Guangchuang Yu
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View article: Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms for single‐cell spatial transcriptomics of mouse brain and lung
Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms for single‐cell spatial transcriptomics of mouse brain and lung Open
Single‐cell spatial transcriptomics enables comprehensive gene expression profiling with precise cellular localization within tissue architecture. To systematically evaluate the compatibility and performance of alternative sequencing platf…
View article: Background bias in functional enrichment analysis: Insights from <i>clusterProfiler</i>
Background bias in functional enrichment analysis: Insights from <i>clusterProfiler</i> Open
View article: ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer
ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer Open
Background Metastatic recurrence poses a significant challenge in cancer treatment, impacting patient survival and prognosis. Understanding the biological mechanisms behind it is essential for improving treatment strategies and patient out…
View article: ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity
ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity Open
Data visualization is essential for exploring and communicating complex biological datasets. As omics data grow in scale and complexity, there is an increasing demand for visualization tools that are both flexible and extensible. We presen…
View article: ivolcano: Interactive Volcano Plot
ivolcano: Interactive Volcano Plot Open
View article: FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency
FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency Open
Biomedical research data visualization faces several challenges, including insufficient expertise and fragmented methodologies, which severely limit research efficiency and result quality. FigureYa is a standardized visualization framework…
View article: Drug-tolerant persister cell in cancer: reversibility, microenvironmental interplay, and therapeutic strategies
Drug-tolerant persister cell in cancer: reversibility, microenvironmental interplay, and therapeutic strategies Open
Drug-tolerant persister (DTP) cells are a subpopulation of cancer cells capable of surviving therapeutic stress through reversible, non-genetic adaptations. These cells contribute to minimal residual disease and eventual tumor relapse. Und…
View article: Gut microbial‐derived 3,4‐dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome
Gut microbial‐derived 3,4‐dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome Open
Polycystic ovary syndrome (PCOS) is a prevalent endocrine and reproductive disorder affecting women of reproductive age. While the gut microbiota has been implicated in PCOS pathophysiology, the role of microbial‐derived metabolites as med…
View article: Adolescents With Severe Obesity Had an Increased Risk of Reporting Symptoms That Indicated They Had Major Depression
Adolescents With Severe Obesity Had an Increased Risk of Reporting Symptoms That Indicated They Had Major Depression Open
Aim This study aimed to compare the severity of depressive symptoms of Hong Kong adolescents with and without obesity and to explore the correlates of depressive symptoms using Patient Health Questionnaire‐9 (PHQ‐9). Methods Participants w…
View article: aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types
aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types Open
Effective data visualization is crucial for researchers, revealing patterns, trends, and insights that might otherwise remain hidden. Integrating related visualizations can reveal correlations and relationships that are not evident when an…
View article: Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications (Small Methods 5/2025)
Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications (Small Methods 5/2025) Open
View article: EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research
EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research Open
Host-microbiome interactions are crucial in maintaining physiological homeostasis and influencing disease progression. While traditional microbiome research, focused on microbial diversity and abundance, provided essential frameworks, the …
View article: Precise Characterization of Cellular States and Spatial Variable Patterns within Spatial Transcriptomics
Precise Characterization of Cellular States and Spatial Variable Patterns within Spatial Transcriptomics Open
Spatial transcriptomics enables the simultaneous characterization of gene expression and spatial organization, providing transformative insights into tissue architecture and function. While numerous tools have been developed to identify sp…
View article: <scp>16S rRNA</scp> Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis
<span>16S rRNA</span> Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis Open
Background Chronic actinic dermatitis (CAD) is a refractory photoallergic skin disease characterized by inflammatory infiltration and UV sensitivity. While the role of microbiome dysbiosis has been established in various inflammatory skin …
View article: Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using <i>treeio</i> and <i>ggtree</i>
Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using <i>treeio</i> and <i>ggtree</i> Open
In metabarcoding research, such as taxon identification, phylogenetic placement plays a critical role. However, many existing phylogenetic placement methods lack comprehensive features for downstream analysis and visualization. Visualizati…
View article: Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0
Enhancing immuno-oncology investigations through multidimensional decoding of tumor microenvironment with IOBR 2.0 Open
The use of large transcriptome datasets has greatly improved our understanding of the tumor microenvironment (TME) and helped develop precise immunotherapies. The growing application of multi-omics, single-cell RNA sequencing (scRNA-seq), …
View article: Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease
Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease Open
Review Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease Shenghe Wang 1,2, Guangchuang Yu 3 and Liwei Xie 1,4,5,* 1 State Key Laboratory of Applied Microbiology Southern China, Guangdong Provi…
View article: Thirteen years of clusterProfiler
Thirteen years of clusterProfiler Open
View article: mirrorselect: Test CRAN/Bioconductor Mirror Speed
mirrorselect: Test CRAN/Bioconductor Mirror Speed Open
View article: tigeR: Tumor immunotherapy gene expression data analysis R package
tigeR: Tumor immunotherapy gene expression data analysis R package Open
Immunotherapy shows great promise for treating advanced cancers, but its effectiveness varies widely among different patients and cancer types. Identifying biomarkers and developing robust predictive models to discern which patients are mo…
View article: Reducing language barriers, promoting information absorption, and communication using fanyi
Reducing language barriers, promoting information absorption, and communication using fanyi Open
Interpreting genes of interest is essential for identifying molecular mechanisms, but acquiring such information typically involves tedious manual retrieval. To streamline this process, the fanyi package offers tools to retrieve gene infor…
View article: Decoding the brain: Unveiling comprehensive cellular atlases through multiomics mega-data
Decoding the brain: Unveiling comprehensive cellular atlases through multiomics mega-data Open
View article: Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis
Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis Open
Objective Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome–metabolome interface in AS. Ba…
View article: Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic
Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic Open
Neural fields can efficiently encode three-dimensional (3D) scenes, providing a bridge between two-dimensional (2D) images and virtual reality. This method becomes a trendsetter in bringing the metaverse into vivo life. It has initially ca…
View article: Resolving tumor evolution: a phylogenetic approach
Resolving tumor evolution: a phylogenetic approach Open
View article: shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals
shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals Open
The molecular clock model is fundamental for inferring species divergence times from molecular sequences. However, its direct application may introduce significant biases due to sequencing errors, recombination events, and inaccurately lab…
View article: Robust expansion of phylogeny for fast-growing genome sequence data
Robust expansion of phylogeny for fast-growing genome sequence data Open
Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. ‘TIPars’ was developed for such challenge integrating parsimony analysis with pr…
View article: ggVennDiagram: Intuitive Venn diagram software extended
ggVennDiagram: Intuitive Venn diagram software extended Open
Highlights of ggVennDiagram include: (1) Subset/Region filling Venn diagram up to seven sets; (2) Upset plot with unlimited sets; (3) Venn Calculator for two or more sets; (4) Provide as R package, Shiny App, and TBtools plugin.
View article: Editorial: Single-cell and spatial-omics in delineating immune-related diseases
Editorial: Single-cell and spatial-omics in delineating immune-related diseases Open
EDITORIAL article Front. Cell Dev. Biol., 16 January 2024Sec. Molecular and Cellular Pathology Volume 12 - 2024 | https://doi.org/10.3389/fcell.2024.1365242
View article: IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research
IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research Open
The use of large transcriptome datasets has greatly improved our understanding of the tumor microenvironment (TME) and helped develop precise immunotherapies. The increasing popularity of multi-omics sequencing, single-cell transcriptome s…