Y.-H. Taguchi

Reduced Detection of Human Orphan Gene Transcripts in Disease Tissue Relative to Expression- and Detection- Matched Controls

Human orphan genes are poorly annotated and lowly expressed, which makes their behavior in disease difficult to establish. We analyzed paired normal and disease RNA-seq libraries from four cohorts, quantified against a combined reference in which 2190 of 198,507 transcripts are orphan. Cohorts were first screened for l...

Novel two-stage deep learning-based approach applied to gene expression data pertaining to esophageal adenocarcinoma boosting biological knowledge discovery

Tensor Decomposition-Based Unsupervised Feature Extraction Applied to Bioinformatics.

This chapter presents tensor decomposition (TD)-based unsupervised feature extraction (FE) as a robust framework for feature selection in bioinformatics and provides a versatile and effective approach for extracting meaningful biological insights from complex, high-dimensional datasets.

Comprehensive Guide to Gene Expression Analysis from Bulk and Single-Nucleus Transcriptomes.

This chapter covers quality control, normalization, sparse data handling, and transcript quantification for both bulk and snRNA-seq, along with strategies to address challenges such as multi-mapped reads and batch effects, and examines how artificial intelligence and machine learning techniques can improve data process...