Medical Scientist Training Program

Tips for thesis students

thesis faq

Here are some things to think about as you work your way through the process of picking a thesis lab and completing your thesis. Some of these points came up during the recent "Navigating through the thesis years" session. Others are questions that I've been frequently asked in one-on-one sessions. This list was written with combined degree students in mind, but most of the issues are generic. The idea is that you are doing a thesis project to prepare you for a career as a physician-investigator. Your training for that role began before you got to Penn and will continue after you leave the MD-PhD program. This is a step, not the entire journey - but it is an important step. It is also one of those rare times that you will be able to focus on a research project with a minimum of other distractions and competing pressures. Make sure that you've picked a lab environment that will contribute to your training in a positive way. For many of you, your next sustained lab experience will be after you've completed your clinical training. When you re-enter a lab at that point you will be building the basis for your next step - a faculty position with independent funding. Come see me if you want to discuss any of this.

- Skip Brass

Lab Rotations

What is the purpose of doing lab rotations?

The primary goal is to find a thesis advisor and lab. There are valid secondary goals including learning new approaches to research, but the biggest goal is finding the right thesis lab.


How may lab rotations should I do?

The number is set by your graduate group, but feel free to discuss it with them if you feel you've found the right place sooner. The final decision is made by the graduate group. Also, don't forget that your choice of a thesis advisor has to be approved by both the graduate group and the CD program director.


Thesis Issues

What are the goals of doing a doctoral thesis?

  • Learn how to ask interesting and significant questions.
  • Learn how to reduce the questions to a set of experiments.
  • Learn how to evaluate the results.
  • Learn how to present the results in written and oral form.
  • Learn survival skills for a successful career as an independent investigator.


When should I start my thesis research?

For CD students in BGS graduate groups, shoot for middle of the third year. Take longer if you need it to find the right lab. Take less if possible and appropriate. Officially, you are not a thesis student until you pass your qualifying exams at the end of year 3, but many CD students are already working on their thesis projects before that.


What is the best topic for a thesis? Should it be "safe"? Should it be risky?

You'll get different opinions from different faculty members. My view is that you should pick a project that you care about in an area that you find interesting. Pick one that is challenging and meaningful to you. Ask yourself: if you answer the questions that you've posed, will you care about the answer when you have it? Take risks, but back up your "risky project" with one that is more predictable. Don't rely on a single high risk, high impact project coming through as your thesis - it might not. These are issues that will come up over and over as you move through your career. Now is a good time to start thinking about them.


Should I pick a project in an area that I want to work on for the rest of my career?

Not necessarily - even assuming you know what you want to work on for the rest of your career. Your interests will almost certainly change as time goes by. Pick something that you care about and that will help you meet the goals of doing a thesis.


How long should it take?

As long as necessary to accomplish the goals and have an identifiable body of creative work. Most CD students take 7-8 years for the entire program. The key is to be focused and efficient, and to work hard.


Who decides when I'm done?

Your thesis committee in consultation with your thesis advisor. The decision is usually based on evidence that you've mastered the field, achieved the goals that are listed above and made a scholarly contribution to the field.


How many publications will I need to have?

There is no set number, but in general the graduate groups expect 1 or 2 first author papers. There have been exceptions, but no one views that as a desirable outcome.


Thesis Advisors

Should I work in a big lab or a small lab?

Either can be fine. Make sure that the training and experience you will get in that lab meets the goals of doing a thesis. A good predictor is the experience that other students have had in that lab, so talk ahead of time with the grad students and postdocs who are already there. Maggie can tell you whether any of the senior CD students have done their thesis with that faculty member. Talk to them - and talk frankly with the faculty member.


Is it OK to do my thesis with a junior faculty member?

Definitely. Working with junior faculty can be a wonderful experience. They are often around the lab more. On the other hand, they will have had much less experience as an advisor than will most senior faculty. The issue of tenure should always be considered and discussed with them. In basic science departments this comes up after 5-6 years. In clinical departments, the tenure decision can be postponed as long as 9 years. The difference in the time allowed is because of the assumption that faculty members in clinical departments will spend at least some time doing clinical work. Many faculty members in clinical departments are on the clinical educator track and not under consideration for tenure, but most who do lab research are on the tenure track. A faculty member who fails to earn tenure may be asked to leave. It is always appropriate to discuss with a potential thesis advisor issues that might result in him or her leaving before you finish your thesis. That includes whether they are actively thinking about moving for reasons other than tenure.


How often should I expect to meet with my thesis advisor?

Regularly, but the norm varies considerably. I would suggest that a meaningful conversation at least once per week - preferably one-on-one. This is an important issue that should be discussed in advance before you decide to work with that person.


What is the purpose of having a thesis advisor?

To teach you, guide you and collaborate with you. All choices of thesis advisor by CD students are subject to approval by the CD program director as well as your graduate group.


Can I do my thesis with a faculty member outside my graduate group?

Generally, no — but a graduate group may approve it under exceptional conditions.


Can I do my thesis with a faculty member at another University?

No. The idea is that you came to Penn for an integrated MD-PhD education to prepare you to be a physician-investigator. You have to be present on campus for that to happen.


Who supports me while I'm doing my thesis?

Mostly your thesis advisor, so be sure to discuss that point with him or her before you sign on. They have to have an assured source of funding for you. Some of you will be appointed to training grants or win individual fellowships.


Thesis Committees

What is the purpose of my thesis committee?


  • serve as a resource
  • oversee your progress
  • determine when you are done
  • when necessary, mediate and resolve conflicts.


How often should I meet with my thesis committee?

The CD program expects you to have thesis committee meetings every 6 months, beginning no later than 6 months after you start (the 6 plus 6 rule). Let Maggie know each time one happens.


When is the best time to schedule my next committee meeting?

Immediately after the last one. Don't wait until your paper has been accepted by Nature. Don't put it off because you are having problems making progress. Don't wait until the 6 months are up - it takes planning to bring your committee members together. Remember that these meetings are for your benefit.


Who should be on my thesis committee?

Faculty members with relevant expertise and a willingness to contribute to your education. They should not be picked solely because they are collaborators or solely because they are "FOA's" (Friends of your Advisor). Different graduate groups have different rules about the number of committee members that you will need.


Who should chair my thesis committee?

An experienced member of the senior faculty who has trained his or her own graduate students, is willing to spend time with you, and willing to take an active role in your education. The chair's responsibilities include making sure that your committee keeps track of the "bigger picture" of the progress of your education. That's why it should be someone who has served previously on thesis committees and who has had multiple graduate students of their own. Like so many things that faculty members are expected to do, there is no specific training for this role.


What should happen before each thesis committee meeting?

You should prepare a presentation that lasts for about 20 min (you'll be interrupted so it will always take longer) that will remind everyone of 1) how far along in the program you are, 2) your project goals, 3) your progress (or lack of progress) since the last meeting, 4) problems you are wrestling with and 5) your plans for the next 6 months - subject to everyone's agreement.


What should happen after each thesis committee meeting?

Your committee chair should submit a written report after every meeting. Copies should go to 1) you, 2) your advisor, 3) the graduate group, and 4) the CD office. Meeting with the committee chair after each committee meeting is highly recommended as a way to make sure that everyone is on the same page. This can be done right after the committee meeting.


Returning to Clinics

Is it true that I can only return to med school at certain times of the year?

No, students can return to med school at any time throughout the year.  However, for each student there will be certain times that are more or less optimal.  Visit the Final Two Years of the Program page for more information.


If I'm undecided about my clinical interests is there anything I can do to help while I'm still in thesis lab?

Yes. Take advantage of the Clinical Connections program. Meet with your CD Program Advisor for advice and/or set up an appointment with me to discuss the pros and cons of different fields. Set up appointments with key faculty members in areas of interest to you to discuss your career goals and seek their advice. Just an hour or two a week networking or participating in Clinical Connections can help you narrow down the best possibilities for you and minimize the anxiety of returning to the clinics. Keep in mind that there are advantages to selecting a clinical area in which physician-investigators are a well-established career model. If you intend to be a laboratory investigator, choose a field where any future clinical responsibilities will fit comfortably with the time you will spend doing research.


Do I really have to defend my thesis before going back to finish med school?

Yes. In fact, you need the program director's permission to do otherwise. Why? Because the pressures to focus on completing your clinical education are great, the hours are long and the opportunities to devote thoughtful time to the completion of your project, the composition of your thesis and your public defense are minimal. If you encountered unexpected obstacles or delays, you would likely then leave the program with only your MD, despite having completed 90+% of the PhD.  It’s not worth taking the risk of never being able to finish.