| 摘要 | 第1-7页 |
| Abstract | 第7-11页 |
| Chapter 1 Introduction | 第11-21页 |
| ·Background | 第11-14页 |
| ·Syllabus of the results | 第14-21页 |
| Chapter 2 Elements of RNA structures and RNA-RNA interaction problems | 第21-45页 |
| ·Representation and combinatorics of RNA structures | 第21-27页 |
| ·Energy model of RNA secondary structures | 第27-29页 |
| ·RNA-RNA interaction problems | 第29-34页 |
| ·Partition function and base pairing probabilities | 第34-45页 |
| Chapter 3 Canonical joint structures prediction over multiple sequence alignments | 第45-75页 |
| ·Canonical joint structures over MSAs | 第45-48页 |
| ·(R,S)-compatible joint structures | 第48-49页 |
| ·Energy model of canonical joint structures | 第49-51页 |
| ·Grammar and partition function of canonical joint strutures | 第51-62页 |
| ·The Bolzmann sampling and base pairing probabilities | 第62-66页 |
| ·Conclusion and Discussion | 第66-75页 |
| Chapter 4 Topological enumeration of RNA structures | 第75-93页 |
| ·Genus of linear chord diagram | 第75-80页 |
| ·Construction of shadows | 第80-93页 |
| Bibliography | 第93-99页 |
| 致谢 | 第99-101页 |
| 个人简介 | 第101页 |
