Earlier this week, I posted Part 1 of this series, which focused on the importance of meeting with your thesis committee as you near the end of your Ph.D. So at this point, you’ve met with your committee, they think you’re ready to defend, and you’ve decided collectively what you need to do before that defense date. In this post, I will be moving on to…

Part 2 of 5 in The Beginning of the End: Drafting a thesis outline, organizing references, and communicating with your adviser about expectations.

I decided to combine these three steps into one blog post because they all kind of go along with the same idea of PREPARE EARLY.

Before getting started, I just wanted to give special shout outs to Liron Bendor, a recent graduate of the Genetics Ph.D. program, and Dr. Melissa Rolls, Chair of the MCIBS program, for all of their advice that helped me to write this post. You can actually see even more advice from Dr. Rolls on writing your thesis by clicking here!


1. Drafting a thesis outline

A Ph.D. thesis is, from my understanding, on average 120-130 pages, so it’s not exactly a document you can just sit down and start writing without thinking ahead about it first. So what’s the easiest way to organize your thoughts before you write? Make an outline!

Based on the theses that have come out of my lab, it’s my understanding that a thesis contains six main parts: abstract, introduction, materials/methods, results, discussions/conclusions, and references. Depending on your lab/adviser’s style, these parts may be organized a bit differently, but you will certainly need all of them in one way or another.

Side note: Don’t take my advice on making an outline as the truth for any and every program. Make sure to check with your adviser/program chair/other students in your program/lab to see the way a thesis is usually organized for your discipline!!


Abstract: Now, an abstract isn’t something you can necessarily outline, so we’re going to skip that and come back to it in a later post about the actual process of writing

Introduction: The introduction is the section that students often find is one of the hardest parts of writing your thesis because it requires you to not only have a comprehensive background knowledge of your field but also to be able to concisely review that background knowledge. Here are some tips on what an introduction should entail and how you should be outlining/writing it:

  • Covers all the background information for someone to understand the field that your work is contributing to
  • Includes your key questions and hypotheses
  • Add figures/diagrams as needed to help illustrate key points
  • Ends with a paragraph that previews the rest of the thesis by describing chapters and how they relate to the published work as well as collaborations involved in the work
  • Outline topics you need to cover and then break those topics down into individual sections
    • Advice from Liron Bendor: “For each section, I wrote down everything I could remember about that topic then read ~10 review papers per topic, and supplemented my remembered information with essential information from the papers (citing all the way!).”
  • Can start outlining this chapter at any point after your comprehensive exam!!
  • DOES NOT include a list of anything and everything that closely relates to your research project(s) — remember, you want to be CONCISE!

BPj7r9YCEAESdRoMaterials & Methods: Since you had to write your first lab report back in high school or maybe even your freshman year of college, you’ve always had to include a materials and methods section. I can’t tell you how many times I have gone to past lab members’ theses in order to figure out how they did an experiment, so just like you’ve always learned, this section is meant to allow someone to repeat exactly what you did. This section is also something you can start working on simply by organizing the different reagents and protocols you use — trust me, this will be a LIFE SAVER down the road because you won’t be rummaging through freezers and your notebooks trying to figure out where a reagent came from or how much 1X PBS you used to wash your cells. This section will obviously differ based on different labs, but make sure you include items like antibodies, chemicals, kits, primer sequences, etc. for materials and ALL of your protocols!

Also, depending on how you’ve decided to organize your thesis, you can either have this section separately or you can include a materials and methods chapter within specific results chapters if you have multiple projects that are pretty different from each other. Once you get your outline set up, you can better see which would make more sense for you.

Results: The results section can also be pretty difficult, especially if you don’t have much experience in science writing. However, if you’ve already been writing up manuscripts, then you should have a pretty good idea of how to do this. Results sections are often framed around your figures, so getting your figures/tables organized is the first step in writing a results section. If you can’t see the figures/results in front of you, how are you going to describe them!? However, a results section is so much more than just describing what a bar graph shows you, so remember these important tips:

  • Set up the question/reasoning as to WHY you did each experiment, which includes your hypothesis
  • Have a summary sentence/paragraph at the end of each section to wrap everything up
  • Write out the titles of figure legends — this will help you to outline your results section as a whole!

Depending on how you’ve decided to organize your thesis and if you’ve already published papers/are in the process of writing them up (and you’re the first author!), you can actually make each chapter one of those papers! As long as it’s okay with your adviser, of course. Just make sure to include if that chapter is the published paper word-for-word, if it’s the paper plus some additional data, or if it’s only part of the paper. Also, if you’re using results that you yourself did not obtain, make sure to acknowledge him/her specifically and exactly what he/she did!!

Discussions/Conclusions: In my opinion, this is the real meat of any piece of scientific writing as it describes what your results really mean not only to your hypotheses/experimental questions but to the field as a whole. When outlining this section, be sure to include:

  • The main conclusions from each major question
  • How these conclusions have advanced the field
  • What questions still need to be answered
  • If you can, a model that summarizes your findings
2. Organizing your references

Throughout your entire thesis, you will accumulate HUNDREDS of references. If you haven’t already started to organize your references throughout graduate school, I highly suggest making use of a reference manager. Don’t know how? Check out this blog post that Molly wrote!

3. Communicating with your adviser about expectationsunnamed

Once you’ve got a solid outline of your thesis drafted, sit down with your adviser and go over this outline to see if you’re missing anything major and also to see if he/she likes the way you’ve organized it. This is also a good opportunity to start talking about expectations:

  • How many pages/words should the thesis be?
  • How many chapters should there be?
  • How long should each section (introduction, results, etc.) be? You might be thinking a 40-page introduction section is perfect while he/she thinks 20 is plenty.

If you don’t have access to theses from previous lab members, you can ask your adviser for them to see as a reference. Also during this meeting would be a good idea to talk about a timeline. Your thesis is due to your committee two weeks before your defense, but your adviser will likely want to see it before then, but how much earlier than then? If this is your first major writing experience, my guess is at least a month before your defense. However, a 120-130 page document is a lot to edit at once, so you should try setting up a timeline of when you will get specific chapters to your adviser. Working on deadlines like this will likely also keep you motivated to keep writing!


Coming up next in Part 3 of 5 of The Beginning of the End is understanding the formatting guidelines required by the Graduate School! I’ve heard from quite a few sources that they can be confusing, so I’m going to try to break this down into a more simplified format. Stay tuned!

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