PUBLICATIONS
Selected Publications
Chai, H., Tjong, H., Li, P., Liao, W., Wang, P., Wong, C.H., Ngan, C.Y., Leonard, W.J., Wei, C.-L., and Ruan, Y. (2023). ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. Nature Communications 14, 213.
Zheng, M., Tian, S.Z., Capurso, D., Kim, M., Maurya, R., Lee, B., Piecuch, E., Gong, L., Zhu, J.J., Li, Z., Wong, C.H., Ngan, C.Y., Wang, P., Ruan, X., Wei, C.-L., and Ruan, Y. (2019). Multiplex chromatin interactions with single-molecule precision. Nature 566, 558-562.
Tang, Z., Luo, Oscar J., Li, X., Zheng, M., Zhu, Jacqueline J., Szalaj, P., Trzaskoma, P., Magalska, A., Wlodarczyk, J., Ruszczycki, B., Michalski, P., Piecuch, E., Wang, P., Wang, D., Tian, Simon Z., Penrad-Mobayed, M., Sachs, Laurent M., Ruan, X., Wei, C.-L., Liu, Edison T., Wilczynski, Grzegorz M., Plewczynski, D., Li, G., and Ruan, Y. (2015). CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell 163, 1611-1627.
Kieffer-Kwon, K.-R., Tang, Z., Mathe, E., Qian, J., Sung, M.-H., Li, G., Resch, W., Baek, S., Pruett, N., Grøntved, L., Vian, L., Nelson, S., Zare, H., Hakim, O., Reyon, D., Yamane, A., Nakahashi, H., Kovalchuk, Alexander L., Zou, J., Joung, J.K., Sartorelli, V., Wei, C.-L., Ruan, X., Hager, Gordon L., Ruan, Y., and Casellas, R. (2013). Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation. Cell 155, 1507-1520.
Li, G., Ruan, X., Auerbach, Raymond K., Sandhu, Kuljeet S., Zheng, M., Wang, P., Poh, Huay M., Goh, Y., Lim, J., Zhang, J., Sim, Hui S., Peh, Su Q., Mulawadi, Fabianus H., Ong, Chin T., Orlov, Yuriy L., Hong, S., Zhang, Z., Landt, S., Raha, D., Euskirchen, G., Wei, C.-L., Ge, W., Wang, H., Davis, C., Fisher-Aylor, K.I., Mortazavi, A., Gerstein, M., Gingeras, T., Wold, B., Sun, Y., Fullwood, Melissa J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., and Ruan, Y. (2012). Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell 148, 84-98.
Handoko, L., Xu, H., Li, G., Ngan, C.Y., Chew, E., Schnapp, M., Lee, C.W.H., Ye, C., Ping, J.L.H., Mulawadi, F., Wong, E., Sheng, J., Zhang, Y., Poh, T., Chan, C.S., Kunarso, G., Shahab, A., Bourque, G., Cacheux-Rataboul, V., Sung, W.-K., Ruan, Y., and Wei, C.-L. (2011). CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genetics 43, 630-638.
Ruan, Y. (2011). Presenting the Human Genome: Now in 3D! Science 331, 1025-1026.
Fullwood, M.J., Liu, M.H., Pan, Y.F., Liu, J., Xu, H., Mohamed, Y.B., Orlov, Y.L., Velkov, S., Ho, A., Mei, P.H., Chew, E.G.Y., Huang, P.Y.H., Welboren, W.-J., Han, Y., Ooi, H.S., Ariyaratne, P.N., Vega, V.B., Luo, Y., Tan, P.Y., Choy, P.Y., Wansa, K.D.S.A., Zhao, B., Lim, K.S., Leow, S.C., Yow, J.S., Joseph, R., Li, H., Desai, K.V., Thomsen, J.S., Lee, Y.K., Karuturi, R.K.M., Herve, T., Bourque, G., Stunnenberg, H.G., Ruan, X., Cacheux-Rataboul, V., Sung, W.-K., Liu, E.T., Wei, C.-L., Cheung, E., and Ruan, Y. (2009). An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58-64.
Wei, C.-L., Wu, Q., Vega, V.B., Chiu, K.P., Ng, P., Zhang, T., Shahab, A., Yong, H.C., Fu, Y., Weng, Z., Liu, J., Zhao, X.D., Chew, J.-L., Lee, Y.L., Kuznetsov, V.A., Sung, W.-K., Miller, L.D., Lim, B., Liu, E.T., Yu, Q., Ng, H.-H., and Ruan, Y. (2006). A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome. Cell 124, 207-219.