In order of their appearance in the final document...
- Chapter 1 - Introduction. This is essentially an executive summary. You should briefly describe all contributions your thesis makes to your field, provide at least one "gee-whiz" result, and lay out a roadmap for the rest of the thesis ("In Chapter 2, I present the background... In Chapter 3, I discuss my work on X...."). It is acceptable to make claims without proof, since you will be defending these later on.
- Chapter 2 - Background. This is essentially a literature review, and demonstrates your understanding of the field and the context surrounding your work. For bioinformatics theses, this covers both the biomedical domain and the area of informatics or computation your work involves. You should present an intellectual framework in which your work fits - what has been done, the advantages and limitations of this previous work, the potential avenues for improvement, and where you come in. Ideally, this chapter could be published as a review article with very little modification.
- GENERAL THEME: Several projects
Chapter 3 - Methods, Results, and Discussion from paper 1
Chapter 4 - Methods, Results, and Discussion from paper 2
(Chapter 5 - Methods, Results, and Discussion from paper 3, if applicable)
FOCUSED THEME: Single project
Chapter 3 - Methods
Chapter 4 - Results/Discussion
(Chapters 5 and 6 - Methods and Results/Discussion for approach 2, if applicable)
In general, you do not want to reuse text from your published papers verbatim, despite how tempting this can be. Papers are very strict and limit what you can express, so you should see your thesis as an opportunity to pontificate and give voice to your ideas. You should also form your thesis into a detailed guide of everything you tried, even some of the things that didn't work, so that it can be a reference to future generations of grad students who may pursue extensions of your research.
- Chapter 6 or 7, depending on type of thesis - Summary chapter. Describe overall contributions to the relevant domains. (For biomedical informatics theses, describe the overall contributions to biology or medicine, and the overall contributions to informatics or engineering. If applicable, you may also describe core contributions to computer science.) Here is where you also discuss the limitations of the work, the unsolved problems, and your best ideas for how to solve them.
- Appendices - supplementary material. Almost anything goes, but you should definitely include all key data and datasets (information needed to recreate the major results from your thesis). Ideally, all data relevant to your thesis (and other related work, if possible) will be stored and/or made available either on the web or as a physical copy, though this is mostly for the advisor as a reference for future students. If you have any proofs or supplementary material, these should be in an appendix. You can also include additional work or papers published unrelated to your thesis.
More specific advice on how to actually write each chapter was not covered and probably warrants its own post. Note that this is my advisor's take on the Ph.D. thesis; I'm sure there are some other interpretations, which would be interesting to hear! How much does the thesis vary by field?