OHSU researchers assemble most extensive atlas of human gene mutations
With hundreds of tissue donors, it is the most extensive guide ever created; could lead…
Browsing: Publications
PUREE – accurate pan-cancer tumor purity estimation from gene expression data
Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion…
RNA extraction method impacts quality metrics and sequencing results in FFPE samples
Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are being increasingly used in molecular cancer research. Compared…
TEMPOmap – a method that uncovers subcellular RNA profiles across time and space at the single-cell level
TEMPOmap can follow thousands of newly made RNA molecules within a cell simultaneously, revealing new…
Nano-tRNAseq – quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult…
Single-cell RNA sequencing determines the evolutionary age of individual cell types
A research team led by Dr Chaogu ZHENG from the School of Biological Sciences at…
Comparison of whole transcriptome sequencing of fresh, frozen, and FFPE cardiac tissue
The use of fresh tissue for molecular studies is preferred but often impossible. Instead, frozen…
Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer
Established prognostic tests based on limited numbers of transcripts can identify high-risk breast cancer patients…
scMSGL – kernelized multiview signed graph learning for single-cell RNA sequencing data
Characterizing the topology of gene regulatory networks (GRNs) is a fundamental problem in systems biology.…
cellDancer – a scalable deep neural network that locally infers velocity for each cell from its neighbors
RNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq)…