Comprehensive and scalable quantification of splicing differences with MntJULiP | Genome Biology
Tools for differential splicing detection have failed to provide a comprehensive and consistent view of splicing variation. Researchers present MntJULiP, a novel method for comprehensive and accurate quantification of splicing differences between two or more conditions. MntJULiP detects both changes in intron splicing ratios and changes in absolute splicing levels with high accuracy, and can find classes of variation overlooked by other tools.
Identification of spatially variable genes with graph cuts | Nature Communications
Single-cell gene expression data with positional information is critical to dissect mechanisms and architectures of multicellular organisms, but the potential is limited by the scalability of current data analysis strategies. Here, researchers present scGCO, a method based on fast optimization of hidden Markov Random Fields with graph cuts to identify spatially variable genes.
APPRIS principal isoforms and MANE Select transcripts define reference splice variants | Bioinformatics
Selecting the splice variant that best represents a coding gene is a crucial first step in many experimental analyses, and vital for mapping clinically relevant variants. This study compares the longest isoforms, MANE Select transcripts, APPRIS principal isoforms, and expression data, and aims to determine which method is best for selecting biological important reference splice variants for large-scale analyses. Proteomics analyses and human genetic variation data suggest that most coding genes have a single main protein isoform. They show that APPRIS principal isoforms and MANE Select transcripts best describe these main cellular isoforms, and find that using the longest splice variant as the representative is a poor strategy.