RNA-Seq and XAI Can be Used as Tools to Aid Pathologists in the Process of Cancer Diagnosis.

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...

Computational approaches and data analysis tools for comprehensive non-coding small RNA profiling in liquid biopsies

This thesis demonstrates that the integration of refined isomiR and tRF profiles within targeted liquid biopsy populations (TEPs and PD), supported by advanced bioinformatics tools like miRGalaxy, significantly enhances the accuracy and sensitivity of cancer diagnosis.

Identification of altered biological processes in heterogeneous RNA-sequencing data by discretization of expression profiles

AI/ML-Driven Gene Analysis: New Perspectives on Variant Calling in Normal Human Tissue Using scRNA-seq Data.

This chapter introduces a practical protocol that contrasts a conventional variant-calling approach with a modern AI/ML-based method using single-cell RNA sequencing (scRNA-seq) data, and demonstrates that AI-based methods, such as DeepVariant, provide enhanced accuracy and confidence in genotype prediction compared to...

MicroRNAs and Their Profiling via Single-Cell Sequencing Technologies.

The potential of single-cell miRNA profiling to contribute to precision medicine and therapeutic development is outlined, including its possible use in biomarker discovery, monitoring tumor heterogeneity, and informing personalized treatment strategies.

Comprehensive and bias-aware analysis of small RNA NGS data for biomarker detection with caRNAge

Aim: Small RNA sequencing (small RNA-Seq) is a widely used and important method for biomarker discovery in extracellular vesicles (EVs), which carry small RNAs among their cargo and protect them from degradation in liquid biopsies. However, existing computational tools for small RNA-Seq data are not tailored to EV-RNA....