Article
Medicine, General & Internal
Ming-Wang Zhang, Zhi-Hong Zhu, Zhi-Kuan Xia, Xin Yang, Wan-Ting Luo, Jun-Hong Ao, Rong-Ya Yang
Summary: Invasive Trichosporon asahii infection in immunodeficient hosts often leads to high mortality, but the pathogenesis is still unknown. This study identified a circRNA-associated competing endogenous RNA network during T. asahii infection, shedding light on the interaction between T. asahii and host cells.
MILITARY MEDICAL RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Yining Liu, Lei Chen, Tianqi Liu, Xiangqian Su, Lin Peng, Jiangbo Chen, Fei Tan, Pu Xing, Zaozao Wang, Jiabo Di, Beihai Jiang, Hong Qu
Summary: This study identified 694 circRNA-mRNA pairs in colorectal cancer patients, showing the regulatory roles between circular RNAs and their corresponding mRNAs, with some of them associated with patient survival time.
Article
Oncology
Daiwei Wan, Sentai Wang, Zhihua Xu, Xinquan Zan, Fei Liu, Ye Han, Min Jiang, Airong Wu, Qiaoming Zhi
Summary: This study identified differentially expressed circRNAs and mRNAs in mouse colitis and colitis-associated cancer models through RNA-seq analysis, revealing associations of mmu_circ_0001109 with pro-inflammatory signals and mmu_circ_0001845 with the Wnt signaling pathway. Further analysis showed that human PRKAR2A-derived circRNAs may serve as potential biomarkers for distinguishing and predicting the prognosis of colitis-associated cancer patients.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Caili Li, Meizhen Wang, Xiaoxiao Qiu, Hong Zhou, Shanfa Lu
Summary: This review highlights the regulatory roles of herbal ncRNAs in bioactive compound production. Thousands of miRNA candidates and hundreds of lncRNAs have been identified, with some miRNAs and lncRNAs predicted to regulate the production of bioactive compounds. Further functional analysis of herbal ncRNAs will contribute to the improvement of medicinal plants in terms of quality and quantity.
CURRENT PHARMACEUTICAL BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Pablo Acera Mateos, You Zhou, Kathi Zarnack, Eduardo Eyras
Summary: The development of new high-throughput techniques has played a crucial role in discovering the properties of RNA modifications with the help of machine learning. Despite the challenges, this review provides a comprehensive survey of machine learning methods for detecting RNA modifications and strategies for training and testing these methods. The review also highlights current challenges and open questions in RNA modification analysis, and emphasizes the potential of machine learning in addressing these limitations.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Yaojia Chen, Jiacheng Wang, Chuyu Wang, Mingxin Liu, Quan Zou
Summary: This article introduces deep learning methods for predicting circRNA-disease associations and analyzes the advantages and limitations of seven representative models. Deep learning technology shows great potential for disease diagnosis and treatment.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Jianshi Jin, Taisaku Ogawa, Nozomi Hojo, Kirill Kryukov, Kenji Shimizu, Tomokatsu Ikawa, Tadashi Imanishi, Taku Okazaki, Katsuyuki Shiroguchi
Summary: Developed a multifunctional robot system ALPS for single-cell RNA sequencing of cells observed under multiple imaging modes. Successfully predicted transcriptome-defined cell phenotypes using cell image-based deep learning. This work provides a new approach to determine live-cell whole transcriptome in real time.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shidong Cui, Yijun Luo, Xiaoxuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Fengxiang Wei, Tzong-Yi Lee, Hsien-Da Huang
Summary: circRNAs, important molecules in cancer diagnosis, act as sponges of microRNAs to regulate transcription and translation. The updated CircNet database integrates circRNAs from various sources and predicts target miRNAs to construct high-quality circRNA-miRNA-gene regulatory networks, providing strong data support in the biomedical fields.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: The paper proposes a multi-view contrastive learning model, DeepMCL, for inferring gene regulatory networks from scRNA-seq data. By utilizing a deep Siamese convolutional neural network and attention mechanism, the model integrates information from multiple data sources, improving the accuracy of network inference.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Zerun Lin, Le Ou-Yang
Summary: In this paper, a multi-view contrastive learning model (DeepMCL) is proposed to infer gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data collected from multiple data sources or time points. The experimental results validate the effectiveness of our contrastive learning and attention mechanisms, demonstrating the effectiveness of our model in integrating multiple data sources for GRN inference.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Cell Biology
Andrew Willems, Nicholas Panchy, Tian Hong
Summary: Recent research has shown the significance of microRNA (miRNA) in the development and spread of colorectal cancer. In this study, a miRNA-based metric was developed using validated miRNA-gene target interactions associated with colorectal cancer. By applying this metric with a Cox model, a small set of top-performing genes related to colon cancer was identified. The results demonstrated that the use of the miRNA metric and Cox model significantly improved colon cancer survival prediction and accurately stratified patient risk. Furthermore, the top genes identified were implicated in NOTCH3 signaling and general metabolism pathways, which are crucial in colon cancer progression.
Article
Genetics & Heredity
Xiao-Mao Tian, Bin Xiang, Zhao-Xia Zhang, Yan-Ping Li, Qin-Lin Shi, Mu-Jie Li, Qi Li, Yi-Hang Yu, Peng Lu, Feng Liu, Xing Liu, Tao Lin, Da-Wei He, Guang-Hui Wei
Summary: This study provides insights into the expression profiles and downstream regulatory mechanisms of circRNAs in Wilms tumor, as well as their associations with immune response. The constructed circRNA-miRNA-mRNA network and immune-related prognostic signature improve our understanding of tumor development and progression, and facilitate individualized treatment.
FRONTIERS IN GENETICS
(2022)
Article
Immunology
Ronald J. J. Nowling, Kimani Njoya, John G. G. Peters, Michelle M. M. Riehle
Summary: Various sequencing techniques are used to identify and characterize cis-regulatory elements in the genome. Machine learning models are employed to predict the activity of these elements based on their underlying DNA sequence. DNase-seq and STARR-seq provide more accurate predictions compared to other techniques, suggesting that their activity is largely determined by DNA sequence.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Cell Biology
Xiuchao Geng, Yuhao Zhang, Qiang Li, Wang Xi, Wentao Yu, Liang Shi, Xiaomeng Lin, Shaoguang Sun, Hong Wang
Summary: The study found that 4 circRNAs could be associated with different pathological grades of glioma, serving as potential therapeutic targets.
Article
Cell Biology
Lei Gao, Xiaolong Tang, Qingsi He, Guorui Sun, Chao Wang, Hui Qu
Summary: In this study, we found that the upregulation of circCOG2 in colorectal cancer (CRC) promoted tumor proliferation, migration, and invasion through the miR-1305/TGF-beta 2/SMAD3 pathway. Furthermore, the effect of circCOG2 could be transmitted via exosomes from CRC cells with high metastatic potential to those with low metastatic potential, suggesting a potential therapeutic target for CRC.
CELL DEATH DISCOVERY
(2021)
Article
Cell & Tissue Engineering
Hengyou Weng, Huilin Huang, Huizhe Wu, Xi Qin, Boxuan Simen Zhao, Lei Dong, Hailing Shi, Jennifer Skibbe, Chao Shen, Chao Hu, Yue Sheng, Yungui Wang, Mark Wunderlich, Bin Zhang, Louis C. Dore, Rui Su, Xiaolan Deng, Kyle Ferchen, Chenying Li, Miao Sun, Zhike Lu, Xi Jiang, Guido Marcucci, James C. Mulloy, Jianhua Yang, Zhijian Qian, Minjie Wei, Chuan He, Jianjun Chen
Article
Cell Biology
Huilin Huang, Hengyou Weng, Wenju Sun, Xi Qin, Hailing Shi, Huizhe Wu, Boxuan Simen Zhao, Ana Mesquita, Chang Liu, Celvie L. Yuan, Yueh-Chiang Hu, Stefan Huettelmaier, Jennifer R. Skibbe, Rui Su, Xiaolan Deng, Lei Dong, Miao Sun, Chenying Li, Sigrid Nachtergaele, Yungui Wang, Chao Hu, Kyle Ferchen, Kenneth D. Greis, Xi Jiang, Minjie Wei, Lianghu Qu, Jun-Lin Guan, Chuan He, Jianhua Yang, Jianjun Chen
NATURE CELL BIOLOGY
(2018)
Article
Oncology
Miao He, Huizhe Wu, Qian Jiang, Yinuo Liu, Li Han, Yuanyuan Yan, Binbin Wei, Fangxiao Liu, Xiaolan Deng, Huiying Chen, Lin Zhao, Min Wang, Xin Wu, Weifan Yao, Haishan Zhao, Jianjun Chen, Minjie Wei
MOLECULAR ONCOLOGY
(2019)
Article
Multidisciplinary Sciences
Huilin Huang, Hengyou Weng, Keren Zhou, Tong Wu, Boxuan Simen Zhao, Mingli Sun, Zhenhua Chen, Xiaolan Deng, Gang Xiao, Franziska Auer, Lars Klemm, Huizhe Wu, Zhixiang Zuo, Xi Qin, Yunzhu Dong, Yile Zhou, Hanjun Qin, Shu Tao, Juan Du, Jun Liu, Zhike Lu, Hang Yin, Ana Mesquita, Celvie L. Yuan, Yueh-Chiang Hu, Wenju Sun, Rui Su, Lei Dong, Chao Shen, Chenying Li, Ying Qing, Xi Jiang, Xiwei Wu, Miao Sun, Jun-Lin Guan, Lianghu Qu, Minjie Wei, Markus Muschen, Gang Huang, Chuan He, Jianhua Yang, Jianjun Chen
Article
Biochemistry & Molecular Biology
Huizhe Wu, Wenyan Qin, Senxu Lu, Xiufang Wang, Jing Zhang, Tong Sun, Xiaoyun Hu, Yalun Li, Qiuchen Chen, Yuanhe Wang, Haishan Zhao, Haiyan Piao, Rui Zhang, Minjie Wei
Article
Biochemistry & Molecular Biology
Tong Sun, Zhikun Wu, Xiufang Wang, Yilin Wang, Xiaoyun Hu, Wenyan Qin, Senxu Lu, Dongping Xu, Yutong Wu, Qiuchen Chen, Xiangyu Ding, Hao Guo, Yalun Li, Yuanhe Wang, Boshi Fu, Weifan Yao, Minjie Wei, Huizhe Wu
Article
Cell Biology
Yilin Wang, Ming Zhang, Xiaoyun Hu, Wenyan Qin, Huizhe Wu, Minjie Wei
Article
Oncology
Xiaoyun Hu, Qiuchen Chen, Hao Guo, Kuo Li, Boshi Fu, Yu Chen, Haishan Zhao, Minjie Wei, Yalun Li, Huizhe Wu
Summary: Elevated miR-425 and miR-576 promote colorectal cancer liver metastases (CRLM) by inhibiting PTEN-mediated cellular immune function. They were found to be closely associated with tumor deterioration, especially liver metastases, and may serve as novel biomarkers for CRLM prevention and immunotherapy, as well as upstream inhibitors of the PTEN-P53/TGF-beta function axis.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Senxu Lu, Li Han, Xiaoyun Hu, Tong Sun, Dongping Xu, Yalun Li, Qiuchen Chen, Weifan Yao, Miao He, Zhenning Wang, Huizhe Wu, Minjie Wei
Summary: This study identified the crosstalk between the m(6)A reader IMP2 and lncRNA ZFAS1, which promotes CRC proliferation and progression through enhanced recruitment of OLA1, ATP hydrolysis, and glycolysis. IMP2 and ZFAS1 are overexpressed in CRC and can serve as independent biomarkers for prognostic prediction. ZFAS1 is stabilized by m(6)A modification and plays a critical role in CRC development.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2021)
Review
Cell Biology
Senxu Lu, Xiangyu Ding, Yuanhe Wang, Xiaoyun Hu, Tong Sun, Minjie Wei, Xiaobin Wang, Huizhe Wu
Summary: Recent research suggests that ncRNAs, including miRNA, circRNA, and lncRNAs, are crucial in the development of CRC, with m(6)A methylation playing a key role in ncRNA metabolism. The interaction regulation network among ncRNAs and m(6)A-related regulators remains underexplored, particularly in the context of CRC. Understanding these interactions could provide insights for potential biomarkers and therapeutic targets for improving CRC diagnostic precision and treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Boshi Fu, Cheng Du, Zhikun Wu, Mingwei Li, Yi Zhao, Xinli Liu, Huizhe Wu, Minjie Wei
