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How to write your Ph.D. thesis

Writing a doctoral thesis—the culmination of years of research work—can be a daunting endeavor. But learning from those who have already tackled this task can help you make the process a little smoother. Science Careers asked recent graduates and current students to reflect on their experiences and what did—and didn’t—work for them.

How did you structure your thesis and approach writing it? How long did it take?

In my department, theses must be no longer than 175 pages plus front matter and appendices. They can be written in either the so-called “traditional thesis format,” which largely consists of a general introduction, a literature review, an overall description of the materials and methods, a presentation of all the results, and a general discussion—or in “manuscript format,” where the main chapters are written as standalone publishable articles between a general introduction and discussion. For my thesis, which I started writing just a couple of months ago, I have chosen the manuscript format.
- Leslie Holmes, Ph.D. candidate in biology at Queen’s University in Kingston, Canada

I wasn't given any specific guidelines on the format or content. The most common advice at my university back in Italy was to look at an older thesis and put together something similar. I had published several papers, so I reorganized them into one coherent and logical story—writing a general background introduction, a chapter introducing my research topic more specifically, a description of the common instrumentation and data analysis, several adapted chapters presenting the original work of my research, and a general conclusion. Altogether, my dissertation was approximately 150 pages. The actual writing took 2 months—the time I had before the final submission deadline. I guess I managed to write it because I had to, the alternative being to fail the Ph.D.
- Eleonora Troja, associate research scientist in astrophysics at the University of Maryland in College Park who works at NASA’s Goddard Space Flight Center in Greenbelt, Maryland

In the Netherlands, where I did my Ph.D., theses are commonly structured as an introduction, four chapters of original research work, and a summarizing discussion. Work that is already published or has been submitted does not need to be rewritten. I was quite lucky to have published two research papers and a review of my field that served as the introduction, and I was revising another manuscript that I had submitted to a journal. This meant that I only had to write one more research chapter and the summarizing discussion, which made the total time and effort to complete my thesis manageable. I started by making a very general outline with all my chapter titles. After getting approval from my supervisor, I made a more detailed outline for the two chapters I had left to write. This was especially helpful for the research manuscript. At the time, my co-author (another Ph.D. student) and I were still acquiring and analyzing the data. The outline helped us with our figures, although some of them started as mock figures that were completed later. Altogether my thesis was 135 pages, which is quite average for a Ph.D. thesis at my institution, and it took me approximately 150 working hours over a couple of months.
- Anoek Zomer, postdoctoral fellow in cancer biology at the University of Lausanne in Switzerland and the Ludwig Institute for Cancer Research

My thesis had to be written in publishable chapters. I had a hard time keeping the chapters short enough for manuscript submissions, so at the time of defense my thesis—which consisted of three chapters plus an overall abstract for introduction—was 125 pages, but it ended up being trimmed after that. I focused on producing several manuscript-ready chapters rather than trying to include all the research work that I did. I first organized my data and results into a storyboard by printing all my graphs and laying them out on a giant table. This strategy helped me see how the pieces fit together, which results would be in or out, the best way to display the data, and where the chapter breaks should be. It also helped me identify a few gaps that needed to be filled back in the lab. Altogether it took about 1 year, including a couple months of maternity leave in the early stages, to write the whole thing.
- Sarah Gravem, postdoctoral scholar in marine ecology at Oregon State University in Corvallis

I decided to write my entire dissertation from scratch. I was already working on two manuscripts for journal submission, but both were collaborations, so it made more sense, and it was also easier, to tell the story of my Ph.D. just by itself. I wrote up my scientific results in four different chapters, with additional chapters for the introduction, materials and methods, and conclusion. For each of the results chapters, I went back to my original experiments and computational results to verify the findings and regenerated the figures and tables as required. I made a lot of notes and flowcharts describing what should go into each chapter to guide me during the writing, which later also helped me provide a quick overview at the beginning of each chapter and crosscheck information at the end of the writing process. As I completed the whole thing, I was quite surprised at how much I had written. My thesis was nearly 300 pages, and I almost got concerned about examiners having to read them all. But the “real thesis” was only about 180 pages, with the remainder being appendices, including my two manuscripts under review, references, and lists of figures and tables. I spent about 6 months putting it all together, using the 4-year duration of my stipend as a hard deadline to push myself to finish.
- Katharina F. Heil, research associate in computational neuroscience at the University of Edinburgh in the United Kingdom

My writing got squeezed into a two-and-a-half-week gap between the end of a major research project and my defense date, which had been chosen 6 months earlier. Luckily, my department allows students to use published papers as dissertation chapters and I had published regularly during my Ph.D., so all I really needed to write was my introduction. I chose to put together a brief history of my field. This required tracking down and reading a whole bunch of historical papers. Then I jotted down every thought I had on the subject, producing a bullet list of elements I wanted to cover, logical connections between ideas, references, and even just catchy phrases. Then I made a first attempt to compile all these thoughts into some structured text, focusing on whether I had sufficient material to support my points and how well they flowed. After that, I focused on honing the phrasing itself, using online resources such as spell checkers and grammar books as English is my second language, followed by a final overall polish. With all the figures and numerous supplementary materials, my thesis—which I’ve just successfully written, defended, and submitted—ended up being over 200 pages, which is within the norm in our department.
- Anton Goloborodko, postdoctoral fellow in theoretical biophysics at the Massachusetts Institute of Technology in Cambridge

Who did you get help or feedback from? How involved was your principal investigator (PI)?

When it comes to theses, I find that no one is as helpful as former grad students from your group. When I reached out to our lab's alumni for advice, they helped me understand the overall process of thesis writing, estimate the time it would take to complete different parts, and watch out for potential pitfalls. I also downloaded and skimmed through their theses to get a feel for what the final product was supposed to look like. My PI had been heavily involved in writing each of the papers that went into my thesis, so the need for his input was less critical. Nonetheless, before sitting down to write, I had a conversation with him in which we figured out what the main theme of my thesis should be and which papers to use. Then when the time came to polish my thesis, many of my friends and colleagues, and my wife, who is also a biophysicist, provided invaluable advice.
- Goloborodko

I sent each chapter's methods and results to all my committee members so that we could make sure that the science was complete before I dug into the key scientific messages. My PI made sure we were in touch and made himself available for questions. He also was an excellent and very thorough editor—having somebody who will rip your writing apart and help you trim and organize is critical. Nearer the end, my fellow graduate students also helped me cut a lot of words.
- Gravem

My PI got involved a couple of times: At the beginning when I asked him for advice about how to put a thesis together, and at the end for the final reading of the draft. But I still felt totally lost. So when my best friend told me that he was going to visit his adviser to discuss how to write his thesis, I did not hesitate to tag along. His adviser clarified the expectations of the graduating commission, gave us some useful suggestions, and reassured us that all would be OK. That meeting helped me feel less overwhelmed and more confident. A senior colleague of mine, who was an expert adviser for Ph.D. students at another university, also offered his help, and he reviewed every single chapter of my thesis. I would deal with the revisions while he was moving on to the next chapter, which made it much more manageable and saved a lot of time. At that time, I badly needed someone to tell me that I wasn't doing something totally wrong or stupid.
- Troja

I sent my chapters to my PI one by one as I finished writing them. At times, I would get some feedback relatively straight away by email or through Skype; other times, I would need to send one or two reminders. Setting deadlines for myself, and letting my PI know about them, made me more accountable and helped me stick to my schedule. When I needed concrete tips on specific aspects of the thesis and my PI was really busy, I would just stop by his office. At times, all I needed was a quick “Yes, you are moving in the right direction” to keep going. I also sent individual chapters to people whom I knew had an interest in my research, mainly for proofreading, and I tried to find native English speakers to help me with grammar and spelling. I notified them all ahead of time so that they would have some flexibility on when and how to give me feedback.
- Heil

I was lucky to have a very caring supervisor who literally always had his door open. However, I tried to only request his input when I felt that critical decisions had to be made, for example when I had finished an outline or a chapter. He provided feedback mainly through track changes added to my drafts, which I found very convenient. When I received his input, I tried to deal with the revisions immediately, leaving the comments that required more work for later. By tackling the quick revisions first, I felt that I was making progress, which helped me stay motivated.
- Zomer

How did you make time and mental space to work on your thesis?

To focus on my writing, I had to stop most of my research, though I still performed some minor tasks that did not require significant time and concentration, such as launching computer calculations. Regarding work-life balance, my wife and I have an informal pact that we try not to work after dinner and on weekends. Without proper rest, productivity just drops and you end up feeling miserable. I can't say that this pact was enforced during the thesis writing period, but even in the most intense times, we did get out of town at least once a week for a walk in nearby parks and nature reserves to decompress.
- Goloborodko

During the entire writing period, I kept some other work-related activities going. Especially at the beginning, I remained active as a teaching assistant. Working with students was a nice distraction from my thesis, and it was motivating to see that my work was useful and appreciated by others, especially during unrewarding writing times. I also worked on other research projects in parallel and went to several international conferences and a summer school on citizen science. These activities not only offered a welcome break from the thesis, but also reminded me of how important and interesting my research was. I also made sure to stay active to keep up my positive energy. Going to the gym always brought me back to writing with a clear mind and a healthier feeling. Sometimes I would try to arrange coffee breaks with friends to reward myself with a piece of cake and good company. Other times, planning to visit a museum or try a new restaurant helped me keep going by giving me a nice event to look forward to.
- Heil

I stopped doing most of my fieldwork about a year and a half before my thesis was due, which was about the same time my son was born. After my maternity leave, I spent 6 to 8 hours a day writing from home, with my baby on my lap or sleeping next to me. Once he was in day care at 7 months old, I went to coffee shops nearby so that I could pop over and nurse him at lunchtime. Several times a day, I practiced the Pomodoro Technique where I'd set the timer for 45 minutes and not do anything but write—no emails, no social media, no other tasks. If I thought of something I needed to do, I wrote it down for later. In addition to combining writing with motherhood, other aspects of work-life balance were also extremely important to me. I didn't work most weekends, and I made sure I got outside and exercised or had some fun every day. Letting go of guilt about not working was key. Feeling bad doesn't get you anywhere, and it just makes the experience unenjoyable for you and the people you love or live with.
- Gravem

Early on, it really helped to take a few days away from the lab and just write. I took advantage of the fact that my parents were on holiday and spent a week in their house. I set realistic daily deadlines, and if I met those I treated myself with a little reward, like a short run through the forest or an evening picnic with an old friend. That week proved very productive, and I came back motivated to get the rest of my writing and experiments done. After I returned, I made sure to continue doing some fun activities without necessarily having to achieve something first, as I realized that I should not be too hard on myself. Going for a run between writing spells, for example, allowed me to get some distance from my thesis and helped me to maintain perspective and generate new ideas. But these activities tended to be spontaneous—I didn’t want to put too much on my schedule so that I could continue writing when I was in the flow.
- Zomer

Emotionally, what was the thesis writing process like?

It was really hard, but I did enjoy it. Writing can feel like a very long, lonely tunnel, but the more you practice, the easier it gets.
- Gravem

Starting with the easy task of reformatting my published articles allowed me to make a large amount of progress quickly and feel in control of the writing process while reducing the stress of the approaching deadline. I had a harder time with my thesis introduction, though I really enjoyed digging through the history of my field. I was even happy that I had to do it—this way, I could prioritize it over other tasks. But the extensive reading made writing much more challenging than I expected, and the tight deadline made it less enjoyable. Almost until the very end, I felt like the task was overly ambitious. To reduce stress at that stage, I kept reminding myself that it was a unique chance to focus on the history of research instead of the research itself.
- Goloborodko

Writing my thesis was for sure an experience that I enjoyed. This was the moment when I was finally putting together all my work of the last 5 years, and I was proud of it.
- Zomer

I guess a good work-life balance would have been important; too bad I did not maintain it. All I could feel was panic. For 2 months, I basically did nothing besides writing my thesis and applying for jobs. When I needed a break from the thesis, I switched to my job applications. This was one of the most miserable times of my academic career. Luckily, at the end I got the postdoc I wanted, which made me forget all the stress and frustration.
- Troja

My Ph.D., including the writing period, was an emotional roller coaster. It wasn't always easy, but remembering that every little effort brings you closer to your final goal is crucial to just keep going and survive emotionally. And while writing was daunting at times, I also found it motivating to see just how much research I had done.
- Heil

I'm only at the beginning stages of my writing, but it has been enjoyable so far. This is probably because I will finally have something tangible out of my Ph.D., which is immensely encouraging!
- Holmes

Do you have any further advice about how to make thesis writing as smooth as possible?

My general recommendation is don’t start at the last minute and don’t underestimate the time it will take. A thesis is not only about the science, but also about how to present it. Even though I had published papers containing a lot of material ready to be included in the thesis, I still had to put a lot of effort and time into reformatting the text, and I even had to improve or update some figures. If I could go back in time, I would start writing my thesis in my first year rather than leaving all the work for the last year. The introductory chapters explaining your subject matter can be written before having any data, and in retrospect, I had all the scientific results to write two-thirds of my thesis before the beginning of my last year.
- Troja

When I was studying for orals in my second year, I was very organized about writing my notes and archiving relevant papers, which proved super helpful when writing my thesis. It was also very helpful that in the first few years of my Ph.D. I had written dozens of grant proposals, which gave me an early opportunity to think about how to present the big picture, as well as some text that I could use as a starting point.
- Gravem

The acknowledgments section, and the time it takes, shouldn’t be overlooked. I saw it as my best chance to sum up the nonscientific part of my Ph.D. and express my gratitude to everyone who helped me along the way, and finding the right words took me several days. I chose to leave it until after my defense, when I could write at a much more relaxed pace during the few weeks I had to edit my thesis.

Beware of perfectionism. A doctoral thesis concludes a major part of one's life and there is a tendency to want to make it flawless. In my case, a non-negotiable deadline provided an effective remedy. Other projects or life events may also impose deadlines. If you’re not facing looming deadlines, self-imposed time limits for individual chapters would probably work.

Regarding technical aspects, my department provides a LaTeX template, which was very helpful. It enforces structured writing and deals with all the formatting so that you can focus on content. For example, it handles numbering, so you don't have to update figure numbers every time you insert or delete a figure. And because LaTeX is based on plain text format, I don't have to worry about not being able to open my thesis file a decade from now. LaTeX requires a certain amount of technical expertise, but this can be overcome with a little effort and Googling.

I am also a big fan of cloud services. I used an online LaTeX editor called Overleaf that allowed me to easily share drafts with my supervisor. I started with a free account, and once I reached the storage limits I paid a tiny fee for 1 month of a “Pro” account. I was also happy to discover that Mendeley, the cloud-based literature management software I have been using for the last decade, integrated easily with Overleaf—although Mendeley did break the night before submission, extending my workday to 6 a.m.
- Goloborodko

Try to figure out when your most productive times of the day are. Also, something that I unfortunately learned the hard way is to leave yourself a roadmap before walking away from your writing, especially if it’s going to be for more than a day. Write yourself a note about thoughts and ideas or the findings and questions that you were pondering in your last work session so that you can immediately pick up where you left off. As for the writing itself, I attended some writing boot camps that helped me get started. I also read some books on writing. One that I’d recommend in particular is The Scientist’s Guide to Writing.
- Holmes

Printing out substantial parts of my writing and leaving a bit of time before reading them allowed me to efficiently proofread and adjust things. And when the writing was not going as well as expected, I switched to the figures or formatting. That way, I could still feel that I was moving forward. Even though you may often feel as though progress is very, very slow, focus on just trying to add a little bit of improvement to your thesis every hour and every day.
- Heil

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