Publications

2024

  • 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* (2024) Single-cell transcriptomic analysis of the immune microenvironment in pediatric acute leukemia Cancer Letters
    • [Paper]
  • Xiaochuan Liu^, Wen Jin^, Dengyi Bao, Tongxin He, Wenhui Wang, Zekun Li, Xiaoxiao Yang, Yang Tong, Meng Shu, Yuting Wang, Jiapei Yuan, Yang Yang (2024) DIPAN: Detecting personalized intronic polyadenylation derived neoantigens from RNA sequencing data. Computational and Structural Biotechnology Journal 23, 2057-2066
    • [Paper][Code]
  • Xiaochuan Liu^, Hao Chen^, Zekun Li, Xiaoxiao Yang, Wen Jin, Yuting Wang, Jian Zheng, Long Li, Chenghao Xuan*, Jiapei Yuan*, Yang Yang* (2024) InPACT: A computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nature Communications 15:2583
    • [Paper] [Code]
  • Yuting Wang*, Meng Shu, Tianqiang Wang, Tongxin He, Jiapei Yuan, Yang Yang* (2024) Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers. Int J Cancer doi: 10.1002/ijc.34955
    • [Paper]
  • Zekun Li^, Gerui Liu^, Xiaoxiao Yang^, Meng Shu, Wen Jin, Yang Tong, Xiaochuan Liu, Yuting Wang, Jiapei Yuan*,Yang Yang* (2024) An atlas of cell-type-specific interactome networks across 44 human tumor types. Genome Medicine 16(1):30
    • [Paper][Website]

 

 

2023

  • Yanhong Zhang^, Xiaoxiao Yang^, Mei Lan, Ze Yuan, Shuai Li, Yangping Liu, Cha Han, Ding Ai, Yang Yang*, Yi Zhu*, Bochuan Li* (preprint) Regulation of blood pressure by METTL3 via RUNX1b-eNOS pathway in endothelial cells. bioRxiv
    • [Paper]
  • Yan Li^, Hongyan Liu^, Shuting Ye, Bumei Zhang, Xiaopei Li, Jiapei Yuan, Yongrui Du, Jianmei Wang*, Yang Yang* (2023) The effects of coagulation factors on the risk of endometriosis: A Mendelian randomization study. BMC Medicine 21:195
    • [Paper]
  • Jiapei Yuan^, Yang Tong^, Xiaochuan Liu, Mulin Jun Li, Qiang Zhang*, Yang Yang* (2023) eaQTLdb: An atlas of enhancer activity quantitative trait loci across cancer types. Int J Cancer 153(1):111-119
    • [Paper] [Website]

 

 

2022

  • Jiapei Yuan, Kathleen E. Houlahan, Susmita G. Ramanand, Guemhee Baek, Yang Yang, Yong Chen, Douglas W. Strand, Michael Q. Zhang, Paul C. Boutros, Sora Lee, Ram S. Mani* (2022) Prostate Cancer transcriptomic regulation by germline risk alleles, somatic mutations and 3D-genomic architecture. Cancer Discovery 12(12):2838-2855
  • Haipeng Fu, Tingyu Wang, Xiaohui Kong, Kun Yan, Yang Yang, Jingyi Cao, Yafei Yuan, Nan Wang, Kehkooi Kee, Zhi John Lu, Qiaoran Xi* (2022) A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nature Communications 13(1):3984
  • Xiaoxiao Yang^, Yang Tong^, Gerui Liu^, Jiapei Yuan, Yang Yang (2022) scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse. Nucleic Acids Research 50(D1):D356-D364
    • [Paper] [Website]

 

 

2021

  • Yang Yang, Paul Anirban, Thao-Nguyen Bach, Z. Josh Huang, Michael Q. Zhang* (2021) Single-cell alternative polyadenylation analysis delineates GABAergic neuron types BMC Biology 19,144
    • [Paper] [Code]

 

 

Before 2021

  • 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 and Zhi John Lu (2017) Recurrently deregulated lncRNAs in hepatocellular carcinoma. Nature Communications 8, 14421
  • Yang Yang, Yu-Cheng T. Yang, Jiapei Yuan, Zhi John Lu, Jingyi Jessica Li (2017) Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states. Nucleic Acids Research 45(4):1657-1672
  • Hao Du, Chen Chen, Yan Wang, Yang Yang, Zhuanzhuan Che, Xiaoxu Liu, Siyan Meng, Chenghao Guo, Manman Xu, Haitong Fang, Fengchao Wang, Chengqi Lin, Zhuojuan Luo RNF219 interacts with CCR4–NOT in regulating stem cell differentiation Journal of Molecular Cell Biology 12(11):894-905
  • Maoguo Luo, Jianbo Bai, Bofeng Liu, Peiqiang Yan, Feifei Zuo, Hongyao Sun, Ye Sun, Xuanhao Xu, Zhihong Song, Yang Yang, Joan Massagué, Xun Lan, Zhi Lu, Ye-Guang Chen, Haiteng Deng, Wei Xie, Qiaoran Xi (2019) H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling. Stem Cell Reports 13(4):642-656
  • Jiapei Yuan, Jingrui Li, Yang Yang, Chang Tan, Yumin Zhu, Long Hu, Yijun Qi, Zhi John Lu (2018) Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa Plant Journal 93(5):814-827
  • Xiaochen Xi, Tianxiao Li, Yiming Huang, Jiahui Sun, Yumin Zhu, Yang Yang and Zhi John Lu (2017) RNA Biomarkers: Frontier of Precision Medicine for Cancer. Non-coding RNA 3, 9
  • Dan Gao, Yingjie Han, Yang Yang, James G Herman, Enqiang Linghu, Qimin Zhan, François Fuks, Zhi John Lu, Mingzhou Guo (2017) Methylation of TMEM176A is an independent prognostic marker and is involved in human colorectal cancer development. Epigenetics 12(7):575-583
  • 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 and Kui Li (2017) Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa. Scientific Reports 7:43166