Article
Chemistry, Medicinal
Shuai Wang, Cui Hui, Tiangang Zhang, Peiliang Wu, Toshiya Nakaguchi, Ping Xuan
Summary: An increasing number of studies have shown that dysregulation of lncRNAs is related to the occurrence of various diseases. However, previous methods designed based on the homogeneity assumption ignore the distant affinity nodes. This study presents a novel prediction method, GAIRD, which leverages the heterogeneous information in the network and the decoupled node features. The experimental results demonstrate the superiority of GAIRD over other state-of-the-art methods.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Analytical
Xiaohan Li, Kequan Yu, Fuyu Li, Wenxiang Lu, Ying Wang, Weizhong Zhang, Yunfei Bai
Summary: This study presents a new comprehensive sequencing approach that allows for the capture of both poly(A) and non-poly(A) transcripts, enabling a deeper exploration of the transcriptome.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Fangzhou Xie, Shurong Liu, Junhao Wang, Jiajia Xuan, Xiaoqin Zhang, Lianghu Qu, Lingling Zheng, Jianhua Yang
Summary: The study updated deepBase to version 3.0, providing a comprehensive atlas of small RNAs and lncRNAs by integrating thousands of high-throughput sequencing data. Extracellular patterns of various ncRNAs were profiled for potential noninvasive biomarker discovery. Survival maps of tRFs, miRNAs, snoRNAs, and lncRNAs were constructed by analyzing cancer sample data, and interactive webs were developed to analyze differential expression and biological functions of various ncRNAs in different types of cancers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomas Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos Garcia Giron, Jose Manuel Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martinez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinuri Xu, Yucheng T. Yang, Andrew Yates, Daniel Zerbino, Yan Zhang, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: The GENCODE project annotates human and mouse genes and transcripts with high accuracy, using experimental data and bioinformatic tools, and continues to improve annotation infrastructure and tools for the human and mouse genomes. This includes manual annotation for the mouse reference genome, targeted improvements for SARS-CoV-2 related genes, collaborative projects for reference annotation databases, and the first GENCODE supervised automated annotation of lncRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Xiao-Xin Du, Yan Liu, Bo Wang, Jian-Fei Zhang
Summary: This study introduced a prediction model based on the nearest neighbor concept for lncRNA-disease association prediction, using a new similarity algorithm to improve predictive performance.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Jiajun Qiu, Xiao Ma, Fanyi Zeng, Jingbin Yan
Summary: RNA editing is a crucial process in which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after transcription. Studies have shown that RNA editing plays a critical role in cancer and aging, but its function in human early embryo development remains unclear. Analysis of single-cell RNA sequencing data revealed differential RNA editing rates among early embryo developmental stages, with a significant reprogramming of editing rates at the 8-cell stage. Furthermore, RNA editing was found to more likely occur on RNA splicing sites during human early embryo development.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Bo Wang, Xinwei Wang, Xiaodong Zheng, Yu Han, Xiaoxin Du
Summary: Non-coding RNAs play a decisive role in biological processes and have been found to regulate each other, contributing to various complex human diseases. In this study, a new method, JSCSNCP-LMA, was used to successfully predict the associations between lncRNA and miRNA.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Yuanlang Hu, Tao Hao, Hanwen Yu, Wenbin Miao, Yi Zheng, Weihua Tao, Jingshen Zhuang, Jichang Wang, Yujuan Fan, Shiqi Jia
Summary: RNA-RNA interactions play a crucial role in regulating gene expression and biological processes. The novel biochemical technique, lhCLIP, enables the transcriptome-wide identification of intra- and intermolecular RNA-RNA interactions mediated by a specific RNA-binding protein (RBP). Using lhCLIP, the study uncovered a diverse landscape of intermolecular RNA interactions recognized by hnRNPK in human cells, which may impact RNA splicing. This study demonstrates the potential and applicability of lhCLIP as a user-friendly method for discovering RNA-RNA interactions mediated by a particular protein of interest.
Article
Biochemistry & Molecular Biology
Dezhong Lv, Zhenghong Chang, Yangyang Cai, Junyi Li, Liping Wang, Qiushuang Jiang, Kang Xu, Na Ding, Xia Li, Juan Xu, Yongsheng Li
Summary: TransLnc is a database that provides experimentally supported and predicted lncRNA peptides in multiple species, with hundreds of thousands of peptides recorded. Various types of evidence supporting the coding potential of lncRNAs are integrated, and users can access lncRNA peptides in 34 tissues and predicted tumor neoantigens.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Xiaoli Liu, Yakun Wang, Ju Yuan, Fang Liu, Xiaoyou Hong, Lingyun Yu, Chen Chen, Wei Li, Wei Ni, Haiyang Liu, Jian Zhao, Chengqing Wei, Haigang Chen, Yihui Liu, Xinping Zhu
Summary: This study provides important evolutionary insights into the sex determination system in turtles, particularly the temperature-dependent sex determination, through the generation of a high-quality genome assembly of the Asian yellow pond turtle.
SCIENTIFIC REPORTS
(2022)
Review
Chemistry, Multidisciplinary
Imliyangla Longkumer, Seema Mishra
Summary: Long noncoding RNAs (lncRNAs) are a promising class of RNAs, and their sequence-structure-function relationship is similar to that of proteins. Although some lncRNAs have been well-studied, there are still many emerging lncRNAs that remain unknown. The low sequence conservation of lncRNAs has led researchers to decipher their conserved structure in order to understand their functional mechanisms.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Oncology
Min-Qiu Lu, Yu-Qin He, Yin Wu, Hui-Xing Zhou, Yuan Jian, Wen Gao, Li Bao, Wen-Ming Chen
Summary: This study aimed to explore the potential effects of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) patients using two detection methods: high-throughput sequencing and microarray. The study found that certain lncRNAs were aberrantly expressed in MM and identified the top 5 common pathways associated with MM. Furthermore, three microRNAs (miRNAs) were found to constitute competing endogenous RNA (ceRNA) networks in MM. The combination analysis significantly increased our understanding of lncRNAs in MM and identified more overlapping differentially expressed lncRNAs as potential therapeutic targets.
FRONTIERS IN ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Cheng Guo, You Duan, Weidong Ye, Wanting Zhang, Yingyin Cheng, Mijuan Shi, Xiao-Qin Xia
Summary: FishGET is an effort to collect and curate fish RNA-seq data in order to discover new RNAs and provide comprehensive transcriptome annotations. Through various steps including transcript assembly, meta-assembly, WGCNA, functional annotations, neighbor location annotation, lncRNA type annotation, and homology annotation, we obtained a total of 1362 RNA-seq paired-end data from 97 different studies of 8 fish species. To facilitate research on fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to access all information and utilize dynamic interactive visualization services.
Article
Multidisciplinary Sciences
Duc-Hau Le
Summary: Enhancer functional interaction network was constructed to predict disease-enhancer associations using the RWDisEnh method, which outperformed other network diffusion methods and accurately predicted novel enhancers linked to diseases.
Article
Multidisciplinary Sciences
Kai Ma, Xiang Luo, Liqun Han, Yu Zhao, Aisajan Mamat, Ning Li, Chuang Mei, Peng Yan, Rui Zhang, Jianfang Hu, Jixun Wang
Summary: The development of walnut female flower buds is a crucial feature that affects kernel yield and fruit quality. Research has shown that circadian rhythm is associated with flower bud development, impacting the understanding of the walnut transcriptome and genome annotation. These findings provide important insights into clarifying the process of flower bud development in walnuts.
Article
Genetics & Heredity
Kuo Yang, Kezhi Lu, Yang Wu, Jian Yu, Baoyan Liu, Yi Zhao, Jianxin Chen, Xuezhong Zhou
Summary: This study introduced a network-based machine-learning framework for identifying disease candidate genes and functional modules, which demonstrated superior performance in effectively addressing the impact of incomplete interactome networks and obtaining reliable rankings of candidate genes.
Article
Biochemistry & Molecular Biology
Lianhe Zhao, Jiajia Wang, Yanyan Li, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang, Mingqing Xu, Runsheng Chen, Yi Zhao, Shunmin He
Summary: NONCODE is a comprehensive database focusing on the collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. The latest version, NONCODEV6, not only covers lncRNAs in plants and animals, but also provides updated human lncRNA-disease relationships, tissue expression profiles and predicted function of lncRNAs in common plants, as well as conservation annotation of lncRNAs at transcript level for 23 plant species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
ShuangSang Fang, Lei Dong, Liu Liu, JinCheng Guo, LianHe Zhao, JiaYuan Zhang, DeChao Bu, XinKui Liu, PeiPei Huo, WanChen Cao, QiongYe Dong, JiaRui Wu, Xiaoxi Zeng, Yang Wu, Yi Zhao
Summary: Pharmacotranscriptomics has been used to evaluate drug efficacy and discover new drug targets. In the field of traditional Chinese medicine (TCM), there is a growing trend towards high-throughput transcriptomic screens for molecular effects of herbs/ingredients. HERB is a database that integrates gene targets for TCM herbs/ingredients and modern drugs, supporting the modernization of TCM and rational drug discovery efforts.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Oncology
Jin-Cheng Guo, Qing-Shuang Wei, Lei Dong, Shuang-Sang Fang, Feng Li, Yi Zhao
Summary: Through analysis of autophagy-related genes, we established a signature of 5 ATG genes that can effectively predict the prognosis of patients with lower-grade gliomas, showing superior predictive ability compared to existing clinical indicators and IDH mutation status.
FRONTIERS IN ONCOLOGY
(2021)
Article
Immunology
Lu Yang, Yanbing Zhu, Dan Tian, Song Wang, Jincheng Guo, Guangyong Sun, Hua Jin, Chunpan Zhang, Wen Shi, M. Eric Gershwin, Zhongtao Zhang, Yi Zhao, Dong Zhang
Summary: The study used single-cell RNA sequencing to analyze DNT cells, revealing transcriptional characteristics and functional roles of different subsets, which contributes to a better understanding of their roles in the immune system.
JOURNAL OF AUTOIMMUNITY
(2021)
Article
Immunology
Duancheng Guo, Yuan Wang, Yan Cheng, Shengyou Liao, Jian Hu, Fang Du, Gang Xu, Yongqiang Liu, Kathy Q. Cai, Martin Cheung, Brandon J. Wainwright, Q. Richard Lu, Yi Zhao, Zeng-jie Yang
Summary: The research demonstrates that astrocytes in relapsed MB mainly originate from the transdifferentiation of tumor cells, which depends on Sox9 and the BMP signaling pathway. Inhibiting BMP signaling pharmacologically suppresses the transdifferentiation of MB cells into astrocytes, thus suppressing tumor relapse.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Dechao Bu, Haitao Luo, Peipei Huo, Zhihao Wang, Shan Zhang, Zihao He, Yang Wu, Lianhe Zhao, Jingjia Liu, Jincheng Guo, Shuangsang Fang, Wanchen Cao, Lan Yi, Yi Zhao, Lei Kong
Summary: Gene set enrichment analysis is crucial for extracting biological insights from genome-scale experiments. The latest version of KOBAS, KOBAS-i, introduces a machine learning-based method CGPS, expands exploratory visualization of enriched results, and increases the number of supported species.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yuwei Zhang, Dechao Bu, Peipei Huo, Zhihao Wang, Hao Rong, Yanguo Li, Jingjia Liu, Meng Ye, Yang Wu, Zheng Jiang, Qi Liao, Yi Zhao
Summary: ncFANs v2.0 is an online platform that offers multiple computational methods for ncRNA functional annotation, including functional modules for different networks. It provides convenience for biological researchers to unravel the regulatory mechanisms of ncRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Haitao Luo, Dechao Bu, Lijuan Shao, Yang Li, Liang Sun, Ce Wang, Jing Wang, Wei Yang, Xiaofei Yang, Jun Dong, Yi Zhao, Furong Li
Summary: By analyzing full-length single-cell RNA sequencing data of T cells across different cancer types, a comprehensive catalog and functional repertoires of lncRNAs in human T cells were established. Overlooked lncRNAs expressed in T cells were identified, providing insight into the regulation of T cell functions and potential new biomarkers for cancer immunotherapies. The study offers a new perspective and resource for investigating T cell regulation in cancer immunity and developing novel cancer immunotherapies.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Oncology
Xinkui Liu, Yang Wu, Yingying Zhang, Dechao Bu, Chao Wu, Shan Lu, Zhihong Huang, Yurong Song, Yi Zhao, Fengying Guo, Peizhi Ye, Changgeng Fu, Liangliang Shen, Jingyuan Zhang, Haojia Wang, Xianchun Duan, Jiarui Wu
Summary: This study established a predictive immunotherapy signature of CKI on TNBC by analyzing gene expression changes and immune cell infiltration in TNBC cells. The signature, including five prognostic genes, showed good performance in predicting mortality risks of TNBC patients and guiding treatment strategies.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao, Xiaoxi Zeng, Shunmin He, Runsheng Chen
Summary: Piwi-interacting RNAs are small noncoding RNAs with diverse functions, and piRBase is a curated resource aimed at assisting functional analysis of piRNAs. The latest release, piRBase v3.0, includes over 181 million unique piRNA sequences from 44 species, along with disease-related piRNAs and regulatory relationship visualizations. The web interface has been redesigned for a better user experience, and new content such as gold standard piRNA sets and expression data has been added.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Yixuan Qiao, Lianhe Zhao, Chunlong Luo, Yufan Luo, Yang Wu, Shengtong Li, Dechao Bu, Yi Zhao
Summary: Digital pathology research utilizes computational technologies to improve the efficiency of diagnosis and treatment, with artificial intelligence algorithms having significant advantages in data analysis. This article investigates the use of hematoxylin-eosin stained tissue slide images to address the imbalance of healthcare resources and discusses the opportunities and challenges of artificial intelligence.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Yu Zheng, Huaxia Luo, Xueyi Teng, Xinpei Hao, Xiaoyu Yan, Yiheng Tang, Wanyu Zhang, Yuanxin Wang, Peng Zhang, Yanyan Li, Yi Zhao, Runsheng Chen, Shunmin He
Summary: The updated NPInter database provides valuable and informative ncRNA interaction information for biological researchers, including RNA-DNA interactions, RNA interactions between SARS-CoV-2 virus and its host, and the expression specificity of long noncoding RNAs in different cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Dechao Bu, Yan Xia, JiaYuan Zhang, Wanchen Cao, Peipei Huo, Zhihao Wang, Zihao He, Linyi Ding, Yang Wu, Shan Zhang, Kai Gao, He Yu, Tiegang Liu, Xia Ding, Xiaohong Gu, Yi Zhao
Summary: The historical use of herbs for treating diseases has been validated in modern medicine systems, providing a resource for drug innovation. FangNet platform utilizes network pharmacology and bioinformatics to assess herb importance and facilitate active ingredient discovery.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Lianhe Zhao, Qiongye Dong, Chunlong Luo, Yang Wu, Dechao Bu, Xiaoning Qi, Yufan Luo, Yi Zhao
Summary: DeepOmix is a flexible, scalable, and interpretable deep learning framework for extracting relationships between clinical survival time and multi-omics data. This method outperforms other prediction methods and demonstrates the functional module nodes associated with prognostic results in a case study on Lower Grade Glioma.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)