Insider Information: Applying to Quantitative Biology PhD Programs

By Hersh K. Bhargava, James Fraser • November 13, 2022



The landscape of life science PhD programs and their admissions processes can be incredibly opaque. As former applicants who are now admissions committee members / grad program leaders, we want to share a behind-the-scenes look to help aspiring scientists make the most informed decisions and craft the best applications possible. We have seen great candidates fail due to not understanding the (perhaps unfortunate, but nevertheless ubiquitous) peculiarities of academia, and it’s our goal to prevent you from making the same mistakes!

Who we are: Hersh is a 4th year Biophysics PhD candidate at UCSF, and James is a Professor at UCSF and Associate Director of the UCSF Biophysics Graduate Program. We both serve on the Biophysics program’s Admissions Committee.

Who this is for: People interested in PhD programs in quantitative life science fields, including: Biophysics, Computational Biology, Biochemistry, Synthetic Biology, Systems Biology, Chemical Biology, Bioengineering, etc.

Who this is not for: People interested in PhD programs outside of life science (a good heuristic is those that are not NIH funded) vary dramatically in their structure and admissions criteria; your mileage may vary. Programs outside the United States are also beyond the scope of this post.

Disclaimer: We’ll use UCSF and the UCSF Biophysics Graduate Program as frequent examples, but will aim to paint the overall picture with respect to peer grad schools/programs. The opinions expressed here are our own, and do not necessarily reflect those of our institutions.

Housekeeping Note: Hereafter we will refer to quantitative biology PhDs and programs simply as PhDs and programs, unless specified otherwise.

What is the point of getting a PhD?

Life science PhD students advance the frontiers of science and medicine, which is an inherently worthwhile pursuit. Practically speaking, however, the value of getting a PhD is largely in the doors it opens for your post-PhD career.

Fundamentally, a PhD is a research degree and will prepare you to conduct scientific research in your field. Thus, PhDs are required for many life science research roles.

There are also jobs that a PhD can help you attain, even if the degree is not required. While getting a PhD is rarely the most efficient way to achieve these roles, they’re worth noting as you consider the possible trajectories your life could take.

Our Advice: Don’t get a PhD if you’re not seriously interested in one of the ‘doors opened directly’ mentioned below. There is almost certainly a far more efficient path.

Doors opened directly by a PhD

  • A doctorate (PhD or MD) is a hard requirement for becoming a research professor at a university. This is what PhD programs traditionally prepare students to do.
  • Nearly all biotech and pharma R&D roles with title Scientist or higher require a PhD.
  • Having a PhD is a major asset (and in many cases all but required) if you plan to start a biotech company.

Doors opened indirectly by a PhD

  • Many people learn to code in the course of their PhD, opening the door to data science and potentially software engineering roles.
  • Many people learn field-specific and/or general skills that make them attractive candidates in consulting, venture capital, finance, etc.
  • A PhD is an excellent education for careers in science writing, policy, and journalism.
  • Many, many other careers/jobs, this is obviously not an exhaustive list. Look at PhD program alumni pages.

Structure of a PhD Program

By far the most significant part of grad school is: leading a significant, novel research project under the guidance of your PhD advisor and publishing the results. Before you can do that, you have to figure out what the project will be, who your advisor will be, and possibly take courses in relevant topics.

PhD Finances & Logistics

  • All respectable PhD programs pay their students a stipend intended to cover their cost of living. This typically ranges from $35k-45k per year based on the local cost of living. Programs typically also cover health insurance, may provide stipends to support relocation, laptops, etc.
  • PhD students do not pay tuition (that is covered by program/advisor).
  • Many schools offer subsidized housing, which may be well below the market rate.
  • Time off/vacation is typically not set, and expectations should be discussed with your advisor.
  • Graduation is typically subject to specific requirements (e.g. submitting a paper and/or writing a thesis, but the final decision is usually up to the advisor).

PhD Program Timeline

The following is a rough timeline of what happens in a PhD program.

  • G1 (first year): 3-month rotations in the labs of ~3 faculty of your choosing. The goal is for you to figure out who your PhD advisor will be, and to some extent for the prospective advisors to evaluate you.
  • G1-G3: Required coursework, typically 1) to bring you up to the undergraduate level in topics relevant to your research and 2) to bring you up to the graduate level in the immediate field of your PhD program.
    • Amount of required coursework ranges from practically none to quite a lot.
    • Usually concentrated in G1.
  • G2: Develop a proposal of your thesis research and defend it in a qualifying exam.
    • Structure and difficulty of qualifying exams ranges dramatically between programs.
  • G3-G5: Conduct thesis project and publish a paper.
  • G4-G6: Graduate. Average is closer to 5-6 years. Typically dependent on research success with a major influence being the discretion of your advisor.

Note: Most programs allow you to leave after 2 years (usually anytime after you pass quals) with a Masters of Science degree in your field. This is a great safety net; in essence enabling you to get paid to obtain a M.S. (though we don’t recommend you use this as a loophole to get a free masters).

Note that a huge component of the student experience depends on the graduate advisor. Once coursework and teaching requirements are done, essentially all decisions are at your advisor’s discretion; after the first 1-2 years, it often matters very little which PhD program you are in and very much whose lab you are in.

Scorecard for Evaluating PhD Programs

A lot of the elements of PhD programs vary significantly between programs. Consider the following list when evaluating programs.


  • Faculty you’re interested in potentially working with
    • Note that faculty may not be taking students, so having multiple backup options is important.
  • How much mandatory coursework?
    • Ranges from minimal to significant amount of time. Too much can interfere with rotations, research, etc.
  • Structure of qualifying exam?
    • Ranges from moderate to high amount of effort. E.g. outside proposal vs inside + outside proposal.


  • Program funding policy and guarantees
    • Some programs guarantee funding for 5 years even if the advisor becomes insolvent.

Resources & Environment

  • Research resources at the institution
    • Presence of a hospital / School of Medicine
    • If your research requires expensive/scarce equipment (e.g. cryoEM, synchrotron), what is availability like?
  • Geographical scientific hotspots – confluence of multiple universities + industry
  • How many faculty at the institution excite or inspire you? Look at the visiting seminar series – does the institution attract speakers that you find exciting? We believe the value of being in a lively scientific environment is tremendous.
  • Commitment to causes important to you – diversity, student unions, etc.

Other Elements

  • Finances: How does the stipend compare with the local cost of living?
  • Historical data on time to degree and career outcomes

The Landscape of PhD Programs

Graduate programs are created for a variety of reasons, and there is little rationality to the overall landscape of PhD programs. The history of science is to blame here – while Biology has been around for a few centuries, Molecular Biology is only ~50 years old, and Computational Biology is still newer. PhD programs are created over time, but rarely eliminated. As a result, it can be very confusing to choose where to apply. Worse yet, there may be many overlapping programs within a single university, and each university may limit you to applying to a single program.

Should I choose an umbrella or a specific program?

The most obvious distinction among PhD programs is between umbrella programs and subfield-specific programs. Umbrella programs, like UCSF Tetrad or Berkeley MCB are typically large (>20 students per year), and have clearly-defined subcategories (e.g. immunology, Biochemistry, etc.). Specific programs, like UCSF Biophysics or Berkeley Computational Biology are typically smaller (≤20 students per year), and are somewhat more flexible in structure.

In our view, the most important aspect of a grad program is which faculty members’ labs students are permitted to join. Both umbrella and specific programs vary in this regard, and either type can be very permissive. For example, UCSF Biophysics allows students to join the lab of any UCSF faculty member. Students are free to rotate anywhere, and it is easy to add new program faculty if a student intends to join their lab.

For most prospective applicants, there is likely an umbrella program and at least one specific program at most universities that is suitable based on research interest. We recommend you consider what types of people you want to be surrounded by – specific programs present an opportunity to be surrounded by peers with related interests. On the other hand umbrella programs expose you to a broad range of ideas and enable you to move between fields without leaving your classmates behind. Consider also that in a specific program for a more quantitative field your peers are more likely to have relevant computational or mathematical skills.

It’s worth noting that specific programs can sometimes be less competitive than umbrella programs, probably because many applicants are indecisive or unclear about the landscape of subfield-specific programs. It is a competitive advantage to have a concrete sense of your research interests. Many institutions post their admission statistics publicly, and if they don’t you should consider contacting them so you can make an informed decision. Also, note that many schools only allow you to apply to a single program, so choose wisely.

Other considerations in choosing a program

  • Some programs actively welcome people with no biology experience but experience in another science field (e.g. physicists, computer scientists, etc. new to biology).
  • The name of the field on your diploma. This mostly matters if you leave life science research.
  • Program-specific policies for coursework, etc.
  • How well is the program managed? An absentee program director in a small program can make life very difficult. Bureaucracy in a large program can be similarly annoying.

Our Advice

  • Talk to current students and ask them about what’s good and bad about their program. PhD students are typically responsive to cold emails from well-intentioned prospective applicants.
  • Whichever program you apply to, make sure you tailor your application to that program and explain in your personal statement why it’s a great fit for you.
  • If in doubt apply to more institutions (assuming you’d actually go if admitted) - note UCSF only allows one program to be selected on application. The application questions are typically the same, you just need to tailor a paragraph to the specific school and faculty of interest. You can always turn down interviews. If $ is limiting, most schools will waive their application fee if you ask.
  • If in doubt about your credentials (but not about going to grad school), just apply. It will not be held against you, there is almost no memory from year to year of rejected applicants, and you might just get in.

General structure of the admissions process & implications for applicants

Structure of the admissions process

This is a generalized description of what happens behind the scenes of PhD admissions.

  1. Reading: The stack of applications goes to a group of readers, who assign each application a numerical score and provide written feedback to justify their decision. There are typically multiple readers per application. The readers include program faculty and sometimes also students.
    • At UCSF Biophysics, all readers are on the admissions committee.
  2. Interviewee Selection: The Admissions Committee (a 5-15 person group of faculty and in some cases students) places each application into the INTERVIEW or REJECT bucket. Typically at least one of the readers of each application is on the admissions committee.
    • The Committee typically discusses candidates in descending order of average reader score, and if there are many applications may choose to interview/reject applicants above/below a threshold score.
    • The number of interview slots is based on how many students the program wants to have in the cohort (which depends on funding, yield rate, etc.).
    • The admissions committee may make final decisions by vote or at the discretion of the Program Director.
    • The vast majority of rejections are made at this stage. After this stage the process typically becomes more two-sided, with the school wanting to impress the applicant and vice versa.
  3. Interviews: Candidates invited to interview are assigned ~3-5 faculty members with whom to have ~30 minute interviews. Student research interests and faculty preferences are typically taken into account in assigning interviewers.
    • Acceptance rate from this stage is typically >50-80%.
    • Many programs take care to have each student interviewed by at least one member of the Admissions Committee.
    • Some programs have student interviewers.
    • Interviewers again score the applicant numerically and give written feedback.
    • Some grad programs combine their visit and interview weekends, while others save the visit weekend for admitted students. Note that during combined visit+interview weekends, most programs direct students and faculty to report any noteworthy (for better or worse) impressions of candidates even if not during an interview.
  4. Final Decisions: The Admissions Committee meets to discuss the interview results, placing candidates into ACCEPT, WAITLIST, and REJECT buckets. The process is very similar to (2).

Implications for applicants

The most important consequence of this structure is that the program faculty are the decision makers at essentially every step. As there is no accepted formula for predicting the success of grad students by application, the preferences of faculty members vary dramatically. A prime example is the consideration of undergraduate grades – some faculty see GPA as a valuable indicator of academic aptitude, others as a potential red or green flag only, and still others as a useless variable.

In our estimation, the most widespread approach of faculty evaluators is trying to estimate the likelihood that a candidate will be committed to and successful in their PhD. The most obvious evidence is prior success in PhD-like endeavors (i.e. multi-year research projects, ideally resulting in publications, presentations at conferences, etc.). However, past success in any difficult pursuit – overcoming conditions in school or a job, significant commitment to interesting side projects, etc. – is a green flag in the eyes of most readers/interviewers. Letters of recommendation can play a significant role as well: a glowing recommendation from someone who is a known quantity (personally or by reputation) to the application reader is a powerful signal.

Our Advice

  • If you have a strong track record of research experience and even publications, center around that. If not, focus on convincing the admissions committee that you have a high chance of succeeding as a researcher, that you have a good reason to get a PhD from the program, and that you aren’t going to drop out halfway through.
  • Put yourself in the mind of the average professor in your field. Now, try to convince them to go to the trouble of speaking up for you in their 23rd year of peer pressure induced service on the admissions committee. Don’t be cliche – imagine how many applications start with some version of how interested you were in science as a kid.

Specific Advice on PhD Interviews

PhD interviews are conducted primarily by program faculty. Some programs include student interviewers, typically at least G3s. The most basic purpose of the interviews is to verify that the positive signals (e.g. depth of research experience and commitment to grad school) from candidates’ written applications are confirmed in face-to-face interactions. Consider that candidates could have had someone else write their written statements, but interviews are hard to cheat. Beyond this confirmation, candidates can stand out by presenting their own experience in a highly polished way, articulating a clear and engaging rationale for why they want to attend the institution in question, and asking insightful questions about the program and interviewer’s research.

While interviewers typically have broad discretion regarding structure, a typical interview involves the following elements in a 30 minute session:

  1. Q: Tell me about yourself and your interests
  2. Q: Tell me about your most meaningful research experience?
  3. Q: Why do you want to pursue a PhD in X field
  4. Q: What do you want to work on in grad school?
  5. Interviewer talks about their own research program
    1. Professors love to talk. Don’t be surprised if half the interview is consumed by this section.
    2. Don’t be afraid to interrupt and ask simple clarifying questions.
  6. Q: What questions do you have for me?

Interviewees often struggle to figure out how to prepare for each interview. This is especially tricky since many programs only finalize interview schedules day of or the day prior. A common misconception is that you are expected to be deeply familiar with your interviewers’ research. In reality, it’s perfectly normal to ask them to explain their interest and research program. We recommend reflecting on the following:

General Advice (figure out well in advance)

  • Practice a ~5 minute summary of your research, interests, and motivation for grad school.
    • Try to emphasize your contribution to your projects.
  • Consider preparing a visual aid (a couple slides on a tablet or laptop, or a printed sheet of paper). This shows motivation.

For each interviewer (figure out once you have your schedule - some schools will not give very far in advance and therefore have low expectations of how much you have prepared)

  • Figure out the high-level summary of their work: Prof X applies Y techniques to understand Z.
  • Read the title and abstract of 1-2 recent papers. Research descriptions on lab websites are often decades out of date, so search Pubmed and sort by most recent. A good PubMed query would be “Smith JM[lastau]” for senior author papers by JM Smith.
  • Have at least one question in mind to ask the interviewer. It can be a softball regarding the program or their opinion on the state of their field, or a specific question about their research.
  • Evaluate whether the interviewer is an expert in the field of your research experience, or an outsider, and practice talking accordingly.
    • Everyone likes to understand what someone is saying, and nobody likes being inundated with jargon they don’t understand. Err on the side of simplicity. If in doubt, imagine you are explaining your research to an AP biology teacher.


We hope this post has helped you understand the landscape and structure of PhD programs in quantitative biology. To summarize, we encourage you to apply soon, be picky and pragmatic, and keep in mind whom you’re writing for (i.e. university professors). Best of luck!