Colette Felton
A5033485094- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- RNA regulation and disease
University of California, Santa Cruz
2022-2025
Santa Cruz County Office of Education
2023
University of California System
2023
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, consortium generated over 427 million sequences from complementary DNA direct RNA datasets, encompassing human, mouse manatee species. Developers utilized these data address challenges in transcript isoform detection, quantification de novo detection. study revealed that...
Abstract The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. consortium generated over 427 million sequences from cDNA and direct RNA datasets, encompassing human, mouse, manatee species, using different protocols sequencing platforms. These data were utilized by developers address challenges in transcript isoform detection quantification, as well de novo identification....
Abstract Although most cancer variant profiling is done with short-read-based methods, many cancers are driven by structural variants that difficult to detect these methods. Our current approach understanding driver mutations also limited single and rarely considers the context in which they expressed. Alterations expression splicing of genes containing can both impact their tumorigenicity allow them develop resistance therapies. We present FLAIR3, generates a custom transcriptome from...
Abstract Background RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these variants a variety of diseases. Aberrant splicing and single nucleotide (SNVs) have been demonstrated to alter transcript stability, localization, function. In particular, the upregulation ADAR, an enzyme that mediates adenosine-to-inosine editing, previously linked increase invasiveness lung adenocarcinoma cells associated with regulation. Despite functional...
ABSTRACT Genome-wide identification of chromatin organization and structure has been generally probed by measuring accessibility the underlying DNA to nucleases or methyltransferases. These methods either only observe positioning a single nucleosome rely on large enzymes modify cleave DNA. We developed adduct sequencing (Add-seq), method probe treating with small molecule angelicin, which preferentially intercalates into not bound core nucleosomes. show that Nanopore angelicin-modified is...
U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA alterations; however, full-length altered mRNA isoforms associated with mutation are largely unknown. To better understand impact on isoform fate function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells without a S34F mutation. We identified 49,366 multi-exon transcript isoforms, more than half...
Abstract Gene fusions are important cancer drivers and drug targets, but difficult to reliably identify with short-read RNA-sequencing. Long-read RNA sequencing data more likely span a fusion breakpoint provide sequence context around the breakpoint. This allows for reliable identification of gene detecting alternative splicing in fusions. Notably, has been shown be mechanism resistance altered levels oncogenicity. Here, we present FLAIR-fusion, computational tool their isoforms from...