Thesis Preparation

A student can write a traditional thesis or a manuscript-based thesis. In the department, the vast majority of students write manuscript-based thesis.

  • Traditional thesis: you write the full story of your PhD, with exactly the data/results you need and that you did. It follows a classic plan, see official guidelines.
  • Manuscript-based thesis: you write introduction, and links between your manuscripts, and a discussion/conclusion. But then you include the manuscript as it is in press. You can include only manuscripts in which you are first author (or co-author with non-thesis researchers).

Important rules

If two students in the thesis program are co-authors, only one can put it in their thesis. Officially, a paper can only be part in one thesis, for some copyright reasons. You can put data and results, but not the “manuscript” as is if it’s also part of another thesis. This applies if the students are writing a manuscript-based thesis (see next paragraph).

Frequently Asked Questions

Can a review be one of the chapters? No, but it would do a good introduction.

Other information

At the PhD level you are expected to present a completely original project proposal. This means you expect to get results that no one has ever published in a peer reviewed journal before. Sounds daunting, but as I have mentioned, your supervisor can (and should!) give you some guidance. They are the experts in this field, not you (yet) so they will know what has been done and what others in the field are interested in finding out. Your proposal should be double-spaced with the following sections:

▪   Title page: the full title (sometimes working title) of the project, your name, any accompanying authors (for example, if your proposal is based on unpublished work from people in your lab), supervisor, date and department.

▪   Introduction: This is a concise summary of background information that someone not in your field would need to know in order to understand your proposal. For example: If you are proposing to use a study population to map a disease modifying gene you may want to write a section on the disease (symptoms, incidence, current findings etc), a section on the population and why they are suitable for your use, a section describing the effectiveness of the method you will use to map the gene, etc.

▪   Rationale, Hypothesis and Objectives: This can be made into one section or divided into three, depending on length. If you’re wordy, go with three sections for clarity, if you can keep it short, go with one. Here you’ll have to state why you think it’s important to pursue each objective. You will likely end up using already published data (or your own previous unpublished data) as precedent. You may also want to include potential problems you expect to encounter (although many times people choose to exclude this and let their committee ask then at the qualifying exam in order to take up time, this is a useful tip!). The hypothesis should be pretty self-explanatory by now, however some projects (like the mapping one I just described) don’t lend themselves well to creating a “real” hypothesis since you have no idea what you’ll find. In this case talk to your supervisor and work out what seems most appropriate, the answer will likely be based on what others have written in published reports on the subject. Objectives, again, are pretty self-explanatory. The “standard” PhD thesis has three objectives; presumably each objective will contain enough research to publish one paper on. Many people I have seen graduate from the department plan it like this: one objective=one publication=one chapter of final thesis. Don’t feel panicked though if you have less than three or many more than three objectives. You may end up combining a couple into one paper (or chapter) or expanding one or two as you collect more and more data. In any case, your goal is to make attainable objectives and to state them in a concise, easy to understand manner.

▪   Progress and methods: This may be the bulk of your proposal if you are a candidate for “switching over” (ie. an MSc student planning to switch to the PhD program without first finishing the MSc), and have already accumulated two years worth of data. It will include any work you’ve already done towards your objectives. Also in this section you will describe the methods you used in order to achieve each objective. Now, this doesn’t mean you have to write each primer sequence, each buffer recipe or anything, but if you’re using a technique not considered “standard lab protocol”, you may want to describe how it works in order to convince people it’s the right one to use.

▪   Future work: If you are a PhD student with a Masters from elsewhere and are doing the QE within your first 15 months, this is your crucial section. It will include rationale and methods for each objective you plan on finishing. Again, the methods don’t have to be super detailed, but it has to be clear why you are using them. Here you will mention precedent from the literature that backs up your decision to pursue each objective. You can get a bit creative in this section so don’t feel bad if some of the experiments you suggest here don’t end up getting done for our thesis. Each project can turn in a different direction if the results lead one way or another.

▪   Conclusion: Sum up your project and what you expect to accomplish. Now for the big finish state how this research will impact the scientific community and the general public. Don’t be afraid to be confident here, make sure people understand that your work is important (this comes in useful when applying for funding!). There’s an element of salesmanship when it comes to your work, so don’t sell yourself short!

▪   References: Also, standard fare. As for formatting, most times it’s authors choice, but stick to one of the more standard styles and keep it consistent the whole way through.

▪   Figures and Tables: Sometimes these are needed as part of your rationale, pointing to work you’ve already done or someone has recently done that backs you up. A picture speaks a thousand words, as they say, so this is a good way to drive home important points. Don’t go overboard though, you don’t need a figure for every result you talk about, just pick the big ones and/or ones that are better understood visually rather than verbally.

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