A5001641983- Cancer Immunotherapy and Biomarkers
- Pancreatic and Hepatic Oncology Research
- Peptidase Inhibition and Analysis
- Cancer-related molecular mechanisms research
- Extracellular vesicles in disease
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Radiomics and Machine Learning in Medical Imaging
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- MicroRNA in disease regulation
- Genomics and Chromatin Dynamics
- Ovarian cancer diagnosis and treatment
- Histone Deacetylase Inhibitors Research
- Bioactive natural compounds
- Glycosylation and Glycoproteins Research
- Genetic Mapping and Diversity in Plants and Animals
- Genetic Associations and Epidemiology
- Cancer, Lipids, and Metabolism
- Galectins and Cancer Biology
- vaccines and immunoinformatics approaches
- Cancer-related gene regulation
- CRISPR and Genetic Engineering
Huazhong University of Science and Technology
2019-2025
West China Medical Center of Sichuan University
2023-2025
Wuhan National Laboratory for Optoelectronics
2022
The distribution and abundance of immune cells, particularly T-cell subsets, play pivotal roles in cancer immunology therapy. T cells have many subsets with specific function current methods are limited estimating them, thus, a method for predicting comprehensive is urgently needed research. Here, Immune Cell Abundance Identifier (ImmuCellAI), gene set signature-based method, introduced precisely the 24 cell types including 18 from expression data. Performance evaluation on both sequencing...
Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a step for revealing functions TFs and their regulations on gene expression. accumulated data chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the across different conditions. In this study, we constructed database named hTFtarget, which integrated huge human TF target resources (7190 ChIP-seq samples...
Abstract Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve signal-to-noise ratio identify potential insights on gene level. However, platforms exploring cancer multi-omics data using GSA methods lacking. In this study, we upgraded our GSCALite to GSCA (gene analysis, http://bioinfo.life.hust.edu.cn/GSCA) for at genomic, pharmacogenomic immunogenomic levels. improved GSCA, integrated expression, mutation,...
Abstract Small non‐coding RNAs (ncRNAs) are functional molecules contained within extracellular vesicles (EVs) that modulate various physiological and pathological processes. This study provides a comprehensive expression profile of seven types small ncRNAs in serum‐ plasma‐derived EVs under conditions. Both large (lEVs) (sEVs) contain high proportions miRNAs (∼28.2% lEVs ∼20.8% sEVs) ribosomal (∼24.0% ∼19.1% sEVs). enriched with more transfer RNA (∼38.8%) than sEVs, whereas sEVs have...
Abstract Extracellular vesicles (EVs) packing various molecules play vital roles in intercellular communication. Non-coding RNAs (ncRNAs) are important functional and biomarkers EVs. A comprehensive investigation of ncRNAs expression EVs under different conditions is a fundamental step for discovery application Here, we curated 2030 small RNA-seq datasets human (1506 sEV 524 lEV) 24 over 40 diseases. We performed unified reads dynamic assignment algorithm (RDAA) considering mismatch...
Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. Much work is currently being conducted to investigate the mechanisms of ICB at transcriptional level. Integrating data produced by these studies will help us give more insight into transcriptomic features therapy. We collected transcriptome and ICB-treated patient samples from Gene Expression Omnibus, ArrayExpress, The Cancer Genome Atlas, dbGaP databases. On basis information, all are...
Abstract Summary Transcription factors (TFs) and microRNAs (miRNAs) are two kinds of important regulators for transcriptional post-transcriptional regulations. Understanding cross-talks between the their targets is critical to reveal complex molecular regulatory mechanisms. Here, we developed FFLtool, a web server detecting potential feed forward loop (FFL) TF-miRNA-target regulation in human. In integrated comprehensive regulations TF-target miRNA-target, functional modules: (i) The ‘FFL...
Abstract Platelets are reprogrammed by cancer via a process called education, which favors development. The transcriptional profile of tumor-educated platelets (TEPs) is skewed and therefore practicable for detection. This intercontinental, hospital-based, diagnostic study included 761 treatment-naïve inpatients with histologically confirmed adnexal masses 167 healthy controls from nine medical centers (China, n = 3; Netherlands, 5; Poland, 1) between September 2016 May 2019. main outcomes...
Abstract The distribution and abundance of immune cells, particularly T-cell subsets, play pivotal roles in cancer immunology therapy. There are many subsets with specific function, however current methods limited estimating them, thus, a method for predicting comprehensive is urgently needed research. Here we introduce Immune Cell Abundance Identifier (ImmuCellAI), novel gene set signature-based method, precisely the 24 cell types including 18 from expression data. Performance evaluation on...
Current non-confocal non-line-of-sight (NLOS) imaging faces the problems of low resolution and limited scene adaptability. We propose a NLOS method based on spherical-slice transform from spatial temporal frequency to space time. Simulation experimental results show that proposed has high-resolution reconstruction without artifact interference, shape distortion, position offset. Furthermore, it strong After GPU acceleration, time can be reduced several hundred milliseconds for PF32 photon...
Type 2 diabetes (T2D) is a long-term metabolic disorder disease characterized by high blood sugar and relative lack of insulin. Previous studies have demonstrated that Dendrobium has potent glucose-lowing effects may serve as add-ons or alternatives to classic medications for T2D prevention treatment, but the underlying molecular mechanisms were still unclear. We performed biochemical transcriptional profiling (RNA sequencing [RNA-seq] microRNA [miRNA-seq]) analyses on pancreas liver...
Esophageal cancer (EC), gastric (GC), and colorectal (CRC) are three major digestive tract tumors with higher morbidity mortality due to significant molecular heterogeneity. Altered IgG glycosylation has been observed in inflammatory activities disease progression, the glycome profile could be used for stratification. However, N-glycome profiles these cancers have not systematically investigated. Herein, subclass-specific CRC, GC, EC was comprehensively characterized by liquid...
Abstract Extracellular vesicles (EVs) carrying various small non-coding RNAs (sncRNAs) play a vital roles in cell communication and diseases. Correct quantification of multiple sncRNA biotypes simultaneously EVs is challenge due to the short reads (<30 bp) could be mapped types. To address this question, we developed an optimized assignment algorithm (ORAA) dynamically map multi-mapping type with higher proportion. We integrated ORAA processing steps into EVAtool Python-package...
<div>Abstract<p>Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. Much work is currently being conducted to investigate the mechanisms of ICB at transcriptional level. Integrating data produced by these studies will help us give more insight into transcriptomic features therapy. We collected transcriptome and ICB-treated patient samples from Gene Expression Omnibus, ArrayExpress, The Cancer Genome Atlas, dbGaP databases. On...
<div>Abstract<p>Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. Much work is currently being conducted to investigate the mechanisms of ICB at transcriptional level. Integrating data produced by these studies will help us give more insight into transcriptomic features therapy. We collected transcriptome and ICB-treated patient samples from Gene Expression Omnibus, ArrayExpress, The Cancer Genome Atlas, dbGaP databases. On...
Extracellular vesicles (EVs) play crucial role in mediating intercellular communication. Small RNA is an important component EVs. However, the proportion of small sequencing (smRNA‐seq) reads EVs mapped to human genome much lower than that cells, suggesting existence many nonhuman sequences there no systematic study on EV fragments unmapped genome. Herein, using smRNA‐seq data, landscape exogenous cargoes portrayed. The results show distribution sequence 1838 samples; average 21.82% are...
Abstract Background: Morpho-physiological alternations of platelets provided a rationale to harness RNA sequencing tumor-educated (TEPs) for preoperative diagnosis cancer. Timely, accurate, and non-invasive detection ovarian cancer in women with adnexal masses presents significant clinical challenge. Patients Methods: This intercontinental, hospital-based, diagnostic study included 761 treatment-naïve inpatients histologically confirmed 167 healthy controls from nine medical centers (China,...
Supplementary Figure from ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics Transcriptome Profiles
Supplementary Data from ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics Transcriptome Profiles
Supplementary Figure from ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics Transcriptome Profiles