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1. Epigenetic analysis of cell-free DNA by fragmentomic profiling

Author

Zhou, Qing, Kang, Guannan, Jiang, Peiyong, Qiao, Rong, Lam, W. K. Jacky, Yu, Stephanie C. Y., Ma, Mary-Jane L., Ji, Lu, Cheng, Suk Hang, Gai, Wanxia, Peng, Wenlei, Shang, Huimin, Chan, Rebecca W. Y., Chan, Stephen L., Wong, Grace L. H., Hiraki, Linda T., Volpi, Stefano, Wong, Vincent W. S., Wong, John, Chiu, Rossa W. K., Chan, K. C. Allen, and Lo, Y. M. Dennis

Published
2022

4. High-resolution analysis for urinary DNA jagged ends

Author

Xie, Tingting, Wang, Guangya, Ding, Spencer C., Lee, Wing-Shan, Cheng, Suk Hang, Chan, Rebecca W. Y., Zhou, Ze, Ma, Mary-Jane L., Han, Diana S. C., Teoh, Jeremy Y. C., Lam, W. K. Jacky, Jiang, Peiyong, Chiu, Rossa W. K., Chan, K. C. Allen, and Lo, Y. M. Dennis

Published
2022
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13. Supplementary Table 2 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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14. Supplementary Figure 1 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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15. Supplementary Figure Legends 1-3 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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16. Supplementary Figure 2 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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17. Data from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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18. Supplementary Figure 3 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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19. Supplementary Table 1 from A Novel 19q13 Nucleolar Zinc Finger Protein Suppresses Tumor Cell Growth through Inhibiting Ribosome Biogenesis and Inducing Apoptosis but Is Frequently Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Liang, Pei, primary, Geng, Hua, primary, Wang, Zhaohui, primary, Li, Lili, primary, Cheng, Suk Hang, primary, Ying, Jianming, primary, Su, Xianwei, primary, Ng, Ka Man, primary, Ng, Margaret H.L., primary, Mok, Tony S.K., primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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20. Data from KRAB Zinc Finger Protein ZNF382 Is a Proapoptotic Tumor Suppressor That Represses Multiple Oncogenes and Is Commonly Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Geng, Hua, primary, Cheng, Suk Hang, primary, Liang, Pei, primary, Bai, Yan, primary, Li, Jisheng, primary, Srivastava, Gopesh, primary, Ng, Margaret H.L., primary, Fukagawa, Tatsuo, primary, Wu, Xiushan, primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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21. Data from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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22. Supplementary Information from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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23. Supplementary Figure 2 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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24. Supplementary Figure 5 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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25. Supplementary Figure 4 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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26. Supplementary Figure Legends 1-6, Table 1 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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27. Supplementary Table 1 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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28. Supplementary Figure 3 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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29. Supplementary Table 1 from KRAB Zinc Finger Protein ZNF382 Is a Proapoptotic Tumor Suppressor That Represses Multiple Oncogenes and Is Commonly Silenced in Multiple Carcinomas

Author

Cheng, Yingduan, primary, Geng, Hua, primary, Cheng, Suk Hang, primary, Liang, Pei, primary, Bai, Yan, primary, Li, Jisheng, primary, Srivastava, Gopesh, primary, Ng, Margaret H.L., primary, Fukagawa, Tatsuo, primary, Wu, Xiushan, primary, Chan, Anthony T.C., primary, and Tao, Qian, primary

Published
2023
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30. Supplementary Figure 6 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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31. Supplementary Figure 1 from Sirtuin 1 Is Upregulated in a Subset of Hepatocellular Carcinomas where It Is Essential for Telomere Maintenance and Tumor Cell Growth

Author

Chen, Juan, primary, Zhang, Bin, primary, Wong, Nathalie, primary, Lo, Anthony W.I., primary, To, Ka-Fai, primary, Chan, Anthony W.H., primary, Ng, Margaret H.L., primary, Ho, Cecilia Y.S., primary, Cheng, Suk-Hang, primary, Lai, Paul B.S., primary, Yu, Jun, primary, Ng, Ho-Keung, primary, Ling, Ming-Tat, primary, Huang, Ai-Long, primary, Cai, Xue-Fei, primary, and Ko, Ben C.B., primary

Published
2023
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32. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

Author

Sun, Kun, Jiang, Peiyong, Chan, K. C. Allen, Wong, John, Cheng, Yvonne K. Y., Liang, Raymond H. S., Chan, Wai-kong, Ma, Edmond S. K., Chan, Stephen L., Cheng, Suk Hang, Chan, Rebecca W. Y., Tong, Yu K., Ng, Simon S. M., Wong, Raymond S. M., Hui, David S. C., Leung, Tse Ngong, Leung, Tak Y., Lai, Paul B. S., Chiu, Rossa W. K., and Lo, Yuk Ming Dennis

Published
2015

34. Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis

Author

Wang, Guangya, primary, Lam, W K Jacky, additional, Ling, Lowell, additional, Ma, Mary-Jane L, additional, Ramakrishnan, Saravanan, additional, Chan, Don C T, additional, Lee, Wing-Shan, additional, Cheng, Suk Hang, additional, Chan, Rebecca W Y, additional, Yu, Stephanie C Y, additional, Tse, Irene O L, additional, Wong, Wai Tat, additional, Jiang, Peiyong, additional, Chiu, Rossa W K, additional, Allen Chan, K C, additional, and Lo, Y M Dennis, additional

Published
2022
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35. Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma

Author

Yu, Stephanie C Y, primary, Deng, Jiaen, additional, Qiao, Rong, additional, Cheng, Suk Hang, additional, Peng, Wenlei, additional, Lau, So Ling, additional, Choy, L Y Lois, additional, Leung, Tak Y, additional, Wong, John, additional, Wong, Vincent Wai-Sun, additional, Wong, Grace L H, additional, Jiang, Peiyong, additional, Chiu, Rossa W K, additional, Chan, K C Allen, additional, and Lo, Y M Dennis, additional

Published
2022
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36. Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma

Author

Che, Huiwen, Jiang, Peiyong, Choy, L.Y. Lois, Cheng, Suk Hang, Peng, Wenlei, Chan, Rebecca W.Y., Liu, Jing, Zhou, Qing, Lam, W.K. Jacky, Yu, Stephanie C.Y., Lau, So Ling, Leung, Tak Y., Wong, John, Wong, Vincent Wai-Sun, Wong, Grace L.H., Chan, Stephen L., Chan, K.C. Allen, and Lo, Y.M. Dennis

Abstract

Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements. Analysis of plasma cfDNA using long-read sequencing reveals an uneven distribution of long molecules from across the genome. Long cfDNA molecules show overrepresentation in euchromatic regions of the genome, in sharp contrast to short DNA molecules. We observe a stronger relationship between the abundance of long molecules and mRNA gene expression levels, compared with short molecules (Pearson's r= 0.71 vs. −0.14). Moreover, long and short molecules show distinct fragmentation patterns surrounding CpG sites. Leveraging the cleavage preferences surrounding CpG sites, the combined cleavage ratios of long and short molecules can differentiate patients with hepatocellular carcinoma (HCC) from non-HCC subjects (AUC = 0.87). We also investigated knockout mice in which selected nuclease genes had been inactivated in comparison with wild-type mice. The proportion of long molecules originating from transcription start sites are lower in Dffb-deficient mice but higher in Dnase1l3-deficient mice compared with that of wild-type mice. This work thus provides new insights into the biological properties and potential clinical applications of long cfDNA molecules.

Published
2024
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38. Single-Molecule Sequencing Enables Long Cell-Free DNA Detection and Direct Methylation Analysis for Cancer Patients

Author

Choy, L Y Lois, primary, Peng, Wenlei, additional, Jiang, Peiyong, additional, Cheng, Suk Hang, additional, Yu, Stephanie C Y, additional, Shang, Huimin, additional, Olivia Tse, O Y, additional, Wong, John, additional, Wong, Vincent Wai Sun, additional, Wong, Grace L H, additional, Lam, W K Jacky, additional, Chan, Stephen L, additional, Chiu, Rossa W K, additional, Chan, K C Allen, additional, and Lo, Y M Dennis, additional

Published
2022
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40. Effects of nucleases on cell-free extrachromosomal circular DNA

Author

Sin, Sarah T.K., primary, Deng, Jiaen, additional, Ji, Lu, additional, Yukawa, Masashi, additional, Chan, Rebecca W.Y., additional, Volpi, Stefano, additional, Vaglio, Augusto, additional, Fenaroli, Paride, additional, Bocca, Paola, additional, Cheng, Suk Hang, additional, Wong, Danny K.L., additional, Lui, Kathy O., additional, Jiang, Peiyong, additional, Chan, K.C. Allen, additional, Chiu, Rossa W.K., additional, and Lo, Y.M. Dennis, additional

Published
2022
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45. Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma

Author

Vong, Joaquim S L, primary, Ji, Lu, additional, Heung, Macy M S, additional, Cheng, Suk Hang, additional, Wong, John, additional, Lai, Paul B S, additional, Wong, Vincent W S, additional, Chan, Stephen L, additional, Chan, Henry L Y, additional, Jiang, Peiyong, additional, Chan, K C Allen, additional, Chiu, Rossa W K, additional, and Lo, Y M Dennis, additional

Published
2021
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50. Additional file 3 of Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

Author

Liu, Lei, Wang, Yulin, Yang, Yu, Wang, Depeng, Cheng, Suk Hang, Zheng, Chunmiao, and Zhang, Tong

Abstract

Additional file 2: Methods. Fig. S1. Genome quality evaluation of hybrid assembly workflows. Fig. S2. Assemblies comparison among three activated sludge studies. Fig. S3. Phylogeny of the recovered 552 bacterial genomes in the Shatin activated sludge. Fig. S4. Taxonomic distribution of reconstructed high-quality/complete MAGs. Fig. S5. Metabolisms associate with sulfur cycle in the wastewater treatment plant. Fig. S6. Association networks between biosynthetic gene clusters and the corresponding lineages. Fig. S7. Distribution of the biosynthetic gene clusters identified across the dominant taxonomic groups. Fig. S8. Association networks between genomes with (a) / without (b) identified antibiotic resistance genes and the diverse biosynthetic gene clusters.

Published
2021
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