CHEN LAB
Welcome to the Chen Lab at the
Genome Institute of Singapore
About
We are a group of researchers at the Genome Insitute of Singapore 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 tissues.
Such 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.
People
Shiji, Nigel CHOU, Ph.D.
Senior Scientist I
Wan Yi SEOW
Senior Research Officer I
Xinrui ZHOU, Ph.D.
Senior Scientist I
Yen Ling LEE
Lead Research Officer II
Dao Tuc Tu, Ph.D.
Scientist
Jiao, CAO, Ph.D.
Scientist
Jose Guijarro Nuez
A*STAR ARAP-MRC DTP Scholar (PhD student)
Former Members
Vipul Singhal, 2018-2024. Integrated Biosciences
Nigel Chou Shiji, 2017-2023. GIS Fellow at Genome Institute of Singapore
Lurong Wang, 2022-2024. Research Officer at Genome Institute of Singapore
Jiamin Toh, 2019-2024. Research Officer at Genome Institute of Singapore
Norbert Ha, 2019-2024. Biomedical Scientist at Delta Electronics
Jack Petts-Lewis, 2021-2023. Graduate Student at University of Warwick
Lingfan Jiang, 2019-2023. Research Scientist at KLA
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
Zhou, X.*, Seow, W. Y.*, Ha, N., Cheng, T. H., Jiang, L. F., Boonruangkan, J., Goh, J. J. L., Prabhakar, S., Chou, N.#, Chen, K. H.#, Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes, Nature Communications, (2024) DOI: 10.1038/s41467-024-46669-y.
Singhal, V.*, Chou, N.*, Lee, J., Yue, Y., Liu, J., Chock, W. K., Lin, Li, Chang, Y., Teo, E., Lee, H. K., Chen, K. H.#, Prabhakar, S.#, BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis, Nature Genetics, (2024) DOI: 10.1038/s41588-024-01664-3.
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).