A5083681157- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- CAR-T cell therapy research
- Biosimilars and Bioanalytical Methods
- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Neuroinflammation and Neurodegeneration Mechanisms
- Cancer Cells and Metastasis
- Cell Image Analysis Techniques
10X Genomics (United States)
2023
University of British Columbia
2020-2022
Canada's Michael Smith Genome Sciences Centre
2020-2021
Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available provide transcriptome single-cell, spatial, or targeted situ analysis. Here, we combine these to explore heterogeneity large, FFPE human breast cancer sections. This integrative approach allowed us differences exist between distinct tumor regions identify biomarkers involved progression towards...
Abstract Chimeric antigen receptor T cell (CAR-T) expansion and persistence vary widely among patients predict both efficacy toxicity. However, the mechanisms underlying clinical outcomes patient variability are poorly defined. In this study, we developed a mathematical description of responses wherein transitions memory, effector exhausted states coordinately regulated by tumor engagement. The model is trained using data from CAR-T products in different hematological malignancies identifies...
Abstract Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent processing and quality control, probe–gene mappings across microarray technologies. Thus, extensive curation reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created help address these issues. consists a database curated datasets, analytical software, web interface services. Here we...
Transcriptionally profiling minor cellular populations remains an ongoing challenge in molecular genomics. Single-cell RNA sequencing has provided valuable insights into a number of hypotheses, but practical and analytical challenges have limited its widespread adoption. A similar approach, which we term single-cell type (sctRNA-seq), involves the enrichment pool cells, yielding cell type-level resolution transcriptomes. While this approach offers benefits terms mRNA sampling from targeted...
Abstract Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent processing and quality control, probe-gene mappings across microarray technologies. Thus, extensive curation reprocessing is necessary prior to any reuse. The Gemma bioinformatics system was created help address these issues. consists a database curated datasets, analytical software, web interface, services. Here we...
<h3>Background</h3> Tissue array technology enables screening of multiple tissue samples on a single microscopic slide and is an assistive tool in the field oncology, given its ability to investigate cancer markers high-throughput manner. Studying tumor tissues with high resolution situ technologies further unlocks potential profile microenvironment cell heterogeneity at subcellular resolution. Here, we used Xenium Analyzer (10x Genomics) characterize gene expression profiles formalin fixed...
ABSTRACT Voltage gated calcium channels (VGCCs) regulate the influx of ions in many cell types, but our lack knowledge about plethora VGCC splice variants remains a gap understanding channel function. A recent advance profiling gene variation is to use long-read RNA-sequencing technology. We sequenced Cacna1e transcripts from rat thalamus using Oxford Nanopore sequencing, yielding full structure 2,110 variants. However, we observed that only 154 were likely encode for functional based on...