RNA plays a central role in biology, but there is still much to learn about the molecule’s life cycle in the cell. In recent years, scientists have devised methods that can take snapshots of messenger RNAs...
Read More »RIP-PEN-seq – RNA immunoprecipitation coupled with sequencing of paired ends of ncRNAs
A kink-turn (K-turn) is a three-dimensional RNA structure that exists in all three primary phylogenetic domains. Reseaerchers at Sun Yat-sen University have developed the RIP-PEN-seq method to identify the...
Read More »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 in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Researchers at the Centre for Genomic Regulation (CRG), Spain ...
Read More »How to choose normalization methods (TPM/RPKM/FPKM) for mRNA expression
Why do mRNA expression values need to be normalized? The unification of mRNA expression value measurements across studies, or the normalization of mRNA data, is a significant problem in biomedical and life science research. The abundance of transcripts is measured ...
Read More »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 yet are approved only for...
Read More »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. The advent of single cell...
Read More »transXpress – a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails...
Read More »Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction
Dimensionality reduction and visualization play an important role in biological data analysis, such as data interpretation of single-cell RNA sequences (scRNA...
Read More »BarleyExpDB – an integrative gene expression database for barley
RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge...
Read More »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) data. Conventional RNA...
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