Salgado J., Bates C.J., Chen K.H., Chang A.C., Han J.C., Strano M.S., & Choi J.H. Understanding oligonucleotide-templated nanocrystals: Growth mechanisms and surface properties. ACS Nano 6, 8136–8143 (2012).

Bates, M., Dempsey, G. T., Chen, K. H. & Zhuang, X. Multicolor super-resolution fluorescence imaging via multi-parameter fluorophore detection. ChemPhysChem 13, 99–107 (2012).

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 (2011).

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 (2011).

Ishitsuka, Y., Okumus, B., Arslan, S., Chen, K. H. & Ha, T. Temperature-independent porous nanocontainers for single-molecule fluorescence studies. Anal. Chem. 82, 9694–9701 (2010).

Mateo-Alonso, A., Ehli, C., Chen, K. H., Guldi, D. M. & Prato, M. Dispersion of single-walled carbon nanotubes with an extended diazapentacene derivative. J. Phys. Chem. A 111, 12669–12673 (2007).

Choi, J. H., Chen, K. H. & Strano, M. S. Aptamer-capped nanocrystal quantum dots: A new method for label-free protein detection. J. Am. Chem. Soc. 128, 15584–15585 (2006).

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