Searching journal content for articles similar to Jiang et al. 22 (4): 593.

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  1. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ..., Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China 200438 ↵7 These authors contributed equally to this work. Corresponding author: hongliyan@smmu.edu.cnAbstractHepatitis B virus (HBV) integration is a key driver of hepatocellular carcinoma (HCC) occurrence and progression...
  2. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    ...↵3 These authors equally contributed to this work. Corresponding author: danxie@scu.edu.cnAbstractSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high...
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  3. Editorial: Long reads decipher genomes and transcriptomes and offer novel insights into biology and diseases
    • Ana Conesa,
    • Alexander Hoischen,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: xi-xiv; doi:10.1101/gr.280665.125
    ...-specific effects on splicing in human lymphoblastoid cell lines. Zeng et al. (2025) demonstrate a combined DNA and RNA analysis in hepatitis B virus-driven hepatocellular carcinoma that examines the transcriptional consequences of somatically integrated viral DNA, including fusion gene detection. Wang et al. (2025...
  4. Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
    • Kosuke Hashimoto,
    • Ana Maria Suzuki,
    • Alexandre Dos Santos,
    • Christophe Desterke,
    • Agnese Collino,
    • Serena Ghisletti,
    • Emilie Braun,
    • Alessandro Bonetti,
    • Alexandre Fort,
    • Xian-Yang Qin,
    • Enrico Radaelli,
    • Bogumil Kaczkowski,
    • Alistair R.R. Forrest,
    • Soichi Kojima,
    • Didier Samuel,
    • Gioacchino Natoli,
    • Marie Annick Buendia,
    • Jamila Faivre,
    • and Piero Carninci
    Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
    ...CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors Kosuke Hashimoto 1 , Ana Maria Suzuki 1 , Alexandre Dos Santos 2 , 3 , Christophe Desterke 2 , 3 , Agnese...
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  5. Research: Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma
    • Zhengyan Kan,
    • Hancheng Zheng,
    • Xiao Liu,
    • Shuyu Li,
    • Thomas D. Barber,
    • Zhuolin Gong,
    • Huan Gao,
    • Ke Hao,
    • Melinda D. Willard,
    • Jiangchun Xu,
    • Robert Hauptschein,
    • Paul A. Rejto,
    • Julio Fernandez,
    • Guan Wang,
    • Qinghui Zhang,
    • Bo Wang,
    • Ronghua Chen,
    • Jian Wang,
    • Nikki P. Lee,
    • Wei Zhou,
    • Zhao Lin,
    • Zhiyu Peng,
    • Kang Yi,
    • Shengpei Chen,
    • Lin Li,
    • Xiaomei Fan,
    • Jie Yang,
    • Rui Ye,
    • Jia Ju,
    • Kai Wang,
    • Heather Estrella,
    • Shibing Deng,
    • Ping Wei,
    • Ming Qiu,
    • Isabella H. Wulur,
    • Jiangang Liu,
    • Mariam E. Ehsani,
    • Chunsheng Zhang,
    • Andrey Loboda,
    • Wing Kin Sung,
    • Amit Aggarwal,
    • Ronnie T. Poon,
    • Sheung Tat Fan,
    • Jun Wang,
    • James Hardwick,
    • Christoph Reinhard,
    • Hongyue Dai,
    • Yingrui Li,
    • John M. Luk,
    • and Mao Mao
    Genome Res. September 2013 23: 1422-1433; Published in Advance June 20, 2013, doi:10.1101/gr.154492.113
    ...Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma Zhengyan Kan 1 , 13 , Hancheng Zheng 2 , 13 , Xiao Liu 2 , 3 , 13 , Shuyu Li 4 , 13 , Thomas D. Barber 4 , Zhuolin Gong 2 , Huan Gao...
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  6. Research: DNA methylation at hepatitis B viral integrants is associated with methylation at flanking human genomic sequences
    • Yoshiyuki Watanabe,
    • Hiroyuki Yamamoto,
    • Ritsuko Oikawa,
    • Minoru Toyota,
    • Masakazu Yamamoto,
    • Norihiro Kokudo,
    • Shinji Tanaka,
    • Shigeki Arii,
    • Hiroshi Yotsuyanagi,
    • Kazuhiko Koike,
    • and Fumio Itoh
    Genome Res. March 2015 25: 328-337; Published in Advance February 4, 2015, doi:10.1101/gr.175240.114
    ...of Tokyo, Tokyo 113-8655, Japan Integration of DNA viruses into the human plays an important role in various types of tumors, including hepatitis B virus (HBV)–related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epis are unknown...
  7. Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
    • Huiwen Che,
    • Peiyong Jiang,
    • L.Y. Lois Choy,
    • Suk Hang Cheng,
    • Wenlei Peng,
    • Rebecca W.Y. Chan,
    • Jing Liu,
    • Qing Zhou,
    • W.K. Jacky Lam,
    • Stephanie C.Y. Yu,
    • So Ling Lau,
    • Tak Y. Leung,
    • John Wong,
    • Vincent Wai-Sun Wong,
    • Grace L.H. Wong,
    • Stephen L. Chan,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
    ...carcinoma (HCC) from subjects without HCC. Thus, we collected SMRT sequencing data using plasma samples from 20 healthy individuals, 19 hepatitis B virus (HBV) carriers, and 48 patients with HCC (Supplemental Table S2). Median values of 1,021,412, 286,492, and 712,223 high-quality circular consensus...
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  8. Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
    • Stephanie N. Schauer,
    • Patricia E. Carreira,
    • Ruchi Shukla,
    • Daniel J. Gerhardt,
    • Patricia Gerdes,
    • Francisco J. Sanchez-Luque,
    • Paola Nicoli,
    • Michaela Kindlova,
    • Serena Ghisletti,
    • Alexandre Dos Santos,
    • Delphine Rapoud,
    • Didier Samuel,
    • Jamila Faivre,
    • Adam D. Ewing,
    • Sandra R. Richardson,
    • and Geoffrey J. Faulkner
    Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
    ...malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole...
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  9. Research: Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors
    • Mi Ni Huang,
    • Willie Yu,
    • Wei Wei Teoh,
    • Maude Ardin,
    • Apinya Jusakul,
    • Alvin Wei Tian Ng,
    • Arnoud Boot,
    • Behnoush Abedi-Ardekani,
    • Stephanie Villar,
    • Swe Swe Myint,
    • Rashidah Othman,
    • Song Ling Poon,
    • Adriana Heguy,
    • Magali Olivier,
    • Monica Hollstein,
    • Patrick Tan,
    • Bin Tean Teh,
    • Kanaga Sabapathy,
    • Jiri Zavadil,
    • and Steven G. Rozen
    Genome Res. September 2017 27: 1475-1486; Published in Advance July 24, 2017, doi:10.1101/gr.220038.116
    ...that are produced by molds growing in grain, peanuts, or other food. Aflatoxin exposure is thought to be a major public health risk in parts of Africa and Asia, partly by synergizing with hepatitis B to dramatically increase risk of hepatocellular carcinoma (HCC) (Kensler et al. 2003; IARC Working Group...
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  10. Method: Detection and characterization of jagged ends of double-stranded DNA in plasma
    • Peiyong Jiang,
    • Tingting Xie,
    • Spencer C. Ding,
    • Ze Zhou,
    • Suk Hang Cheng,
    • Rebecca W.Y. Chan,
    • Wing-Shan Lee,
    • Wenlei Peng,
    • John Wong,
    • Vincent W.S. Wong,
    • Henry L.Y. Chan,
    • Stephen L. Chan,
    • Liona C.Y. Poon,
    • Tak Y. Leung,
    • K.C. Allen Chan,
    • Rossa W.K. Chiu,
    • and Y.M. Dennis Lo
    Genome Res. August 2020 30: 1144-1153; Published in Advance August 14, 2020, doi:10.1101/gr.261396.120
    ...analyzed a cohort in a previously published study (Jiang et al. 2020), consisting of healthy control subjects (n = 8), patients infected with chronic hepatitis B virus (HBV, n = 17), and patients with hepatocellular carcinoma (HCC, n = 34), using bisulfite sequencing. This experimental protocol involved...
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