x

Contents

7

EEG-based BCI Systems in Neuropsychiatric Diseases

174

Emine Elif Tülay

7.1

Introduction

. . . . . . . . . . . . . . . . . . . . . . . . . . .

174

7.2

Understanding the Brain-Computer Interface (BCI)

. . . . .

175

7.2.1

What is BCI? . . . . . . . . . . . . . . . . . . . . . . .

175

7.2.2

History of EEG-based BCI

. . . . . . . . . . . . . . .

176

7.2.3

Categories of EEG-based BCI . . . . . . . . . . . . . .

177

7.2.4

Hardware and Software Technology of EEG-based BCI

Systems . . . . . . . . . . . . . . . . . . . . . . . . . .

178

7.3

Phases of EEG-based BCI Systems

. . . . . . . . . . . . . .

179

7.3.1

Acquisition of EEG Signals . . . . . . . . . . . . . . .

179

7.3.2

Encoding Paradigms for EEG-based BCI

. . . . . . .

179

7.3.3

Pre-processing of EEG Signals

. . . . . . . . . . . . .

180

7.3.4

Feature Extraction Methods for EEG-based BCI . . .

181

7.3.5

Artificial Intelligence Techniques in EEG-based BCI

Systems for Neural Decoding . . . . . . . . . . . . . .

182

7.4

Current BCI Systems Applications . . . . . . . . . . . . . . .

184

7.4.1

Control of Computer Systems and External Devices

.

185

7.4.2

Decoding Mental States in Neuropsychiatric Diseases .

185

7.5

Challenges and Future Perspectives

. . . . . . . . . . . . . .

187

7.6

Conclusion

. . . . . . . . . . . . . . . . . . . . . . . . . . . .

188

7.7

Acknowledgment . . . . . . . . . . . . . . . . . . . . . . . . .

189

Bibliography

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

189

8

Bioinformatics of Brain Diseases

198

Tuba Sevimoglu

8.1

Introduction

. . . . . . . . . . . . . . . . . . . . . . . . . . .

198

8.2

Analyzing the Brain Transcriptome

. . . . . . . . . . . . . .

199

8.2.1

Microarrays . . . . . . . . . . . . . . . . . . . . . . . .

199

8.2.2

RNA-seq Technologies . . . . . . . . . . . . . . . . . .

201

8.3

Repositories

. . . . . . . . . . . . . . . . . . . . . . . . . . .

202

8.4

Data Analysis and Visualization Tools . . . . . . . . . . . . .

202

8.5

Bioinformatics Studies on Brain Diseases and Disorders

. . .

204

8.5.1

Microarray Studies . . . . . . . . . . . . . . . . . . . .

205

8.5.2

RNA-seq Studies . . . . . . . . . . . . . . . . . . . . .

208

8.6

Integration of Brain Transcriptomics and Imaging Data

. . .

212

8.7

Future Perspectives

. . . . . . . . . . . . . . . . . . . . . . .

213

8.8

Conclusion

. . . . . . . . . . . . . . . . . . . . . . . . . . . .

214

Bibliography

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

214

9

Complex Brain Networks: A Graph-Theoretical Analysis

224

Kayhan Erciyes

9.1

Introduction

. . . . . . . . . . . . . . . . . . . . . . . . . . .

224

9.2

Brain Network Construction

. . . . . . . . . . . . . . . . . .

225

9.3

Analysis Parameters . . . . . . . . . . . . . . . . . . . . . . .

227