A5100373200- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Respiratory viral infections research
- Extracellular vesicles in disease
- SARS-CoV-2 detection and testing
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Sparse and Compressive Sensing Techniques
- Advanced Data Compression Techniques
- Advanced Fluorescence Microscopy Techniques
- Advanced Biosensing Techniques and Applications
- Mitochondrial Function and Pathology
- Hydrocarbon exploration and reservoir analysis
- Computational Drug Discovery Methods
- Traumatic Brain Injury and Neurovascular Disturbances
- Scientific Computing and Data Management
- RNA and protein synthesis mechanisms
- Advanced Adaptive Filtering Techniques
- Coal Combustion and Slurry Processing
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Enhanced Oil Recovery Techniques
University of Michigan
2023-2025
Boston University
2020-2024
Wellcome Sanger Institute
2024
University School
2021
ShanghaiTech University
2021
University of Utah
2019
Abstract Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, various technical artifacts present in scRNA-seq data and should assessed before performing downstream analyses. While several tools have been developed perform individual quality control (QC) tasks, they are scattered different packages across programming environments. Here, streamline the process of generating visualizing QC metrics for data, we built...
Many datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While biospecimen experimental information is often captured, detailed metadata standards related data matrices analysis workflows currently lacking. To address this, we develop the matrix (MAMS) serve as a resource for centers, repositories, tool developers. We define fields parameters commonly utilized in analytical developed rmams package extract MAMS from...
Abstract Summary Cells differentiate to their final fates along unique trajectories, often involving multi-potent progenitors that can produce multiple terminally differentiated cell types. Recent developments in single-cell transcriptomic and epigenomic measurement provide tremendous opportunities for mapping these trajectories. The visualization of data relies on dimension reduction methods such as UMAP simplify high-dimensional down an understandable two-dimensional (2D) form. However,...
Abstract The sand erosion detection sensor in the outlet pipe of subsea tree is an effective tool to assess extent which trees are affected by during offshore oil and gas extraction operations. has intricate structures numerous pipeline components, necessitating study optimal installation position ensure sensitivity sensor. This paper carries out a simulation determine tree. By integrating correlation analysis, experimental data comparison other methods, this analyzes verifies that...
Abstract Nearby cells within tissues communicate through ligand-receptor signaling interactions. Emerging spatial transcriptomic technologies provide a tremendous opportunity to systematically detect signaling, but no method operates at cellular resolution in the context. We developed CytoSignal infer locations and dynamics of cell-cell communication from data. is based on simple insight that protein-protein interaction occurs specific tissue location when ligand receptor are expressed close...
Analysis of single-cell RNA sequencing (scRNA-seq) data can reveal novel insights into the heterogeneity complex biological systems. Many tools and workflows have been developed to perform different types analyses. However, these are spread across packages or programming environments, rely on underlying structures, only be utilized by people with knowledge languages. In Single-Cell Toolkit 2 (SCTK2), we integrated a variety popular various aspects scRNA-seq analysis. All run in R console...
Abstract Repetitive head impacts (RHI) sustained from contact sports are the largest risk factor for chronic traumatic encephalopathy (CTE). Currently, CTE can only be diagnosed after death and multicellular cascade of events that trigger initial hyperphosphorylated tau (p-tau) deposition remain unclear. Further, symptoms endorsed by young individuals with early disease not fully explained extent p-tau deposition, severely hampering development therapeutic interventions. Here, we show RHI...
The identification of gene regulatory networks (GRN) governing distinct cell fates in multilineage cellular differentiation systems is critical importance for understanding fate decision. Single-cell RNA-sequencing (scRNA-seq) provides a powerful tool the quantification gene-level co-variation across state manifold. However, accurate GRN reconstruction hampered by sparsity scRNA-seq data introducing substantial technical noise. Moreover, high dimensionality typical datasets limits...
Abstract SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in the airway epithelium. The similarities differences of VE (ACE2, TMPRSS2, CTSL) across nasal bronchial compartments have not been fully characterized using matched samples from large cohorts. Gene data 793 1673 brushes obtained individuals participating lung cancer screening or diagnostic workup revealed that smoking status (current versus former) was only clinical factor...
A large number of genomic and imaging datasets are being produced by consortia that seek to characterize healthy disease tissues at single-cell resolution. While much effort has been devoted capturing information related biospecimen experimental procedures, the metadata standards describe data matrices analysis workflows them relatively lacking. Detailed schema needed facilitate sharing interoperability across groups promote provenance for reproducibility. To address this need, we developed...
Recent work has shown the promise of cold flow technology for transporting waxy crude oils below their wax appearance temperatures. The thermal flux that results due to difference between temperature transported oil and ambient is minimized in implementation flow, thus significantly lowering deposition on pipeline walls. Restarting pipelines carrying under conditions an important consideration. In previous from our laboratory, we have gelled restart pressures water-free systems are lower...
The polymerase chain reaction (PCR)-based gene targeting method, which can delete a specific or introduce tags, has been widely utilized to study function in fission yeast. One of the critical steps this method is design primers for amplifying DNA fragments deletion tagging modules and checking integration those at designated loci. Although primer tool Pombe PCR Primer Program (PPPP) available Schizosaccharomyces pombe, there no such publicly application other three yeast species, S....
Abstract Single-cell RNA sequencing (scRNA-seq) can be used to gain insights into cellular heterogeneity within complex tissues. However, a variety of technical artifacts present in scRNA-seq data and need assessed before downstream analyses performed. While several algorithms tools have been developed perform individual quality control (QC) tasks, they are scattered different packages across programming environments. Comprehensive pipelines streamline the process generating visualizing QC...
Background : SARS-CoV-2 infection and disease severity are influenced by viral entry (VE) gene expression patterns in airway epithelium. The similarities differences of VE (ACE2, TMPRSS2, CTSL) across nasal bronchial compartments has not been fully characterized using matched samples from large cohorts. Results Gene data 793 1,673 brushes obtained individuals participating lung cancer screening or diagnostic workup revealed that smoking was the only clinical factor significantly reproducibly...
Abstract Summary Cells differentiate to their final fates along unique trajectories, often involving multi-potent progenitors that can produce multiple terminally differentiated cell types. Recent developments in single-cell transcriptomic and epigenomic measurement provide tremendous opportunities for mapping these trajectories. The visualization of data relies on dimension reduction methods such as UMAP simplify high-dimensional down into an understandable two-dimensional (2D) form....
Abstract The identification of gene regulatory networks (GRNs) is crucial for understanding cellular differentiation. Single-cell RNA sequencing data encode gene-level covariations at high resolution, yet sparsity and dimensionality hamper accurate scalable GRN reconstruction. To overcome these challenges, we introduce NetID leveraging homogenous metacells while avoiding spurious gene–gene correlations. Benchmarking demonstrates superior performance compared to imputation-based methods. By...
Primary graft dysfunction (PGD) and chronic lung allograft (CLAD) are critical challenges in transplantation. Dysregulated gene expression epigenomic states mesenchymal cells (MCs) play a key role these conditions, but further work is needed to elucidate the biomarkers molecular drivers. Single-cell multi-omic technologies offer an unprecedented opportunity address this gap by jointly measuring chromatin accessibility diseased healthy cells. We performed single-cell profiling genetic...
Summary Analysis of single-cell RNA-seq (scRNA-seq) data can reveal novel insights into heterogeneity complex biological systems. Many tools and workflows have been developed to perform different types analysis. However, these are spread across packages or programming environments, rely on underlying structures, only be utilized by people with knowledge languages. In the Single Cell Toolkit 2.0 (SCTK2.0), we integrated a variety popular various aspects scRNA-seq All run in R console using an...
Analysis of single-cell RNA-seq (scRNA-seq) data can reveal novel insights into heterogeneity complex biological systems. Many tools and workflows have been developed to perform different types analysis. However, these are spread across packages or programming environments, rely on underlying structures, only be utilized by people with knowledge languages. In the Single Cell Toolkit 2.0 (SCTK2.0), we integrated a variety popular various aspects scRNA-seq All run in R console using an...
Abstract Coronavirus Disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 SARS-CoV-2), which infects host cells with help from the Viral Entry (VE) proteins ACE2, TMPRSS2, and CTSL 1–4 . Proposed risk factors for viral infection, as well rate of disease progression, include age 5,6 , sex 7 chronic obstructive pulmonary 7,8 cancer 9 cigarette smoking 10–13 To investigate whether proposed increase infection modulation VE genes, we examined gene expression...