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Publications

Publications on PubMed and Google Scholar

#(co-)first-author; *(co-)corresponding author.



2024

21. Jiapei Yuan#*, Yang Tong#, Le Wang, Xiaoxiao Yang, Xiaochuan Liu, Meng Shu, Zekun Li, Wen Jin, Chenchen Guan, Yuting Wang, Qiang Zhang*, Yang Yang*. A compendium of genetic variations associated with promoter usage across 49 human tissues. Nature Communications. 2024 Oct 9;15(1):8758.

20. Jiapei Yuan#*, Jingliao Zhang#, Beibei Zhao, Fang Liu, Tianfeng Liu, Yongjuan Duan, Yumei Chen, Xiaojuan Chen, Yao Zou, Li Zhang, Ye Guo, Wenyu Yang, Yang Yang, Jun Wei*, Xiaofan Zhu*, Yingchi Zhang*. Single-cell transcriptomic analysis of the immune microenvironment in pediatric acute leukemia. Cancer Letters. 2024 Jun 4:217018.

19. Xiaochuan Liu#, Wen Jin#, Dengyi Bao, Tongxin He, Wenhui Wang, Zekun Li, Xiaoxiao Yang, Yang Tong, Meng Shu, Yuting Wang, Jiapei Yuan, Yang Yang*. DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data. Computational and Structural Biotechnology Journal. 2024 Dec;23:2057-2066.

18. Xiaochuan Liu#, Hao Chen#, Zekun Li, Xiaoxiao Yang, Wen Jin, Yuting Wang, Jian Zheng, Long Li, Chenghao Xuan, Jiapei Yuan*, Yang Yang*. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nature Communications. 2024 Mar 22;15(1):2583.

17. Zekun Li#, Gerui Liu#, XiaoXiao Yang#, Meng Shu, Wen Jin, Yang Tong, Xiaochuan Liu, Yuting Wang, Jiapei Yuan*, Yang Yang*. An atlas of cell-type-specific interactome networks across 44 human tumor types. Genome Medicine. 2024 Feb 12;16(1):30.

16. Ahmed Abbas, Khyati Chandratre, Yunpeng Gao, Jiapei Yuan, Michael Q. Zhang*, Ram S. Mani*. ChIPr: accurate prediction of cohesin‑mediated 3D genome organization from 2D chromatin features. Genome Biology. 2024 Jan 12;25(1):15.

15. Yuting Wang*, Meng Shu, Tianqiang Wang, Tongxin He, Jiapei Yuan, Yang Yang*. Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers. International Journal of Cancer. 2024 Apr 13. doi: 10.1002/ijc.34955. Online ahead of print.



2023

14. Jiapei Yuan#, Yang Tong#, Xiaochuan Liu, Mulin Jun Li, Qiang Zhang*, Yang Yang*. eaQTLdb: An atlas of enhancer activity quantitative trait loci across cancer types. International Journal of Cancer. 2023 Jul 1;153(1):111-119.

13. Yan Li#, Hongyan Liu#, Shuting Ye, Bumei Zhang, Xiaopei Li, Jiapei Yuan, Yongrui Du, Jianmei Wang*, Yang Yang*. The effects of coagulation factors on the risk of endometriosis: a Mendelian randomization study. BMC Medicine. 2023 May 25;21(1):195.



2022

12. Jiapei Yuan, Kathleen E Houlahan, Susmita G Ramanand, Sora Lee, GuemHee Baek, Yang Yang, Yong Chen, Douglas W Strand, Michael Q Zhang, Paul C Boutros, Ram S Mani*. Prostate cancer transcriptomic regulation by the interplay of germline risk alleles, somatic mutations and 3D-genomic architecture. Cancer Discovery. 2022, Dec 2;12(12):2838-2855.

11. Xiaoxiao Yang#, Yang Tong#, Gerui Liu#, Jiapei Yuan, Yang Yang*. scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse. Nucleic Acids Research. 2022 Jan 7;50(D1):D356-D364.



2020

10. Susmita G Ramanand#, Yong Chen#, Jiapei Yuan#, Kelly Daescu, Maryou Bk Lambros, Kathleen E Houlahan, Suzanne Carreira, Wei Yuan, GuemHee Baek, Adam Sharp, Alec Paschalis, Mohammed Kanchwala, Yunpeng Gao, Adam Aslam, Nida Safdar, Xiaowei Zhan, Ganesh V Raj, Chao Xing, Paul C Boutros, Johann de Bono, Michael Q Zhang*, Ram S Mani*. The Landscape of RNA Polymerase II Associated Chromatin Interactions in Prostate Cancer. Journal of Clinical investigation. 2020 Aug 3;130(8):3987-4005.



2019

9. Kathleen E Houlahan, Yu-Jia Shiah, Alexander Gusev, Jiapei Yuan, Musaddeque Ahmed, Anamay Shetty, Susmita G Ramanand, Cindy Q Yao, Connor Bell, Edward O'Connor, Vincent Huang, Michael Fraser, Lawrence E Heisler, Julie Livingstone, Takafumi N Yamaguchi, Alexandre Rouette, Adrien Foucal, Shadrielle Melijah G Espiritu, Ankit Sinha, Michelle Sam, Lee Timms, Jeremy Johns, Ada Wong, Alex Murison, Michèle Orain, Valérie Picard, Hélène Hovington, Alain Bergeron, Louis Lacombe, Mathieu Lupien, Yves Fradet, Bernard Têtu, John D McPherson, Bogdan Pasaniuc, Thomas Kislinger, Melvin L K Chua, Mark M Pomerantz, Theodorus van der Kwast, Matthew L Freedman, Ram S Mani, Housheng H He, Robert G Bristow, Paul C Boutros*. Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Nature Medicine. 2019 Oct;25(10):1615-1626.

8. Qian Zheng, Peipei Liu, Ge Gao, Jiapei Yuan, Pengfeng Wang, Jinliang Huang, Leiming Xie, Xinping Lu, Fan Di, Tanjun Tong, Jun Chen, Zhi Lu, Jisong Guan, Geng Wang*. Mitochondrion-processed TERC regulates senescence without affecting telomerase activities. Protein & Cell. 2019 Sep;10(9):631-648.



2018

7. Jiapei Yuan#, Jingrui Li#, Yang Yang, Chang Tan, Yumin Zhu, Long Hu, Yijun Qi*, Zhi John Lu*. Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. The Plant Journal. 2018 Mar;93(5):814-827.

6. Ying Cheng, Peipei Liu, Qian Zheng, Ge Gao, Jiapei Yuan, Pengfeng Wang, Jinliang Huang, Leiming Xie, Xinping Lu, Tanjun Tong, Jun Chen, Zhi Lu, Jisong Guan, Geng Wang*. Mitochondrial trafficking and processing of telomerase RNA TERC. Cell Reports. 2018 Sep 4;24(10):2589-2595.



2017

5. Yang Yang#, Lei Chen#, Jin Gu#, Hanshuo Zhang#, Jiapei Yuan, Qiuyu Lian, Guishuai Lv, Siqi Wang, Yang Wu, Yu-Cheng T Yang, Dongfang Wang, Yang Liu, Jing Tang, Guijuan Luo, Yang Li, Long Hu, Xinbao Sun, Dong Wang, Mingzhou Guo, Qiaoran Xi, Jianzhong Xi, Hongyang Wang, Michael Q Zhang*, Zhi John Lu*. Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications. 2017 Feb 13;8:14421. (ESI highly cited paper).

4. Yang Yang#, Yu-Cheng T Yang#, Jiapei Yuan, Zhi John Lu*, Jingyi Jessica Li*. Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states. Nucleic Acids Research. 2017 Feb 28;45(4):1657-1672.

3. Zhonglin Tang#, Yang Wu#, Yalan Yang, Yu-Cheng T Yang, Zishuai Wang, Jiapei Yuan, Yang Yang, Chaoju Hua, Xinhao Fan, Guanglin Niu, Yubo Zhang, Zhi John Lu*, Kui Li*. Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa. Scientific Reports. 2017 Feb 24;7:43166.



2016

2. Jiapei Yuan#, Ye Zhang#, Jinsong Dong, Yuzhe Sun, Boon L Lim, Dong Liu*, Zhi John Lu*. Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana. BMC Genomics. 2016 Aug 18;17:655.



2014

1. Chao Di#, Jiapei Yuan#, Yue Wu, Jingrui Li, Huixin Lin, Long Hu, Ting Zhang, Yijun Qi, Mark B Gerstein, Yan Guo, Zhi John Lu*. Characterization of stress-responsive lncRNA in Arabidopsis Thaliana by integrating expression, epigenetic and structural features. The Plant Journal. 2014 Dec;80(5):848-61. (ESI highly cited paper, in the top 1% of the academic field of Plant & Animal Science).