Article
Biochemistry & Molecular Biology
Daniel Perez-Cremades, Ana B. Paes, Xavier Vidal-Gomez, Ana Mompeon, Carlos Hermenegildo, Susana Novella
Summary: This study identified a comprehensive regulatory network controlling transcriptomic changes in endothelial cells exposed to estradiol, highlighting the important role of estrogen in regulating endothelial function. The analysis revealed interactions between miRNAs and transcription factors, as well as downstream target genes, involved in key signaling pathways such as hypoxia signaling and cell adhesion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Ran Kang, Zhengtang Tan, Mei Lang, Linqi Jin, Yin Zhang, Yiming Zhang, Tailin Guo, Zhiyun Guo
Summary: EnhFFL is an online database providing data resource for users to browse and search typical enhancer and super-enhancer FFLs. The database covers a wide range of FFLs across different tissues/cell lines of human and mouse, allowing users to browse loops by selecting species, types of tissue/cell line, and types of FFLs. Disease and functional enrichment analysis revealed the significance of master miRNAs in FFLs in tumorigenesis.
PRECISION CLINICAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Yunxia Wang, Ziqi Pan, Minjie Mou, Weiqi Xia, Hongning Zhang, Hanyu Zhang, Jin Liu, Lingyan Zheng, Yongchao Luo, Hanqi Zheng, Xinyuan Yu, Xichen Lian, Zhenyu Zeng, Zhaorong Li, Bing Zhang, Mingyue Zheng, Honglin Li, Tingjun Hou, Feng Zhu
Summary: In this study, a task-specific encoding algorithm for RNAs and RNA-associated interactions was developed, which realized comprehensive RNA feature encoding by introducing novel features and enabled task-specific integration of interacting partners using convolutional autoencoder-directed feature embedding.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
Summary: Access pathways are critical for substrate and product transport in enzymes. A Python3 API called pyCaverDock is introduced to enhance the user experience and facilitate ligand transport analysis. This API simplifies the steps needed to use CaverDock and allows for automation of setup processes.
Article
Cell Biology
Yizeng Yang, Dharmendra Bhargava, Xiao Chen, Taicheng Zhou, Gizem Dursuk, Wenpeng Jiang, Jinshen Wang, Zhen Zong, Sharyn I. Katz, Gwen A. Lomberk, Raul A. Urrutia, Jonathan P. Katz
Summary: In non-transformed human squamous epithelial cells, the decision of whether to arrest or undergo apoptosis in response to stress is mediated by the interaction between p53 and the zinc-finger transcription factor KLF5. The levels of cellular stress determine the specific outcome, with moderate stress leading to cell survival and severe stress resulting in apoptosis.
CELL DEATH & DISEASE
(2023)
Article
Biochemical Research Methods
Amelie Barozet, Kevin Molloy, Marc Vaisset, Christophe Zanon, Pierre Fauret, Thierry Simeon, Juan Cortes
Summary: MoMA-LoopSampler is a sampling method that explores the conformational space of flexible protein loops globally, using a large structural library and reinforcement-learning-based approach. It generates a set of statistically likely loop states satisfying geometric constraints and can sample experimentally observed conformations.
Article
Biochemistry & Molecular Biology
Zhiyong Li, Xiangjin Wei, Xiaohong Tong, Juan Zhao, Xixi Liu, Huimei Wang, Liqun Tang, Yazhou Shu, Guanghao Li, Yifeng Wang, Jiezheng Ying, Guiai Jiao, Honghong Hu, Peisong Hu, Jian Zhang
Summary: The translation explains that Tre6P maintains sugar balance in plants and promotes growth by regulating carbon allocation. The sugar-inducible rice NAC transcription factor OsNAC23 elevates Tre6P levels and represses trehalose levels by directly repressing the transcription of the Tre6P phosphatase gene TPP1. Additionally, OsNAC23 and Tre6P suppress the activity and transcription of SnRK1a, preventing SnRK1a-mediated degradation of OsNAC23. Overexpression of OsNAC23 increases rice yield and photosynthetic rate.
Article
Biotechnology & Applied Microbiology
Rui Dou, Xiong Wang, Jin Zhang
Summary: This study reveals the correlation between the expression of NFE2 family members and the prognosis of ovarian cancer. NFE2L1 is associated with short-term progression-free survival, while NFE2L2 is associated with long-term progression-free survival. NFE2L3 is correlated with overall survival and post-progression survival.
BIOMED RESEARCH INTERNATIONAL
(2022)
Article
Mechanics
Tuhin Subhra Roy, Mintu Nandi, Pinaki Chaudhury, Sudip Chattopadhyay, Suman K. Banik
Summary: In this study, we propose a stochastic framework to analyze fluctuation propagation in classes of coherent feed-forward loops. We consider the contributions of direct and indirect pathways as well as additive and multiplicative integration mechanisms. The analysis of output fluctuations reveals the contributions of different fluctuation terms to the overall output fluctuations.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Biochemical Research Methods
Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker
Summary: The folding of RNA during transcription plays a crucial role in its structure and function. A new algorithm has been developed to track and predict the changes in RNA secondary structure during transcription. This algorithm is deterministic, fast, and capable of folding long RNA sequences.
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Dharmesh D. Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J. Davis
Summary: vissE.Cloud is a webserver for gene-set analysis, offering summarisation and interactive visualisation of GSA results. It allows analysis of gene lists as well as raw single-cell and spatial omics data, making it the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Young Koung Lee, Sunita Kumari, Andrew Olson, Felix Hauser, Doreen Ware
Summary: Zinc finger homeodomain (ZF-HD) transcription factors have important roles in the growth, development, and architecture regulation of plants. In Arabidopsis, ZF-HD TFs negatively regulate miR157 and positively regulate SPL10, creating a feed-forward loop that constitutes a miRNA regulatory module.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Michelle M. Hill
Summary: LipidSuite is an end-to-end differential lipidomics data analysis server that provides a step-by-step workflow for preprocessing, exploratory analysis, differential analysis, and enrichment analysis of untargeted and targeted lipidomics datasets. It supports the upload of three lipidomics data formats and allows users to interactively explore data and conduct various analyses.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Mathematical & Computational Biology
Jimin Pei, Qian Cong
Summary: This study developed the AlphaFold Transmembrane proteins (AFTM) database, which identifies transmembrane regions in human TMPs using high-quality structural models based on the AlphaFold program. A comparison with other databases showed that AFTM performs well in identifying transmembrane regions for multipass TMPs and exhibits more consistent results with experimental structures. Additionally, AFTM identified some proteins previously annotated as TMPs as non-TMPs.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biotechnology & Applied Microbiology
Hyobin Jeong, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, Tobias Roider, Radhakrishnan Sabarinathan, David Porubsky, Sophie A. Herbst, Busra Erarslan-Uysal, Johann-Christoph Jann, Tobias Marschall, Daniel Nowak, Jean-Pierre Bourquin, Andreas E. Kulozik, Sascha Dietrich, Beat Bornhauser, Ashley D. Sanders, Jan O. Korbel
Summary: This study introduces a computational method called scNOVA, which utilizes Strand-seq to analyze structural variations in single cells and infer gene expression. The research reveals the impact of structural variations on gene regulation and signaling pathways, and successfully applies the method to the study of chronic lymphocytic leukemia and T cell acute lymphoblastic leukemia.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chun-Jie Liu, Gui-Yan Xie, Ya-Ru Miao, Mengxuan Xia, Yi Wang, Qian Lei, Qiong Zhang, An-Yuan Guo
Summary: Extracellular vesicles (EVs) contain various molecules that are crucial for intercellular communication, with non-coding RNAs (ncRNAs) playing important roles as functional molecules and biomarkers. EVAtlas is a comprehensive database for ncRNA expression in EVs, providing valuable information on expression profiles under different conditions, sources, and diseases through four functional modules, serving as a key resource in this field.
NUCLEIC ACIDS RESEARCH
(2022)
Letter
Hematology
Xie Gui-Yan, Liu Chun-Jie, Miao Ya-Ru, Xia Mengxuan, Zhang Qiong, An-Yuan Guo
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wen-Kang Shen, Si-Yi Chen, Zi-Quan Gan, Yu-Zhu Zhang, Tao Yue, Miao-Miao Chen, Yu Xue, Hui Hu, An-Yuan Guo
Summary: Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate gene expression. The Animal Transcription Factor Database (AnimalTFDB) has been updated to version 4.0 with new data and functions, including variations in TF genes in human cancers and other diseases, predicted post-translational modification sites on TFs, TF regulation in autophagy, comprehensive TF expression annotation, and improved search functions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jingfa Xiao, Shun-min He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Yingke Ma, Meili Chen, Cuiping Li, Shuai Jiang, Dong Zou, Zheng Gong, Xue-tong Zhao, Yanqing Wang, Junwei Zhu, Shuhui Song, Yunchao Ling, Yiwei Wang, Jiaxin Yang, Xinhao Zhuang, Guangya Duan, Gangao Wu, Xiaoning Chen, Dongmei Tian, Zhaohua Li, Yan-ling Sun, Zhenglin Du, Lili Hao, Yuan Gao, Bixia Tang, Yadong Zhang, Hao Zhang, Zaichao Zhang, Qiheng Qian, Zhewen Zhang, Hailong Kang, Tianhao Huang, Zhiqiang Xia, Xincheng Zhou, Jin-quan Chao, Zhonghuang Wang, Jun-wei Zhu, Sisi Zhang, Weimin Tian, Wenquan Wang, Song Wu, Yue Huang, Mochen Zhang, Guoliang Wang, Xin-chang Zheng, Wenting Zong, Wei Zhao, Peiqi Xing, Rujiao Li, Zhaoqi Liu, Mingming Lu, Fengchun Yang, Jialin Mai, Qianwen Gao, Xiaowei Xu, Hongyu Kang, Li Hou, Yunfei Shang, Qiheng Qain, Jie Liu, Meiye Jiang, Congfan Bu, Jinyue Wang, Jingyao Zeng, Jiao Li, Siyu Pan, Hongen Kang, Xinxuan Liu, Shiqi Lin, Na Yuan, Peilin Jia, Xinchang Zheng, Yanling Sun, Zhuang Xiong, Fei Yang, Xu Chen, Tingting Chen, Caixia Yu, Lili Dong, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yan-qing Wang, Anke Wang, Yaokai Jia, Xuetong Zhao, Yitong Pan, Xiaonan Liu, Rongqin Zhang, Yi Wang, Lina Ma, Xufei Teng, Lun Li, Na Li, Ying Cui, Tong Jin, Enhui Jin, Tao Zhang, Tianyi Xu, Ming Chen, Guangyi Niu, Rong Pan, Tongtong Zhu, Yuan Chu, Jian Sang, Yuanpu Zhang, Zhennan Wang, Yuan-sheng Zhang, Qiliang Yao, Xinran Zhang, Xutong Guo, Zhao Li, Lin Liu, Changrui Feng, Yuxin Qin, Wei Jing, Sicheng Luo, Tong-tong Zhu, Yuansheng Zhang, Zis-han Wu, Qianpeng Li, Pei Liu, Yongqing Sun, Zhuojing Fan, Wen-ming Zhao, Wen-Kang Shen, An-Yuan Guo, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Yu Xue, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Yujie Gou, Miaomiao Chen, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Wan Liu, Ruifang Cao, Guo-qing Zhang, Yuxiang Wei, Chun-Jie Liu, Gui-Yan Xie, Hao Yuan, Tianhan Su, Yong E. Zhang, Chenfen Zhou, Pengyu Wang, Yincong Zhou, Guoji Guo, Qiong Zhang, Shanshan Fu, Xiaodan Tan, Dachao Tang, Weizhi Zhang, Mei Luo, Yubin Xie, Ya-Ru Miao, Xinhe Huang, Zihao Feng, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Dechang Yang, Feng Tian, Ge Gao, Wenyi Wu, Cheng Han, Qinghua Cui, Chunfu Xiao, Chuan-Yun Li, XiaoTong Luo, Qing Tang
Summary: The National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) provides database resources to support global academic and industrial communities. The NGDC constantly expands and updates core database resources by archiving big data, conducting integrative analysis, and providing value-added curation. New database resources have been developed for infectious diseases and microbiology, cancer-trait association, and tropical plants. Additionally, resources for the monkeypox virus and SARS-CoV-2 have been newly constructed and regularly updated. All resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yanbo Yang, Dongyang Wang, Ya-Ru Miao, Xiaohong Wu, Haohui Luo, Wen Cao, Wenqian Yang, Jianye Yang, An-Yuan Guo, Jing Gong
Summary: Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes and play crucial roles in diseases. The updated version 3 of lncRNASNP provides a comprehensive repository of single nucleotide polymorphisms (SNPs) and somatic mutations in lncRNAs, along with their impacts on lncRNA structure and function. The database now includes eight eukaryotic species, expanded SNP data, and several new features, such as SNP effects on miRNA-lncRNA interactions, lncRNA expression profiles, disease and GWAS-associated lncRNAs and variants, experimental and predicted lncRNAs and drug target associations, and SNP effects on lncRNA expression across tumor and normal tissues.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Yue Gao, Chun-Jie Liu, Hua-Yi Li, Xiao-Ming Xiong, Gui-Ling Li, Sjors G. J. G. In't Veld, Guang-Yao Cai, Gui-Yan Xie, Shao-Qing Zeng, Yuan Wu, Jian-Hua Chi, Jia-Hao Liu, Qiong Zhang, Xiao-Fei Jiao, Lin-Li Shi, Wan-Rong Lu, Wei-Guo Lv, Xing-Sheng Yang, Jurgen M. J. Piek, Cornelis D. de Kroon, C. A. R. Lok, Anna Supernat, Sylwia Lapinska-Szumczyk, Anna Lojkowska, Anna J. Zaczek, Jacek Jassem, Bakhos A. Tannous, Nik Sol, Edward Post, Myron G. Best, Bei-Hua Kong, Xing Xie, Ding Ma, Thomas Wurdinger, An-Yuan Guo, Qing-Lei Gao
Summary: Platelets are reprogrammed by cancer through education, which promotes cancer development. Tumor-educated platelets (TEPs) have a distinct transcriptional profile that can be used for cancer detection.
Letter
Cell Biology
Chun-Jie Liu, Hua-Yi Li, Yue Gao, Gui-Yan Xie, Jian-Hua Chi, Gui-Ling Li, Shao-Qing Zeng, Xiao-Ming Xiong, Jia-Hao Liu, Lin-Li Shi, Xiong Li, Xiao-Dong Cheng, Kun Song, Ding Ma, An-Yuan Guo, Qing-Lei Gao
Article
Hematology
Mei Luo, Ya-Ru Miao, Ya-Juan Ke, An-Yuan Geo, Qiong Zhang
Summary: In this study, the researchers integrated RNA sequencing data sets of over 3000 samples from 14 leukemia subtypes and developed a user-friendly data portal called LeukemiaDB, which provides comprehensive information on the transcriptomic landscape of leukemia. The database includes modules for protein-coding genes, long noncoding RNAs, circular RNAs, alternative splicing, and fusion genes. The analysis of data in LeukemiaDB revealed valuable insights into oncogenesis and progression of leukemia.
Article
Public, Environmental & Occupational Health
Jun-Jie Mao, Xiao Zang, Wan-Lu Yue, Pei-Yao Zhai, Qiong Zhang, Chun-Hu Li, Xun Zhuang, Min Liu, Gang Qin
Summary: Given the ageing epidemic of tuberculosis (TB) in China, the first clinically approved next-generation TB vaccine Vaccae, proved to be effective in preventing reactivation from latent infection. This study evaluated the health and economic impacts of introducing Vaccae vaccination to inform policy-makers. The results showed that targeted vaccination among older adults could modestly reduce TB burden, preventing millions of TB cases and deaths over a 20-year period, at an incremental cost-effectiveness ratio of US$4387 per disability adjusted life year averted.
Article
Chemistry, Physical
Yi Wang, Gui-Yan Xie, Qiong Zhang, Xiuqing Zhang, An-Yuan Guo
Summary: Extracellular vesicles (EVs) play a crucial role in intercellular communication, and small RNA is an important component in EVs. A study using EV small RNA sequencing (smRNA-seq) data portrayed the landscape of exogenous RNA cargoes in human EVs. The results revealed the presence of nonhuman sequence fragments in 1838 EV samples, with an average of 21.82% unmapped to the human genome and 12.33% mapped to exogenous reference sequences. The study provides valuable insights into the diverse sources of RNA in the human body.
Article
Computer Science, Cybernetics
Qin Zhao, Jingyi Huang, Gang Liu, Yaru Miao, Pengwei Wang
Summary: This paper proposes a multiinterest and social interest-field framework (MISIF) to improve social recommendations in financial security. By introducing capsule networks, the traditional single-interest representation is extended to user multiinterest embedding, enhancing the expressiveness of user embedding. By constructing social interest fields and integrating social interests based on multiinterest embedding, the framework alleviates noise in social networks and user data sparsity problems. The final prediction scores are obtained by aggregating user multiinterest embedding and additional information through neural networks.
IEEE TRANSACTIONS ON COMPUTATIONAL SOCIAL SYSTEMS
(2023)
