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Articles by Cankun Wang
Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation
Keywords spatial transcriptomics single-cell nasal epithelium inflammation chronic rhinosinusitis remodeling autoimmunity nasal polyp type 2 inflammation Introduction Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease of the nasal and sinonasal cavities.
Brain-derived tau oligomer polymorphs: distinct aggregations, stability profiles, and biological activities - Communications Biology
Abstract Aggregation of microtubule-associated tau protein is a distinct hallmark of several neurodegenerative disorders such as Alzheimer’s disease (AD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP). Tau oligomers are suggested to be the primary neurotoxic species that initiate aggregation and propagate prion-like structures. Furthermore, different diseases are shown to have distinct structural characteristics of aggregated tau, denoted as polymorphs.
scGNN+: Adapting ChatGPT for Seamless Tutorial and Code Optimization
Abstract Foundation models have transformed AI by leveraging large-scale data to efficiently perform diverse tasks, and their applications in bioinformatics are primarily focused on data-centric tasks like cell type annotation and gene expression analysis. However, their potential extends beyond data analysis, offering significant opportunities in software development and optimization, such as code refinement, tutorial generation, and advanced visualization.
Autoencoder to Identify Sex-Specific Sub-phenotypes in Alzheimer's Disease Progression Using Longitudinal Electronic Health Records
The authors have declared no competing interest. This study was partially supported by grants from Centers for Disease Control and Prevention (1U18DP006512), National Institute of Environmental Health Sciences (R21ES032762) and the NIH National Center for Advancing Translational Sciences (UL1TR001427). I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD) - Nature Communications
Abstract Alzheimer’s Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability.
A Single-cell and Spatial RNA-seq Database for Alzheimer's Disease (ssREAD)
Abstract Alzheimer's Disease (AD) pathology has been increasingly explored through single-cell and single-nucleus RNA-sequencing (scRNA-seq & snRNA-seq) and spatial transcriptomics (ST). However, the surge in data demands a comprehensive, user-friendly repository. Addressing this, we introduce a single-cell and spatial RNA-seq database for Alzheimer's disease (ssREAD). It offers a broader spectrum of AD-related datasets, an optimized analytical pipeline, and improved usability.
Abnormal Progenitor Cell Differentiation and Cardiomyocyte Proliferation in Hypoplastic Right Heart Syndrome
References 1. LaPar DJ, Bacha E . Pulmonary atresia with intact ventricular septum with borderline tricuspid valve: how small is too small.Semin Thorac Cardiovasc Surg Pediatr Card Surg Annu. 2019; 22:27–31. doi: 10.1053/j.pcsu.2019.02.007CrossrefMedlineGoogle Scholar 2. Contreras J, Alonzo M, Ye S, Lin H, Hernandez-Rosario L, McBride KL, Texter K, Garg V, Zhao MT .
ssREAD: A Single-cell and Spatial RNA-seq Database for Alzheimer's Disease
Abstract Alzheimer's Disease (AD) is a neurodegenerative malady predominantly affecting the elderly and exhibits its debilitating effects on a dementia-prone population.
Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single‐cell transcriptomic analysis
1 BACKGROUND Human Papillomavirus (HPV) infection causes the most common sexually transmitted diseases and up to 5% of human cancer, including anogenital cancer, and head and neck cancer.1-3 Specifically, persistent HPV infection in the host epithelium is one of the critical steps of cervical cancer development.4, 5 Current prophylactic HPV vaccines have enabled the prevention of initial infection and HPV-associated malignancies.
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
Abstract Deciphering the intricate relationships between transcription factors (TFs), enhancers, and genes through the inference of enhancer-driven gene regulatory networks is crucial in understanding gene regulatory programs in a complex biological system.
Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis
Abstract Human Papillomaviruses (HPVs) are associated with around 5-10% of human cancer, notably nearly 99% of cervical cancer. The mechanisms HPV interacts with stratified epithelium (differentiated layers) during the viral life cycle, and oncogenesis remain unclear. In this study, we used single-cell transcriptome analysis to study viral gene and host cell differentiation-associated heterogeneity of HPV-positive cervical cancer tissue.
A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset
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Bulk and single-cell RNA-sequencing analyses along with abundant machine learning methods identify a novel monocyte signature in SKCM
Yuyao Liu1†, Haoxue Zhang2,3,4†, Yan Mao5, Yangyang Shi6, Xu Wang7, Shaomin Shi5*, Delin Hu1* and Shengxiu Liu2,3,4* 1Department of Burns, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China 2Department of Dermatovenerology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China 3Key Laboratory of Dermatology, Ministry of Education, Hefei, Anhui, China 4Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical...
A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data
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Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
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Author Correction: scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses - Nature Communications
Correction to: Nature Communications https://doi.org/10.1038/s41467-021-22197-x, published online 25 March 2021. In Figure 2, panels (a) and (b) were inadvertently swapped. The correct version of this figure appears below. This has been corrected in the HTML and PDF version of this article. Author information Author notes These authors contributed equally: Juexin Wang, Anjun Ma. Affiliations Department of Electrical Engineering and Computer Science, and Christopher S.
DeepMAPS: Single-cell biological network inference using heterogeneous graph transformer
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Biological network inference from single-cell multi-omics data using heterogeneous graph transformer
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