Our Publications

2022

Wu, F., Xu, L., Tu, Y., Cheung, O. K., Szeto, L. L., Mok, M. T., Yang, W., Kang, W., Cao, Q., Lai, P. B., Chan, S. L., Tan, P., Sung, J. J., Yip, K. Y., Cheng, A. S., & To, K. F. (2022). Sirtuin 7 super-enhancer drives epigenomic reprogramming in hepatocarcinogenesis. Cancer letters, 525, 115–130. doi.org/10.1016/j.canlet.2021.10.039

Li, J., Du, P., Yang, L., Zhang, J., Song, C., Chen, D., Song, Y., Ding, N., Hua, M., Han, K., Song, R., Xie, W., Chen, Z., Wang, X., Liu, J., Xu, Y., Gao, G., Wang, Q., Pu, L., Di, L., Li, J., Yue, J., Han, J., Zhao, X., Yan, Y., Yu, F., Wu, A. R., Zhang, F., Gao, Y. Q., Huang, Y., Wang, J., Zeng, H., Chen, C. (2022). Two-step fitness selection for intra-host variations in SARS-CoV-2. Cell reports, 38(2), 110205. doi.org/10.1016/j.celrep.2021.110205

2021

Jiang, B., Mu, Q., Qiu, F., Li, X., Xu, W., Yu, J., Fu, W., Cao, Y., & Wang, J. (2021). Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors. Nature communications, 12(1), 6692. doi.org/10.1038/s41467-021-27017-w

Song, X., Aw, J., Ma, F., Cheung, M. F., Leung, D., & Herrup, K. (2021). DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response. The Journal of neuroscience : the official journal of the Society for Neuroscience, 41(45), 9286–9307. doi.org/10.1523/JNEUROSCI.0845-21.2021

Zhou, X., Sam, T. W., Lee, A. Y., & Leung, D. (2021). Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations. Nature communications, 12(1), 6462. doi.org/10.1038/s41467-021-26630-z

Huang, Y., Qiao, Y., Zhao, Y., Li, Y., Yuan, J., Zhou, J., Sun, H., & Wang, H. (2021). Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Briefings in bioinformatics, 22(6), bbab195. doi.org/10.1093/bib/bbab195

Yu, K. H., Shi, C. H., Wang, B., Chow, S. H., Chung, G. T., Lung, R. W., Tan, K. E., Lim, Y. Y., Tsang, A. C., Lo, K. W., & Yip, K. Y. (2021). Quantifying full-length circular RNAs in cancer. Genome research, 31(12), 2340–2353. Advance online publication. doi.org/10.1101/gr.275348.121

Li, H., Nam, Y., Huo, R., Fu, W., Jiang, B., Zhou, Q., Song, D., Yang, Y., Jiao, Y., Weng, J., Yan, Z., Di, L., Li, J., Wang, J., Xu, H., Wang, S., Zhao, J., Wen, Z., Wang, J., & Cao, Y. (2021). De Novo Germline and Somatic Variants Convergently Promote Endothelial-to-Mesenchymal Transition in Simplex Brain Arteriovenous Malformation. Circulation research, 129(9), 825–839. doi.org/10.1161/CIRCRESAHA.121.319004

He, L., Ding, Y., Zhao, Y., So, K. K., Peng, X. L., Li, Y., Yuan, J., He, Z., Chen, X., Sun, H., & Wang, H. (2021). CRISPR/Cas9/AAV9-mediated in vivo editing identifies MYC regulation of 3D genome in skeletal muscle stem cell. Stem cell reports, 16(10), 2442–2458. doi.org/10.1016/j.stemcr.2021.08.011

Olivieri, J. E., Dehghannasiri, R., Wang, P. L., Jang, S., de Morree, A., Tan, S. Y., Ming, J., Ruohao Wu, A., Tabula Sapiens Consortium, Quake, S. R., Krasnow, M. A., & Salzman, J. (2021). RNA splicing programs define tissue compartments and cell types at single-cell resolution. eLife, 10, e70692. doi.org/10.7554/eLife.70692

Wang, Y., Yang, Y., Chen, S., & Wang, J. (2021). DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration. Briefings in bioinformatics, 22(5), bbab048. doi.org/10.1093/bib/bbab048

Chen, X., Yuan, J., Xue, G., Campanario, S., Wang, D., Wang, W., Mou, X., Liew, S. W., Umar, M. I., Isern, J., Zhao, Y., He, L., Li, Y., Mann, C. J., Yu, X., Wang, L., Perdiguero, E., Chen, W., Xue, Y., Nagamine, Y., … Wang, H. (2021). Translational control by DHX36 binding to 5’UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nature communications, 12(1), 5043. doi.org/10.1038/s41467-021-25170-w

Kang, T., Zhu, L., Yang, D., Ding, D., Zhu, X., Wan, Y., Liu, J., Ramakrishnan, S., Chan, L. L., Chan, S. Y., Wang, X., Gan, H., Han, J., Ishibashi, T., Li, Q., & Chan, K. M. (2021). The elevated transcription of ADAM19 by the oncohistone H2BE76K contributes to oncogenic properties in breast cancer. The Journal of biological chemistry, 296, 100374. doi.org/10.1016/j.jbc.2021.100374

Wan, Y., & Chan, K. M. (2021). Histone H2B Mutations in Cancer. Biomedicines, 9(6), 694. doi.org/10.3390/biomedicines9060694

Wang, X., Yu, L., & Wu, A. R. (2021). The effect of methanol fixation on single-cell RNA sequencing data. BMC genomics, 22(1), 420. doi.org/10.1186/s12864-021-07744-6

Weng, J., Yang, Y., Song, D., Huo, R., Li, H., Chen, Y., Nam, Y., Zhou, Q., Jiao, Y., Fu, W., Yan, Z., Wang, J., Xu, H., Di, L., Li, J., Wang, S., Zhao, J., Wang, J., & Cao, Y. (2021). Somatic MAP3K3 mutation defines a subclass of cerebral cavernous malformation. American journal of human genetics, 108(5), 942–950. doi.org/10.1016/j.ajhg.2021.04.005

Chen, Y., Cheng, W. Y., Shi, H., Huang, S., Chen, H., Liu, D., Xu, W., Yu, J., & Wang, J. (2021). Classifying gastric cancer using FLORA reveals clinically relevant molecular subtypes and highlights LINC01614 as a biomarker for patient prognosis. Oncogene, 40(16), 2898–2909. doi.org/10.1038/s41388-021-01743-3

Mu, Q., & Wang, J. (2021). CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression. IEEE/ACM transactions on computational biology and bioinformatics, 18(1), 306–311. doi.org/10.1109/TCBB.2019.2944827

Loi, D., Yu, L., & Wu, A. R. (2021). Effective ribosomal RNA depletion for single-cell total RNA-seq by scDASH. PeerJ, 9, e10717. doi.org/10.7717/peerj.10717

Zhang, J., Ding, N., Ren, L., Song, R., Chen, D., Zhao, X., Chen, B., Han, J., Li, J., Song, Y., Di, L., Han, K., Yu, F., Xie, R., Chen, Z., Xie, W., Liu, J., Cen, S., Bi, Y., Wu, A. R., Zhang, F., Chen, C., Zeng, H. (2021). COVID-19 reinfection in the presence of neutralizing antibodies. National science review, 8(4), nwab006. doi.org/10.1093/nsr/nwab006

Lee, C., Cheung, M. F., Li, J., Zhao, Y., Lam, W. H., Ho, V., Rohs, R., Zhai, Y., Leung, D., & Tye, B. K. (2021). Humanizing the yeast origin recognition complex. Nature communications, 12(1), 33. doi.org/10.1038/s41467-020-20277-y

2020

Dong, A., Preusch, C. B., So, W. K., Lin, K., Luan, S., Yi, R., Wong, J. W., Wu, Z., & Cheung, T. H. (2020). A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression. Proceedings of the National Academy of Sciences of the United States of America, 117(51), 32464–32475. doi.org/10.1073/pnas.2005868117

Shi, C. H., & Yip, K. Y. (2020). A general near-exact k-mer counting method with low memory consumption enables de novo assembly of 106× human sequence data in 2.7 hours. Bioinformatics (Oxford, England), 36(Suppl_2), i625–i633. doi.org/10.1093/bioinformatics/btaa890

Chen, C., Li, J., Di, L., Jing, Q., Du, P., Song, C., Li, J., Li, Q., Cao, Y., Xie, X. S., Wu, A. R., Zeng, H., Huang, Y., & Wang, J. (2020). MINERVA: A Facile Strategy for SARS-CoV-2 Whole-Genome Deep Sequencing of Clinical Samples. Molecular cell, 80(6), 1123–1134.e4. doi.org/10.1016/j.molcel.2020.11.030

Fu, A. X., Lui, K. N., Tang, C. S., Ng, R. K., Lai, F. P., Lau, S. T., Li, Z., Garcia-Barcelo, M. M., Sham, P. C., Tam, P. K., Ngan, E. S., & Yip, K. Y. (2020). Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease. Genome research, 30(11), 1618–1632. doi.org/10.1101/gr.264473.120

Du, P., Ding, N., Li, J., Zhang, F., Wang, Q., Chen, Z., Song, C., Han, K., Xie, W., Liu, J., Wang, L., Wei, L., Ma, S., Hua, M., Yu, F., Wang, L., Wang, W., An, K., Chen, J., Liu, H., Gao, G., Wang, S., Huang, Y., Wu, A. R., Wang, J., Liu, D., Zeng, H., Chen, C. (2020). Genomic surveillance of COVID-19 cases in Beijing. Nature communications, 11(1), 5503. doi.org/10.1038/s41467-020-19345-0

Yue, L., & Cheung, T. H. (2020). Protocol for Isolation and Characterization of In Situ Fixed Quiescent Muscle Stem Cells. STAR protocols, 1(3), 100128. doi.org/10.1016/j.xpro.2020.100128

Jiang, Q., Ang, J., Lee, A. Y., Cao, Q., Li, K. Y., Yip, K. Y., & Leung, D. (2020). G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping. Cell reports, 33(4), 108315. doi.org/10.1016/j.celrep.2020.108315

Yi, W., Li, J., Zhu, X., Wang, X., Fan, L., Sun, W., Liao, L., Zhang, J., Li, X., Ye, J., Chen, F., Taipale, J., Chan, K. M., Zhang, L., & Yan, J. (2020). CRISPR-assisted detection of RNA-protein interactions in living cells. Nature methods, 17(7), 685–688. doi.org/10.1038/s41592-020-0866-0

Cao, Q., Zhang, Z., Fu, A. X., Wu, Q., Lee, T.-L., Lo, E., Cheng, A. S., Cheng, C., Leung, D., & Yip, K. Y. (2020). A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Nature Machine Intelligence, 2(8), 447–456. doi.org/10.1038/s42256-020-0205-2

Wan, Y., Liu, J., Zhu, L., Kang, T., Zhu, X., Lis, J., Ishibashi, T., Danko, C. G., Wang, X., & Chan, K. M. (2020). The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma. Signal transduction and targeted therapy, 5(1), 106. doi.org/10.1038/s41392-020-00219-2

Wan, Y., Leung, T., Ding, D., Sun, X., Liu, J., Zhu, L., Kang, T., Yang, D., Zhang, Y., Zhang, J., Qian, C., Huen, M., Li, Q., Chow, M., Zheng, Z., Han, J., Goel, A., Wang, X., Ishibashi, T., & Chan, K. M. (2020). Cancer-associated histone mutation H2BG53D disrupts DNA-histone octamer interaction and promotes oncogenic phenotypes. Signal transduction and targeted therapy, 5(1), 27. doi.org/10.1038/s41392-020-0131-0

Tan, S. Y., Leung, Z., & Wu, A. R. (2020). Recreating Physiological Environments In Vitro: Design Rules for Microfluidic-Based Vascularized Tissue Constructs. Small (Weinheim an der Bergstrasse, Germany), 16(9), e1905055. doi.org/10.1002/smll.201905055