The Hitchhiker’s Guide to Ph.D. Qualifying Exam Prep

Are you wondering where to begin with prepping for Ph.D qualifying exams (especially if you’re a first-gen student)? Read on.

Beginnings can be overwhelming

Once I had a date planned for my Ph.D. qualifying exams, it took me a while to process where to begin. My project and interests felt very interdisciplinary in genomics and I found myself brainstorming how I’d tackle reading papers at the intersections of human evolution, repetitive DNA, microscopy, and computational biology. Even more so, I had to navigate conversations about planning, writing, and preparing for my exam, at the start of the COVID-19 pandemic in March 2020 with my exam date being set for early June. Yikes!

If you’re in a similar position where you might need to take this exam virtually, you’re unsure of where to start, or maybe a bit of both — hopefully this guide will be helpful for you! Here, I’ll share frequently asked questions that other mentees have asked me when preparing for their quals, a timeline of how I balanced out studying, and general tips for preparing for the exam.

An important note is that my qualifying exams were made up of a written portion in the format of a F31 grant (6 pages, not including references), and an oral portion where I discussed my proposed written project. The oral component is given as a presentation to your committee and you should be prepared to answer questions that will be primarily related to the topics you’re proposing. If you’re reading this guide and these two areas don’t apply to you, I’ve provided some general tips that could help you regardless of how your quals are formatted.

Although this guide aims to be comprehensive and reflective of my experience, each person will go through their quals differently. I encourage you to reach out to your mentors, other trainees, and close friends to also hear their perspectives.

FAQ

Q: How long did you study for your quals?

A: I started studying in mid-March of 2020 and persisted on and off until my exam date in June. I took two months to focus on preparing for the exam by reading daily and brainstorming ideas. On some days I’d only read a review or two, and other days I dedicated to writing or designing slides that conveyed my written proposal. I’ll share a timeline of what that looked like for me.

Q: What was the hardest part of preparing your written work?

A: Coming up with independent aims that could be feasible projects. As someone who had mostly done computational work up to the point of preparing for my exam, I was still interested in learning microscopy and imaging techniques despite having done minimal bench work. This felt incredibly intimidating for me at first but one thing that helped me overcome this was chatting with lab mates about the feasibility of my proposals. In addition to this, speaking with my advisors consistently about the feasibility of my aims helped me come up with ideas that were concrete.

Q: What tools would you recommend for preparing your talk? Writing?

A: When preparing for my talk, I used several tools to piece together my thoughts based off of my written proposal.

For preparing figures:

• Biorender — this is an online based tool that does require a monthly subscription but it is incredibly helpful and fast for preparing scientific images. This can be especially helpful for people who are trying to illustrate experiments.
• Clip Studio Paint — this is an art software tool that I frequently use for drawing and creating images independently.
• Procreate — same deal as Clip Studio but this software is for the iPad and would highly recommend it for making clean images.
• Adobe illustrator — this has a bit of a learning curve but in the long run, you can greatly benefit from it to make incredible illustrations and paper figures.

For the presentation:

PowerPoint: I made my slides in powerpoint, but you could also easily do them in Keynote. Now moving forward with my talks, I’m transitioning more to Keynote because they have a clean interface but if you aim to make most of your figures in something like PowerPoint, I would stick to one software in that case.

For writing:

I highly recommend using a reference manager. It will be much easier to save your research articles and organize them for reading and writing. These are some managers I’ve used that have greatly helped me:

• Mendeley
• Endnote
• Zotero

Q: Who are good groups to practice your talk with?

A: It’s really great to practice your talk with labmates if you can get a slot at a lab meeting. But I would say that it’s just as important (if not more important) to try and practice with folks outside your lab if you are able to. Since a lot of people in your lab tend to be experts in your area of research, it’s important to hear and listen to other perspectives because they might be able to ask questions that could be easy to overthink.

I also reached out to my old mentors from undergrad who wanted to hear about my research and they also greatly appreciated it! Funny enough my parents also wanted to see my slides. They’re not scientists and I’m a first-gen college grad so they loved seeing my sketches and work!

Q: Did practicing for your quals disrupt your research?

A: I mostly spent May preparing for my quals by reading and writing. I truthfully did little research at this point but, in my opinion, reading reviews of the field and area of study are just as important as making research progress. If you feel like you can balance your experiments and studying, I would definitely say go for it, but more importantly — you should do what feels right for you. If you want to focus more on your exams, definitely chat with your advisors. I did this early in May and they were able to provide me with the time and space I needed to feel confident about going into the exam.

Q: So what was your exam like? Any scary parts? How long did it take?

A: I was nervous at first, but it quickly felt more conversational once I started presenting my ideas. I did get several questions throughout my talk but they remained on topics and data that I presented. There were some questions that I had a hard time answering and I did get to the point where I had to say ‘You know, I’m not too sure about that.” And that’s totally ok! My exam in total including feedback and receiving the news that I passed took about two and a half hours.

Q: What did you do after your quals? What did it feel like to be done?

A: First of all I called my parents and I legitimately teared up once I got off the zoom call! Knowing that I’d be the first person in my family to go after a Ph.D. was a big deal and passing this exam really validated that I was moving forward. I ended up staying with family for about a month (the remainder of June) to just recharge. I would highly recommend doing the same after your quals if you’re able to.

One thing that’s important to acknowledge is that self-care throughout preparing for quals is essential. Some folks do report that after their quals they do experience feeling depressed, drained, and burned out. It’s important to take things slow, spend time with loved ones, and do hobbies that make you feel good to balance out the energy you just used!

Q: So where should I start?

A: I’d start by making a document that outlines general topic areas you want to focus on. For me, I had a document that included headers such as: FISH, microscopy, computational biology, repetitive DNA, etc. And beneath each heading, I’d search larger review papers to help me get started. It’s VERY easy to go down a rabbit hole with downloading papers. But I’d recommend talking to your advisors, even reading relevant grants they’ve written if they’re willing to share, and parse through literature that you’ve found and see how it lines up with their references. I’ll share some of my guides on this below!

Building a study guide to identify key literature

Here, I’m sharing an example of how I outlined some topics that I covered to search for papers in these areas. Reviews are very important so you can learn general topics about the field. If you need to dive into specific areas of your project, then I would approach those papers as necessary. Again, your advisors, lab mentors, and collaborators can be great resources to help guide you in the direction of papers.

I would also highly recommend setting up 1:1 meetings with your other committee members to see what their expectations are of questions and topics you should be able to cover adequately. This will help you focus on areas of study. Be sure to take good notes after your first committee meeting so that you can ask them about their expectations. This would also be a good time for you to clarify and communicate what you also see as material that is fair game. Don’t be afraid to share areas that you intend to not dive into too much detail due to project relevance, etc.

This is an example of how I went into detail on some reading topics. There’s quite a bit of jargon related to technology development and repetitive DNA here but don’t mind it. This is just an example of how I structured some of my thinking:

Background Reading:

• 3D Genome Organization (history of, methods and technologies, Hi-C, differences between 3C and 4C methods).
• Microscopy (history of FISH, current methods and types of imaging, current tech dev methods, SABER, STORM).
• Repetitive DNA (tandem repeats, satellite DNA, evolution and origin of repetitive DNA, types of LINES and SINES, retrotransposons, Where on chromosomes are each type of repetitive element found commonly? Some facts about repetitive element locations in different model systems? How much of the genome was composed of repetitive DNA?).
• Algorithms (Methods for studying Tandem Repeats, TRF, MREPS, find reviews on current methods, K-mer counting methods).
• Machine learning (PR and ROC, how I implemented these concepts in my project, different types of classification and regression cases).

Timeline

Since I started preparing in mid-March and my exam was in early June, I’ve decided to write out this study timeline as a ten week outline. I’ve also spaced out a number of these items in a way so that you can balance self-care. During this time, definitely take care of yourself and do other things that will make you feel good (exercising, art, hanging out with friends, hiking, baking, reading for fun, etc.)!

However, here are some notes that are unique to the way my quals were structured:

• It’s recommended that you submit your written work three weeks in advance to your committee, so I’ve planned this guide to accommodate that.
• Your experience with preparing and writing your written proposal will likely be highly dependent on the focus of your committee. In my experience, my committee is composed of a good balance of faculty interested in technology development and the biology of genome organization. Here, I was sure to develop a proposal that reiterated why the technology I was developing had feasible and measurable biological applications. Be sure to communicate your interests clearly with committee members and develop a proposal that can address questions they may have.

Week 1 — Searching for literature and organizing your resources

• This is the week that you should take to organize topics of research you’re interested in and get software downloaded and review papers on your citation managers as needed.
• Asking mentors and other peers for how they structured their general exams can be helpful. Here’s a general guide for how these grants are structured.

Week 2 — Reading reviews, connecting with mentors, and complete your aim 1

• Reading big picture reviews and creating timelines of how your new ideas and experiments fall into the big picture of your field of research are key. This can help you craft your introduction and why your project is important!
• Ask your mentors and collaborators on how they structure grants so you can get familiar with the language that is used.
• You can save your introduction as needed when developing the remainder of your aims.

Week 3 — Reading, write aim 2 and aim 3

• Chat with your mentors and peers to see the feasibility of your proposals. This can help you fine tune and scale your writing. See literature to get a sense of how they structure portions of their paper.

Week 4 — Reading, write your introduction and conclusions

• Saving your intro and conclusions are a good way to recap the points you have in aims 1–3. These parts of your proposal are important because they should answer how your work falls into the bigger picture of work in your field. How is your work addressing something that’s needed to understand a biological system, make analyses more efficient, etc?
• This is a good time to circle back with your mentors and committee members to see their expectations and ideas on your project as well.

Week 5 — Reading, make an outline of your powerpoint

• This is a good week to make an outline of what you’ve discussed in writing and send drafts of your written proposal to your advisors. They can help you scope out what’s realistic or what might need to be adjusted accordingly.
• This presentation outline can be as simple as planning out key questions and points you aim to address on each slide. In total I had about 40 slides (including supplementary slides to talk about techniques if needed).

Week 6 — Seek feedback from mentors and peers, schedule a practice talk during week 8

• You should schedule a practice talk accordingly so labmates and peers can provide you with feedback. Don’t be afraid to reach out to others who might be interested in reading your proposal too!
• By this point, your proposal should be wrapping up but it’s ok to use more time as needed in the next week to make adjustments.
• Definitely continue reading background and literature as needed.

Week 7 — Submit your written proposal, continue reading, work on the introduction to your presentation

• Celebrate that you’ve submitted your proposal!
• Take this week a bit more lightly and try to work on communicating your ideas through your slides. Get feedback from your peers as needed.

Week 8 — Finish your talk, and give a practice one by the end of the week

• It’s absolutely ok if you need to make adjustments on how you communicate your science, it’s a learning process and getting feedback from outside your lab will help you with this.
• By making your practice talk, this will also help you go back to literature you need to review if you feel uncomfortable in other areas.

Week 9 — Read areas you feel like you still need to review

• At this point, you should make adjustments to your talk, but also take time to review and look back at the progress you’ve made! . It’s important to review ares you discussed at your first committee meeting.

Week 10 — Exam, practice, decompress with friends

• The day before your exam get plenty of rest and try to spend some time with your friends and family! Feel free to look over your talk to do a practice run, but know that you’ve put in great work!
• Celebrate when it’s over and prep to take a much needed break!

General tips for writing

These are just a collection of tips for writing that helped me put together different parts of my written proposal:

• Read how F31 grants are structured and see other written quals examples from peers.
• Bold key points in your introduction and summary. A lot of times, your readers want you to get to the main point of why your area of research is going to help answer questions in your field. In grants, bolding your thesis statements are much appreciated.
• Reading the introduction to papers is a great way to describe how you could summarize your own aims. A lot of the language used in scientific papers is similar and will help you put words together for explaining introductions, methods, and conclusions.
• Always have people outside of your immediate field of study read your proposal.
• Discuss your ideas with your committee members before your exam.
• Take breaks when you need them. I can’t stress this enough. If you’re hitting a wall on coming up with ideas — walk away from your computer and chat with friends and mentors.
• Add figures to illustrate your ideas. Also space your lines accordingly to make it easier for your readers.

Preparing your talk

• Fewer words and more pictures. Graphics can visually help you convey your ideas. Make sure they accurately reflect your written work. Peers can help you identify if images are confusing.
• How would you walk a friend through your work who hasn’t read your written proposal? This is critical toward setting up the context of why your project is important.
• Home slides. This is important for taking people through parts of your project.
• Be sure to share any data you currently have to show feasibility and your own progress. Make sure your current figures are labeled clearly and are easy to understand. Whenever I show data, I always try to walk people through the axes and provide them with a general summary of what the findings describe.
• Color palettes are important. I highly recommend styling your data in ways that are colorblind-friendly and there are lots of guides on google that can help you stylize your talks in this way.
• Take note at how figures in papers are designed to outline methods.
• Don’t be afraid to animate to guide your talks and help the flow of your talk.
• Acknowledgements. This slide is actually the first one I made and it always felt great to look at as motivation! I included friends and people who were critical toward supporting me this far!

Final Thoughts

Studying for your quals can feel like a long and overwhelming process, but know that you can lean on others and find community with your peers and mentors to navigate imposter syndrome. Know that you’ve made it this far and that you’ve done (and will continue to do) incredible work in your research. I hope that this guide serves you well as a point of reference to get started on preparing for your quals! Best of luck and know that you will absolutely make it!