A5045634893- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
Institute of Organic Chemistry
2024
University of California, Santa Cruz
2019-2021
Determining the layers of gene regulation within innate immune response is critical to our understanding cellular responses infection and dysregulation in disease. We identified a conserved mechanism human mouse via changes alternative first exon (AFE) usage following inflammation, resulting isoforms produced. Of these AFE events, we 95 unannotated transcription start sites mice using de novo transcriptome generated by long-read native RNA-sequencing, one which cytosolic receptor for dsDNA...
Retrons are a retroelement class found in diverse prokaryotes that can be adapted to augment CRISPR-Cas9 genome engineering technology efficiently rewrite short stretches of genetic information bacteria and yeast; however, efficiency human cells has been limited by unknown factors. We identified non-coding RNA (ncRNA) instability impaired Cas9 activity as major contributors poor retron editor efficiency. re-engineered the Eco1 ncRNA incorporate an exoribonuclease-resistant pseudoknot from...
Abstract Determining the layers of gene regulation within innate immune response is critical to our understanding cellular responses infection and dysregulation in disease. We identified a conserved mechanism human mouse via changes alternative first exon (AFE) usage following inflammation, resulting isoform usage. Of these AFE events, we 50 unannotated transcription start sites (TSS) mice using Oxford Nanopore native RNA sequencing, one which cytosolic receptor for dsDNA known inflammatory...
The reproducibility of gene expression measured by RNA sequencing (RNA-Seq) is dependent on the depth. While unmapped or non-exonic reads do not contribute to quantification, duplicate quantification but are informative for reproducibility. We show that mapped, exonic, non-duplicate (MEND) a useful measure RNA-Seq datasets used analysis.
Abstract Gene expression analysis of single samples shows increasing promise for clinical applications. However, obtaining high quality RNA from a human tumor sample can be challenging because medical, surgical, and pathological requirements often lead to sparse or degraded RNA. The variability in presents challenges defining input requirements, which are required calculate sensitivity, specificity reference ranges as Clinical Laboratory Improvement Amendments (CLIA)-approved test. RNA-Seq...
Abstract Background The accuracy of gene expression as measured by RNA sequencing (RNA-Seq) is dependent on the amount performed. However, some types reads are not informative for determining this accuracy. Unmapped and non-exonic do contribute to quantification. Duplicate can be product high or technical errors. Findings We surveyed bulk RNA-Seq datasets from 2179 tumors in 48 cohorts determine fractions uninformative reads. Total sequence depth was 0.2-668 million (median (med.) 61...