Explanipedia

SEdb 3.0: a comprehensive super-enhancer database across multiple species Open

Liyuan Liu, Chenchen Feng, Guorui Zhang, Yu Gao, Mingxue Yin , et al. · 2025

Super-enhancers (SEs) are key DNA cis-regulatory elements that play a central role in regulating tissue/cell-specific gene expression, thereby maintaining cellular identity and function. SEdb 3.0 (http://www.licpathway.net/sedb) provides a…

ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse Open

Fengcui Qian, Zhengyang Yu, Binglong Li, Xiangkun Meng, Ting Cui , et al. · 2025

Chromatin accessibility, which reflects transcriptional activity, is crucial for elucidating gene regulation, cellular function, and disease mechanisms. To provide a more comprehensive chromatin accessibility resource, we have released ATA…

scVMAP: a comprehensive platform for integrating single-cell chromatin accessibility regions with causal variants Open

Zhengmin Yu, Fengcui Qian, Qiao-Li Fang, Xiangkun Meng, Yanyu Li , et al. · 2025

Integrating causal variant effects with single-cell assay for transposase-accessible chromatin with high-throughput sequencing (scATAC-seq) enables a more effective elucidation of the roles and impacts of genetic variations at the single-c…

CCCdb: a comprehensive manually curated database for cell–cell communication in human and mouse Open

Mingcong Xu, Guorui Zhang, Xuan Wang, Yiqing Chen, Chenchen Feng , et al. · 2025

Cell–cell communication (CCC) is central to the organization, function, and plasticity of multicellular life. Advancing experimental technologies and growing insights into complex multicellular systems and disease microenvironments are dri…

GLP-1 receptor agonists: exploration of transformation from metabolic regulation to multi-organ therapy Open

Bing Gong, Chunquan Li, Zhenduo Shi, Fuping Wang, Ruanxian Dai , et al. · 2025

Glucagon-like peptide-1 receptor agonists (GLP-1RAs), initially developed for type 2 diabetes and obesity, have evolved into multi-organ potential therapeutics due to their pleiotropic effects beyond glycemic control. Mechanistically, GLP-…

A systematic review of protein post-translational modifications in sepsis Open

Lishun Yang, Zhenduo Shi, Fuping Wang, Guomin Shi, Chunquan Li , et al. · 2025

PTMs represent a core regulatory mechanism in the pathophysiology of sepsis. A comprehensive understanding of the functions and interactions of various PTMs is of great significance for profoundly elucidating the complexity of sepsis and d…

Identification of sepsis biomarkers through glutamine metabolism-mediated immune regulation: a comprehensive analysis employing mendelian randomization, multi-omics integration, and machine learning Open

Zhenduo Shi, Fuping Wang, Lishun Yang, Chunquan Li, Bing Gong , et al. · 2025

Background Sepsis is a global health challenge associated with high morbidity and mortality rates. Early diagnosis and treatment are challenging because of the limited understanding of its underlying mechanisms. This study aimed to identif…

Evaluation of the therapeutic effect of estrogen replacement therapy combined with autologous serum therapy in controlling severe dry eye disease in perimenopausal women Open

Tao Li, Juan Tang, Xinghuan Wang, Zhiwu Lin, Chunquan Li , et al. · 2025

Open-label pilot study using hydroxytyrosol as dietary supplements in patients with mitochondrial diseases Open

Theodoric Wong, Emily Man, Ian Chi Kei Wong, Xue Li, Hui Zhi , et al. · 2025

Background Mitochondrial Diseases (MDs) refers to a heterogeneous group of inherited metabolic disorders resulting in defective cellular energy production due to abnormal oxidative phosphorylation (OXPHOS) caused by pathogenic mitochondria…

TransAgent: Dynamizing Transcriptional Regulation Analysis via Multi-omics-Aware AI Agent Open

Guorui Zhang, Chao Song, Liyuan Liu, Qiuyu Wang, Chunquan Li · 2025

Transcriptional regulation research, as a core area of life sciences, faces challenges such as scattered multi-omics data, complex joint analysis, and difficulties in integrating data processing tools. To address these issues, we propose T…

TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data Open

Guorui Zhang, Chao Song, Mingxue Yin, Liyuan Liu, Yuexin Zhang , et al. · 2025

It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large…

scEnrich: An online webserver for cell-type identification of scATAC-seq data through comprehensive region enrichment analysis Open

Fu-Juan Dong, Ye Li, Zhicong Liu, Zhengmin Yu, Fengcui Qian , et al. · 2025

FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs Open

Yanyu Li, Fengcui Qian, Guorui Zhang, Xuecang Li, Li‐Wei Zhou , et al. · 2024

Accumulating evidence indicates that long noncoding RNAs (lncRNAs) play important roles in molecular and cellular biology. Although many algorithms have been developed to reveal their associations with complex diseases by using downstream …

sc2GWAS: a comprehensive platform linking single cell and GWAS traits of human Open

Mingxue Yin, Chenchen Feng, Zhengmin Yu, Yuexin Zhang, Ye Li , et al. · 2024

Identifying cell populations associated with risk variants is essential for uncovering cell-specific mechanisms that drive disease development and progression. Integrating genome-wide association studies (GWAS) with single-cell RNA sequenc…

scImmOmics: a manually curated resource of single-cell multi-omics immune data Open

Yanyu Li, Li‐Wei Zhou, Fengcui Qian, Qiao-Li Fang, Zhengmin Yu , et al. · 2024

Single-cell sequencing technology has enabled the discovery and characterization of subpopulations of immune cells with unique functions, which is critical for revealing immune responses under healthy or disease conditions. Efforts have be…

SpatialRef: a reference of spatial omics with known spot annotation Open

Ting Cui, Yanyu Li, Binglong Li, Han Zhang, Tingting Yu , et al. · 2024

Spatial omics technologies have enabled the creation of intricate spatial maps that capture molecular features and tissue morphology, providing valuable insights into the spatial associations and functional organization of tissues. Accurat…

Cross‐modal integration of bulk <span>RNA</span>‐seq and single‐cell <span>RNA</span> sequencing data to reveal T‐cell exhaustion in colorectal cancer Open

Mingcong Xu, Guorui Zhang, Ting Cui, Jiaqi Liu, Qiuyu Wang , et al. · 2024

Colorectal cancer (CRC) is a relatively common malignancy clinically and the second leading cause of cancer‐related deaths. Recent studies have identified T‐cell exhaustion as playing a crucial role in the pathogenesis of CRC. A long‐stand…

scBlood: A comprehensive single-cell accessible chromatin database of blood cells Open

Yu Zhao, Zhengmin Yu, Ting Cui, Lidong Li, Yanyu Li , et al. · 2024

TRAPT: A multi-stage fused deep learning framework for transcriptional regulators prediction via integrating large-scale epigenomic data Open

Guorui Zhang, Chao Song, Mingxue Yin, Liyuan Liu, Y. Zhang , et al. · 2024

It is a challenging task to identify functional transcriptional regulators, which control expression of gene sets via regulatory elements and epigenomic signals, involving context-specific studies such as development and diseases. Integrat…

TFTG: A comprehensive database for human transcription factors and their targets Open

Xinyuan Zhou, Li‐Wei Zhou, Fengcui Qian, Jiaxin Chen, Yuexin Zhang , et al. · 2024

Transcription factors (TFs) are major contributors to gene transcription, especially in controlling cell-specific gene expression and disease occurrence and development. Uncovering the relationship between TFs and their target genes is cri…

Uncertainty-driven and Adversarial Calibration Learning for Epicardial Adipose Tissue Segmentation Open

Kai Zhao, Zhiming Liu, Jiaqi Liu, Jingbiao Zhou, Bihong Liao , et al. · 2024

Epicardial adipose tissue (EAT) is a type of visceral fat that can secrete large amounts of adipokines to affect the myocardium and coronary arteries. EAT volume and density can be used as independent risk markers measurement of volume by …

LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis Open

Guorui Zhang, Chao Song, Shifan Fan, Mingxue Yin, Xinyue Wang , et al. · 2023

Long non-coding RNAs (lncRNAs) possess a wide range of biological functions, and research has demonstrated their significance in regulating major biological processes such as development, differentiation, and immune response. The accelerat…

SCInter: A comprehensive single-cell transcriptome integration database for human and mouse Open

Jun Zhao, Yuezhu Wang, Chenchen Feng, Mingxue Yin, Yu Gao , et al. · 2023

Single-cell RNA sequencing (scRNA-seq), which profiles gene expression at the cellular level, has effectively explored cell heterogeneity and reconstructed developmental trajectories. With the increasing research on diseases and biological…

KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species Open

Chenchen Feng, Chao Song, Shuang Song, Guorui Zhang, Mingxue Yin , et al. · 2023

Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive…

scATAC-Ref: a reference of scATAC-seq with known cell labels in multiple species Open

Fengcui Qian, Li‐Wei Zhou, Yanbing Zhu, Yanyu Li, Zhengmin Yu , et al. · 2023

Chromatin accessibility profiles at single cell resolution can reveal cell type-specific regulatory programs, help dissect highly specialized cell functions and trace cell origin and evolution. Accurate cell type assignment is critical for…

scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse Open

Xuemei Huang, Chao Song, Guorui Zhang, Ye Li, Yu Zhao , et al. · 2023

Gene regulatory networks (GRNs) are interpretable graph models encompassing the regulatory interactions between transcription factors (TFs) and their downstream target genes. Making sense of the topology and dynamics of GRNs is fundamental…

eRNAbase: a comprehensive database for decoding the regulatory eRNAs in human and mouse Open

Chao Song, Guorui Zhang, Xinxin Mu, Chenchen Feng, Qinyi Zhang , et al. · 2023

Enhancer RNAs (eRNAs) transcribed from distal active enhancers serve as key regulators in gene transcriptional regulation. The accumulation of eRNAs from multiple sequencing assays has led to an urgent need to comprehensively collect and p…

Single cell transcriptomics reveal the heterogeneities of TCR Vα7.2+CD161+ and TCR Vα7.2+CD161− T cells in human peripheral blood Open

Mingyang Li, Hua Jin, Ling Wei, Tianzhen Zhang, Shiyang Huang , et al. · 2023

Purpose T cell receptor (TCR) usually determines the specificity and unique function of T cells. Recently, the unconventional T cells with a unique TCR have attracted great attentions because of their clinical importance. TCR Vα7.2 + cells…

Author Correction: Universal DNA methylation age across mammalian tissues Open

Ake T. Lu, Zhe Fei, Amin Haghani, Todd R. Robeck, Joseph A. Zoller , et al. · 2023

Universal DNA methylation age across mammalian tissues Open

Ake T. Lu, Zhe Fei, Amin Haghani, Todd R. Robeck, Joseph A. Zoller , et al. · 2023

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