Article
Cell Biology
Liang Chen, Qingshi Meng, Shen Li, Yue Jiang, Cong Zhang, Shanlong Tang, Ruqing Zhong, Xiangfang Tang, Sheng Zhang, Xiaohui Feng, Yong Zhao, Hongfu Zhang
Summary: This study presents the development and maturation of neonatal cecal cells at a single cell level with transcript, protein, microbiota, and metabolism perspectives. It shows specific trends in the development and maturation of different cecal cell types controlled by transcriptional factors, ligand-receptor pairs, and other factors. The study also reveals the correlation between cecal cell types and microbial diversity in cecal content and mucosal-associated microbiota.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ashley Mae Conard, Nathaniel Goodman, Yanhui Hu, Norbert Perrimon, Ritambhara Singh, Charles Lawrence, Erica Larschan
Summary: TIMEOR is the first web-based and adaptive time-series multi-omics pipeline method that infers the relationship between gene regulatory events across time, addressing the critical need for determining causal regulatory mechanism networks. It integrates time-series RNA-seq, motif analysis, protein-DNA binding data, and protein-protein interaction networks.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Shiqi Li, Xin Chen, Jianfang Chen, Binjian Wu, Jing Liu, Yanzhi Guo, Menglong Li, Xuemei Pu
Summary: This study utilizes two integration strategies to comprehensively analyze GPCRs and reveals that mutations cannot effectively predict expression dysregulation. The correlations between expressions and SCNAs are primarily positive, while correlations of methylation and SCNAs with expressions exhibit bimodal patterns. 32 potential cancer-related GPCRs driven by aberrant SCNA and 144 potential cancer-related GPCRs driven by aberrant methylation are identified. Deep learning models predict over 100 GPCRs as potential oncogenes. The study emphasizes the importance of combining both integration strategies to identify cancer-related GPCRs and reveals the immune-related nature of GPCRs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Min Zhou, Shigang Zheng
Summary: Environmental pollution of heavy metals has become a growing concern in recent years. This review focuses on the response of wheat to heavy metal stress and management strategies to reduce heavy metal uptake and accumulation. The findings provide insights into the challenges and future recommendations for wheat under heavy metal stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Aishwarya Krishnamoorthy, Sebastian Kadener
Summary: circRNAs are covalently closed RNA molecules generated by backsplicing that are tissue-specific, stable, and can regulate gene expression or be translated into protein. With the use of deep sequencing and genetic tools like GAL4-UAS system, research on circRNAs in Drosophila has revealed mechanisms of circRNA production, details of translation, and their physiological functions. The short lifecycle and neurodegeneration models of Drosophila make it a suitable model for studying the role of circRNAs in aging and age-related disorders.
Article
Biochemistry & Molecular Biology
Weiwei Zhou, Minghai Su, Tiantongfei Jiang, Qingyi Yang, Qisen Sun, Kang Xu, Jingyi Shi, Changbo Yang, Na Ding, Yongsheng Li, Juan Xu
Summary: This study developed an integrated spatial omics resource for visualizing and analyzing spatial transcriptomics data in cancer. Currently available datasets from 17 types of cancer were manually curated, and reference single-cell RNA sequencing data were matched in the majority of datasets. The resource provides multiple analytical modules to meet the primary requirements of spatial transcriptomics analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Xin Huang, Ling Li, Suiping Zhou, Dehui Kong, Jie Luo, Lu Lu, Hai-Ming Xu, Xusheng Wang
Summary: This study conducted a systems-level analysis of the mouse kinome by investigating genetic sequence variation, tissue-specific expression patterns, and associations with downstream phenotypes.
Article
Neurosciences
Riho Kobayashi, Shin Nakane, Jun Tomita, Hiromasa Funato, Masashi Yanagisawa, Kazuhiko Kume
Summary: Sleep behavior is observed across species from non-vertebrates to humans. A mutation in the Sik3 gene, known as Sik3-SA, has been found to increase sleep in mice and fruit flies. Further research revealed that overexpression of Sik3-SA in all neurons increased sleep, while overexpression only in PDF neurons affected the circadian rhythm and increased sleep during subjective daytime.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
Mengyuan Kan, Avantika R. Diwadkar, Supriya Saxena, Haoyue Shuai, Jaehyun Joo, Blanca E. Himes
Summary: In the era of post genome-wide association study (GWAS), omics techniques have expanded our understanding of genetic variants by incorporating information beyond the genome. However, raw omics data is not accessible or understandable for experimental researchers without adequate computational resources or omics data analysis experience. To address this issue, we developed an integrated resource of tissue-specific omics results guided by disease-specific knowledge, facilitating the design of experiments that provide biologically meaningful insights into genetic associations.
Article
Multidisciplinary Sciences
Annika F. Barber, Shi Yi Fong, Anna Kolesnik, Michael Fetchko, Amita Sehgal
Summary: Regulation of circadian behavior and physiology by the Drosophila brain clock requires communication from central clock neurons to downstream output regions. Morning and evening clock neurons have time-of-day-dependent connectivity to the pars intercerebralis, which is regulated by specific peptides and fast neurotransmitters. This study provides insights into mechanisms by which clock neurons signal to nonclock cells to drive rhythms of behavior.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Chao Wang, Xu Feng, Dan Su, Zhen Chen, Shimin Wang, Mengfan Tang, Min Huang, Litong Nie, Huimin Zhang, Siting Li, Ling Yin, Randy L. Johnson, Traver Hart, Junjie Chen
Summary: Cell surface proteins are crucial for cancer development, but their functional analysis is limited. In this study, we used a gene library and CRISPR screens to identify a cell surface tumor suppressor involved in the Hippo pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Gastroenterology & Hepatology
Shuai Yang, Ling Qian, Zhixuan Li, Ye Li, Jian Bai, Bo Zheng, Kun Chen, Xinyao Qiu, Guoxiang Cai, Shan Wang, Haiyan Huang, Jianmin Wu, Yanjing Zhu, Qianwen Zhangyang, Lanyun Feng, Tong Wu, Rui Wu, Airong Yang, Kaiting Wang, Ruiru Wang, Yani Zhang, Yan Zhao, Wenwen Wang, Jinxia Bao, Siyun Shen, Ji Hu, Xuan Wu, Tao Zhou, Zhiqiang Meng, Weiwei Liu, Hongyang Wang, Peng Wang, Lei Chen
Summary: This study characterized the immune microenvironment subtypes of liver metastases and identified potential mechanisms using mass cytometry, transcriptomic and whole-exome sequencing. Five distinct immune subtypes were identified, and patients with terminally exhausted or rare T-cell-inflamed characteristics showed worse prognosis. Increased intratumor heterogeneity, somatic mutations in TP53, KRAS, APC, and PIK3CA, and hyperactivated hypoxia signaling contributed to the formation of these aggressive subtypes. SLC2A1 was found to promote immune suppression and escape in liver metastatic lesions through interaction with Spp1 thorn macrophages and regulatory T cells, and also played a role in primary colorectal cancer.
Review
Plant Sciences
Milan Jockovic, Sinisa Jocic, Sandra Cvejic, Ana Marjanovic-Jeromela, Jelena Jockovic, Aleksandra Radanovic, Dragana Miladinovic
Summary: The review emphasizes the importance of systematic approaches to sunflower breeding, highlighting the lack of desirable genetic variation in the field. By integrating information from various omics technologies, a comprehensive understanding of the molecular mechanisms in sunflower can be achieved, leading to more efficient breeding strategies.
Review
Biochemistry & Molecular Biology
Kenichiro Kinouchi, Yohei Mikami, Takanori Kanai, Hiroshi Itoh
Summary: The circadian clock enables organisms to adapt to daily rhythms, with the central clock in the SCN being reset by light and peripheral clocks being entrained by feeding-fasting rhythms. Different diets and feeding times can reprogram circadian rhythms in a tissue specific manner, impacting the availability of nutrients. This understanding at the genomic and epigenomic levels is largely due to advanced technologies like transcriptome, proteome, and metabolome analysis, providing insights into circadian cycles and gene regulation.
MOLECULAR ASPECTS OF MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Chang Zhang, Jiahui Xu, Lijun Chen, Xiaojie Lin
Summary: The circadian rhythm pathway exhibited pathological functions in glioma on a single-gene level. By analyzing multi-omics data, it was found that lower grade glioma (LGG) patients showed higher frequencies of mutations and better survival outcomes related to the circadian rhythm pathway. Quantification of the pathway using a pathway index indicated distinctly altered circadian pathway in LGG patients.
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)
Article
Biochemical Research Methods
Ya-Ru Miao, Mengxuan Xia, Mei Luo, Tao Luo, Mei Yang, An-Yuan Guo
Summary: ImmuCellAI-mouse is an accurate tool for predicting mouse immune cell abundance, utilizing gene expression data and a hierarchical strategy to accurately predict most immune cell types, revealing dynamic changes in immune cell infiltration in a mouse tumor dataset.
Article
Oncology
Zhao Zhang, Mei Luo, Qiang Li, Yuan Liu, Charles Lussier, Jian Zhang, Youqiong Ye, An-Yuan Guo, Leng Han
Summary: This study systematically investigates the impact of enhancer RNAs (eRNAs) on cancer and provides a multidimensional data portal for further research.
Article
Biochemical Research Methods
Gui-Yan Xie, Chun-Jie Liu, An-Yuan Guo
Summary: This article introduces a method for quantifying multiple sncRNA biotypes simultaneously in extracellular vesicles (EVs). An optimized reads assignment algorithm is developed to dynamically map multi-mapping reads to sncRNA types with higher proportions. The method is integrated into the EVAtool tool, which allows for the quantification of sncRNA expression profiles in EV samples.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Bo Wen, Eric J. Jaehnig, Bing Zhang
Summary: OmicsEV is an R package that evaluates the quality of omics data tables by using various methods to assess depth, normalization, biological signal, and other factors. It generates comprehensive visual and quantitative evaluation results to help assess data quality and determine the optimal data processing method and parameters.
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
Multidisciplinary Sciences
Yangyang Yuan, Chenwei Wang, Xuran Zhuang, Shaofeng Lin, Miaomiao Luo, Wankun Deng, Jiaqi Zhou, Lihui Liu, Lina Mao, Wenbo Peng, Jian Chen, Qiangsong Wang, Yilai Shu, Yu Xue, Pengyu Huang
Summary: This study develops a method, central kinase inference, to predict key kinases by integrating quantitative transcriptomic and phosphoproteomic data. The method is more accurate than Kinase-Substrate Enrichment Analysis in predicting known kinases associated with anti-cancer drug resistance. The study also identifies key kinases involved in hepatocyte maturation and hepatic reprogramming.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mei Luo, Lin Ye, Ruimin Chang, Youqiong Ye, Zhao Zhang, Chunjie Liu, Shengli Li, Ying Jing, Hang Ruan, Guanxiong Zhang, Yi He, Yaoming Liu, Yu Xue, Xiang Chen, An-Yuan Guo, Hong Liu, Leng Han
Summary: Autophagy is typically associated with resistance to cancer therapy, but it may also sensitize cancer cells to anti-cancer drugs.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Mei Yang, Ya-Ru Miao, Gui-Yan Xie, Mei Luo, Hui Hu, Hang Fai Kwok, Jian Feng, An-Yuan Guo
Summary: Immune checkpoint blockade (ICB) therapy has shown remarkable clinical benefits for multiple cancer types. The ICBatlas database provides transcriptomic features of ICB therapy by analyzing 1,515 ICB-treated samples from 25 studies across nine cancer types. Users can explore clinical outcomes, treatment-related genes, biological pathways, and immune cell infiltration in relation to ICB therapy response or treatment modules.
CANCER IMMUNOLOGY RESEARCH
(2022)
Editorial Material
Cell Biology
Yu Xue
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
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
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.
