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<!DOCTYPE html>
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<h5><a style="background-color: black">Highly Sensitive Spatial Transcriptomics using FISHnCHIPs</a></h5>
<p><a style="background-color: black">By simultaneously imaging ~2-35 co-expressed genes that are spatially co-localized in tissues, FISHnCHIPs derive similar spatial information as single-gene FISH, but at ~2-20-fold higher sensitivity.</a></p>
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<h5><a style="background-color: black">BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis</a></h5>
<p><a style="background-color: black">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.</a></p>
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<h5><a style="background-color: black">Highly Specific RNA Imaging with Split-FISH</a></h5>
<p><a style="background-color: black">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.</a></p>
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<h5><a style="background-color: black">Spatial Transcriptomics with MERFISH</a></h5>
<p><a style="background-color: black">To image transcripts at high throughput, different species of RNAs are labeled via FISH probes in a combinatorial fashion. These Barcodes are then reconstructed via sequential rounds of hybridization and imaging.</a></p>
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<h1>Who We Are</h1>
<p>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.</p>
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<h1>What We Do</h1>
<p>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. </p>
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<h1>Why We Do</h1>
<p>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. </p>
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<h1 class="display-4">Members</h1>
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<img src="kokhao.png" alt="Kok Hao CHEN, PhD" class="rounded-circle" style="width: 140px; height: 140px"> <a href="https://www.a-star.edu.sg/gis/our-people/faculty-staff/members/kok-hao-chen">
<h4>Kok Hao CHEN, Ph.D.</h4>
<p>Principal Scientist II</p></a>
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<img src="nigel.jpg" alt="Shiji, Nigel CHOU, Ph.D" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Shiji, Nigel CHOU, Ph.D.</h4>
<p>Senior Scientist I</p>
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<img src="wanyi.jpg" alt="Wan Yi SEOW" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Wan Yi SEOW</h4>
<p>Senior Research Officer I</p>
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<img src="xinrui.png" alt="Xinrui ZHOU, Ph.D" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Xinrui ZHOU, Ph.D.</h4>
<p>Senior Scientist I</p>
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<img src="yenling.jpg" alt="Yen Ling LEE" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Yen Ling LEE</h4>
<p>Lead Research Officer II</p>
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<img src="maurice.jpeg" alt="Maurice Youzong LEE, Ph.D" class="rounded-circle" style="width: 140px; height: 140px"> <a href="https://twitter.com/Maurice_Y_Lee">
<h4>Maurice Youzong LEE, Ph.D.</h4>
<p>Scientist</p></a>
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<img src="tu.png" alt="Dao Tuc Tu, Ph.D" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Dao Tuc Tu, Ph.D.</h4>
<p>Scientist</p>
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<img src="caojiao.jpg" alt="Jiao, CAO, Ph.D" class="rounded-circle" style="width: 140px; height: 140px">
<h4>Jiao, CAO, Ph.D.</h4>
<p>Scientist</p>
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<h4>Jose Guijarro Nuez</h4>
<p>A*STAR ARAP-MRC DTP Scholar (PhD student)</p>
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<h1 class="text-black">Former Members</h1>
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<p>● Vipul Singhal, 2018-2024. Integrated Biosciences</p>
<p>● Nigel Chou Shiji, 2017-2023. GIS Fellow at Genome Institute of Singapore</p>
<p>● Lurong Wang, 2022-2024. Research Officer at Genome Institute of Singapore</p>
<p>● Jiamin Toh, 2019-2024. Research Officer at Genome Institute of Singapore</p>
<p>● Norbert Ha, 2019-2024. Biomedical Scientist at Delta Electronics</p>
<p>● Jack Petts-Lewis, 2021-2023. Graduate Student at University of Warwick</p>
<p>● Lingfan Jiang, 2019-2023. Research Scientist at KLA</p>
<p>● Jazlynn Tan, 2022. University of Toronto</p>
<p>● Jeeranan Boonruangkan, 2018-2022. Biofourmis</p>
<p>● Jie Lin Jolene Goh, 2016-2022. Veranome Biosystems</p>
<p>● Mike Jin-An Huang, 2018-2021. 1910 Genetics</p>
<p>● Paul Cheng, 2018-2021. Veranome Biosystems</p>
<p>● Kaviya Selva Raju, 2018-2020. Research Associate at Applied Materials</p>
<p>● Siyi Chen, 2018. Senior Scientist at Maiden Therapeutics</p>
<p>● Christabelle Goh, 2018. Scientist II at Applied Materials</p>
<p>● Ziqing, Winston Zhao, 2018-2019. Assistant Professor at National University of Singapore</p>
<p>● Teck Por Lim, 2018-2019.</p>
<p>● Mei Lun Chow, 2018. Project Officer at Nanyang Technological University</p>
</div>
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<h1 class="text-black">Publications</h1>
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<p><a href="https://www.nature.com/articles/s41467-024-46669-y" target="_blank">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.</a></p>
<p><a href="https://www.nature.com/articles/s41588-024-01664-3" target="_blank">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.</a></p>
<p><a href="https://www.nature.com/articles/s41592-020-0858-0" target="_blank">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.</a></p>
<p><a href="https://www.nature.com/articles/ng.3818" target="_blank">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).</a></p>
<p><a href="https://www.pnas.org/doi/10.1073/pnas.1612826113" target="_blank">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).</a></p>
<p><a href="https://www.science.org/doi/10.1126/science.aaa6090" target="_blank">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).</a></p>
<p><a href="https://pubs.acs.org/doi/10.1021/nn302779m" target="_blank">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).</a></p>
<p><a href="https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cphc.201100735" target="_blank">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).</a></p>
<p><a href="https://pubs.rsc.org/en/content/articlelanding/2011/lc/c0lc00644k" target="_blank">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).</a></p>
<p><a href="https://www.nature.com/articles/nmeth.1768" target="_blank">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).</a></p>
<p><a href="https://pubs.acs.org/doi/10.1021/ac101714u" target="_blank">Ishitsuka, Y., Okumus, B., Arslan, S., Chen,q K. H. & Ha, T. Temperature-independent porous nanocontainers for single-molecule fluorescence studies. Anal. Chem. 82, 9694–9701 (2010).</a></p>
<p><a href="https://pubs.acs.org/doi/10.1021/jp0765648" target="_blank">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).</a></p>
<p><a href="https://pubs.acs.org/doi/10.1021/ja066506k" target="_blank">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).</a></p>
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<p>We’re located on level 5 of the Genome Institute of Singapore, at the Biopolis research campus in the One-North area.</p>
<p>Our mailing address is: Genome Institute of Singapore (GIS), 60 Biopolis Street Level 5, Genome Building, Singapore 138672</p>
<p>Positions available.
Email:chenkh(at) gis.a-star.edu.sg</p>
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