Detection of pathogenic infections in neurological disorders through recycling of gene expression data

1 Introduction
2 Biological background
2.1 Ribonucleic acid (RNA)
2.2 Small RNA
2.3 Sequencing
2.4 Microbiology
2.5 Neurodegenerative diseases
2.6 Pathogens in neurological diseases
3
Bioinformatics background
3.1 Data sources
3.2 Metadata and biological ontologies
3.3 Read alignment
3.4 Comparative analysis
3.5 Metagenomic analysis
3.6 Integrated analysis pipelines
4 Computer science background
4.1 Web development
4.2 Data science and machine learning
5 Small RNA Expression Atlas (SEA)
5.1 Background
5.2 System architecture
5.3 Implementation
5.4 System behavior
5.5 Results
6 Biological discoveries through SEA
6.1 Tissue specificity of small RNA
6.2 User data and Parkinson’s disease
6.3 Pathogens in neurodegenerative diseases
6.4 Sex specificity of small RNA in human body
6.5 Discussion
7 Pathogen detection in RNA-seq data
7.1 Background
7.2 Identification algorithm
7.3 Performance measures
7.4 Evaluation
8 Path(ogen)s to disease
8.1 Analysis pipeline
8.2 Burkholderia stabilis in frontotemporal dementia
8.3 Discussion
9 Conclusion
Bibliography
A SEA JSON communication objects
B Pathonoia algorithms
C Detailed analysis results