Applying to Biology PhD programs

Casey Dunn
19 min readNov 17, 2016


Each year I advise undergraduate students who are applying to grad school, help evaluate grad school applications, and talk with prospective PhD students that are interested in joining my lab. I’ve collected some general thoughts here that I hope are useful to prospective PhD students as they decide how to approach the application process. The advice is most relevant to United States PhD programs in Ecology and Evolutionary Biology (EEB). There are cultural and structural differences between fields (within and outside of Biology) that can lead to different emphasis and priorities, so some of the advice is more generally relevant and some is more specific to EEB departments.

There isn’t one universal PhD experience — each trainee’s experience is highly individualized. This can make it difficult to decide if pursuing a PhD is right for you. There are some critical traits for a succesful and rewarding PhD experience. One of the central tensions is that you must be comfortable and capable of both independent self-guided work and intense collaborations with larger groups. You need to be able to switch between these modes of work quickly and effectively. You must be highly self motivated, prepared to work very hard for extended periods of time, a good self-starter, and able to pick up new skills on your own. You must fundamentally be driven by the joy of discovery, and ready for the many frustations and failures you will encounter on the way to discovery.

Biology PhD training in the United States typically takes about 5 years. It is a combination of class work, self directed study, training in teaching and mentoring, and, centrally, novel research in your field of interest. Tuition, health benefits, and a stipend are usually provided. Details of this support can vary, such as whether you may need to do additional teaching if grant support isn’t available in your later years of study.

Why apply to a Biology PhD program?

The value of getting a PhD can be divided into two broad categories: domain expertise and transferable skills. Each is incredibly rewarding.

Domain expertise focuses on what experts in particular subdisciplines need to know. Many students enter PhD programs because they have a passionate interest in a specialized domain, be it ants or deep sea biology, and they want to train with experts in these fields. I loved learning about siphonophores, invertebrate zoology, developmental biology, and phylogenetics during my PhD training with Günter Wagner.

Transferable expertise includes foundational technical skills (e.g., technical writing, programming, general lab bench skills) and experience approaching big complex problems in the face of uncertainty (e.g., time management, comfort with messy data, the ability to define and measure progress toward goals, working with teams, multitasking). Many PhD students become even more passionate about their transferable expertise than they originally were about the domain focus that led them to get a PhD. I know many recent PhD students, for example, that found in the course of their research that they loved working with large datasets, and then went on to apply their data analysis skills to problems very different than the original problem they set out to work on.

Not all PhD holders will continue to employ and develop their PhD domain expertise throughout their entire professional careers. Most PhD holders will find the transferable skills they develop in their PhD to be a critical foundation for much of their professional lives, regardless of what they do. These transferable skills are valuable in many contexts. Developing these skills in the context of a hard, fun biological problem is a great way to prepare yourself for a wide variety of careers.

Getting a PhD is an important step on the path to becoming a professor, but this doesn’t mean that becoming a professor is necessarilly the most important outcome of getting a PhD. Historically, PhD training has focused on the academic faculty career path above other career paths. A growing number of students now pursue PhDs without the intention of becoming professors. Many PhD training programs and advisors are working to make sure they provide PhD training that serves this broader array of outcomes. If your primary goal for getting a PhD isn’t to go on to be a professor, feel free to talk openly about this early on in the application process. Either you will learn the specifics of what your prospective advisor and department are doing to make sure they meet the needs of broader professional goals, or you will find that the program isn’t right for you.

Post-PhD career paths have sometimes been viewed by academics as binary, the trainee either stays in academia to become a professor or leaves academia to pursue other goals (A). It is critical to recognize academia is one of many alternative post-PhD career paths (B). There should not be an implied stigma of failure if someone with a PhD pursues a career path other than becoming a professor.

Some jargon…

If you have already worked in a research lab you may be familiar with most of the jargon relevant to applying to a PhD. Otherwise, here is a primer. Either way, get ready for plenty of jargon in the course of your PhD.

A graduate school is the academic and administrative organization within the university that oversees graduate education (including PhD and masters training) and oversees the admission process. A department is an academic group of faculty organized around a thematic focus (e.g., ecology and evolution). Each PhD student will have an academic advisor, or more rarely a couple of co-advisors. This advisor is usually a professor with a research group that may include other graduate students, postdoctoral researchers that already have a PhD (a.k.a., postdocs), technicians, undergraduate students, and other members. A research group is often refered to as a lab, even if it doesn’t have a physical laboratory space. Professors are sometimes called by different names depending on what professional capacity is being referred to. They are often referred to as faculty members (particularly in the context of university administration), group leaders (in the organizational sense of overseeing a research group), a principal investigators (PIs, when overseeing work supported by a grant), or a thesis/PhD advisor (in the context of training PhD students in their research group). These titles don’t always perfectly overlap. For example, a postdoc can also be a PI in some cases. A faculty member can be in one or more departments. A curriculum vitae (CV) is a document that explains past education and qualifications. It is essentially a résumé, though with more detail.

How is applying to a PhD program different than applying to be an undergraduate?

When you apply to become an undergraduate student, you are primarilly applying to the institution (i.e., a College or University) and will interact frequently with people across all of campus. In graduate school, you will spend more of your time within a smaller part of the institution. Rather than think of your graduate student application as an application to a university, you should think of it more as an application to a particular department or a particular lab. This means you shouldn’t focus on finding universities that are the right fit for you, you should focus on finding departments and labs that are the right fit.

Graduated students are always formally admitted to the department, but departments differ in whether the student is directly admitted to a specific lab at the time they join the department or join a lab after having been in the department for a year or so. Always feel free to ask for clarification if you aren’t sure which path applies to the department you are interested in. They are quite different, so it is important to understand them as you approach the application process. The graduate school and department will always have a big say in deciding which prospective students to admit, but the role of the potential advisor can be different in these two systems. Regardless of which path the department you apply to uses, you should contact prospective advisors to make sure they are taking a student.

Direct admission to lab — Some departments admit students only when a particular advisor has been pre-identified, with the intention of the student working in the designated lab when they arrive. In this case, the prospective sudent is essentially admitted to a particular lab and the potential advisor plays a big role in deciding whether the student should be admitted to the department.

Rotations — Some departments admit students to the department before a particular advisor has been identified. The student does rotations in several labs when they first arrive. Later, the labs and PhD students will identify the best fits. In these cases, the advisor often doesn’t play as big a role in the original admission decission because it isn’t yet set which advisors will train which students (though they can certainly weigh in if they are interested in a particular incoming student). Even so, before students apply to the department it is just as important that they make sure there are one or more labs in the department that they would be very excited to work with and that these labs expect to take students in the near future.

Some departments have models that are hybrids of these approaches. For example, applicants identify potential advisors during the admission process, still do rotations when they arrive to get to better know the department, and sometimes switch to a different lab that turns out to be a better fit.

How should you decide where to apply?

The most important first step in deciding where to apply is to read the primary scientific literature. Take a deep dive into papers in the research domain you are most interested in pursuing for your PhD work. Even if you think you have identified an advisor that is the best fit before reading any of their papers, still read their papers to make sure the nitty gritty of their work is in alignment with your goals.

Once you find a paper you like, go to the lab websites of the authors and look for other papers of interest. As you zero in on a few labs of interest check out the sites for the departments where they are located. See what other labs in the department are of interest to you and read some of their papers too. Some departments have a focus on particular subfields, with multiple closely collaborating labs. Try and identify any such department clusters in your field of interest. Joining such a cluster can give you more flexibility and training options, though many great labs are not part of a cluster.

When it comes to the specifics of the scientific research program of a lab, there are a few ways to assess fit. I usually think of three distinct types of fit — methods, system (e.g., focal species, simulation framework), and question. I think it is best when the interests of the prospective advisor strongly overlap in at least one or two of these areas, and that really exciting things often happen when there isn’t yet overlap in one of the other areas. For example, the student may anticipate using an established method and system in the lab to ask a new type of question, get at a question the lab is working on in an established system using a new set of methods, or port an established question and set of methods to a new system. You should be very cautious about entering a lab where you don’t anticipate strong overlap in at least one of these areas. If your work isn’t tied in some way to existing work in the lab then there will be fewer training opportunities, funding can be more difficult, and there is less opportunity to collaborate as a team.

A good scientific fit is necessary for a successful graduate student experience, but not sufficient. There are other types of fit that are also critical, but that can be harder to assess. These include the advising style of the advisor, lab culture, and department culture. Your advisor will have a big impact on your day to day frame of mind, training, productivity, and post-PhD professional opportunities (through letter writing in particular). Particularly in the later phases of the application process, talk frankly with a prospective advisor about their advising style. Talk to other students to see what their impression of the advisor’s mentoring style is, and to get a handle on how accessible the advisor is. Advisors are people, and they have very different personalities. Some advisor personalities will work well for some students, others won’t. An advisor personality attribute that is a plus to one student might be a minus to another student.

Feel free to ask about lab culture. Are there regular lab meetings? How do lab members share manuscripts, code, and data? Also ask about the collegiality of the department. Are there regular talks and socials? How much do people interact across labs? Do faculty conflicts ever negatively impact graduate student experience? This will be your community, and you will rely on them in good times and bad.

PhD research projects differ greatly in how independent or collaborative they are (though all projects have elements of both). Some projects are stand-alone research programs, where the student sets most of the parameters and operates very autonomously. Other PhD projects are subparts of much larger highly collaborative projects, where students are frequently working with others to set priorities and the parameters of the project are highly influenced by what else is happening in the lab. There are distinct benefits to each type of projects. Working independently can give more freedom, for example, while working collaboratively gives the opportunity to be part of something much bigger than anyone could do on their own. If you have a strong preference for independent vs. collaborative work, then talk with your prospective advisor in advance. Most labs tend to have more PhD projects of one type than the other.

How will your application be assessed?

The people that evaluate your application will consider a few different things. They look at your past training to make sure you are prepared for their program. They assess your track record (e.g., grades, test scores, and, if applicable, published work) to try to predict your future performance as a PhD student. They try to evaluate how you will work (e.g., can you succeed at both collaborative and independent work?). They are looking at your interests and current skills to assess fit with the projected work and priorities.

Good fit has multiple components. These include the overlap on methods, systems, and questions that I discuss above. A prospective advisor is usually looking for a student that is interested in particular research areas and will help move the lab toward long term goals. Regardless, you should talk openly with potential advisors about the fit between your interests and overall lab goals.

PhD training programs are looking for students who are mature, curious, hard working, and add positively to group dynamics. “Works well with others” has become a cliche in some ways, but is extremely important. Science is collaborative. Doing something else after finishing your undergrad work and before applying to grad school is often looked upon favorably, as it gives you a broader set of expereinces to draw on during your graduate work. Examples include masters studies, working as a research assistant, logging a few years in industry, non-profit work, or even traveling.

PhD training programs are excited about the experiences and skills you bring to the community. You are not a blank slate. Make it clear what you bring with you. Provide specifics on bench, field, computational, statistical, engineering, illustration, microscopy, and any other skills you have. The details are very helpful. I have had several conversations with prospective students where they casually mention toward the end of a call that they are already trained in some technique that will be highly relevant to their work. Make it clear up front what you are bringing to the table, don’t be shy. For example, if you have data analysis skills, don’t just list “data analysis” on your CV. Explain the actual tools you have used and how you have used them. If you have posted code you wrote on GitHub, provide a link to it.

Most applications have an open-format personal statement of some form. In this statement, you should get across both the big picture and little details. Why do you want to go to grad school? What scientific questions are you interested in? What would you bring to the lab in ways of skills, experience? What do you want to get out of grad school? Why are you applying to this lab/ department in particular? Provide the most important information up front, don’t build up to a big point on the last page that some reviewers may not read very closely. Essays that focus on grand general descriptions of why you love the natural world, at the expense of describing the specifics of your experience and goals, are far less helpful for understanding what type of student you will be.

Scientists spend a large fraction of their time writing. Being able to write well and efficiently is very important to your success as a PhD student. The reviewers will be scrutinizing your application for indications of your strengths as a writer. This includes approaching your personal statement as a writing specimen. Publishing a scientific paper is certainly not a requirement for applying to a PhD program, but it is very helpful to your application for several reasons. It shows that you can see a project through from begining to end, it provides a concrete example of your scientific writing, and it shows that you have experience with one of the most important aspects of doing science.

If there is something about your application that will send up flags (e.g., a low GPA), your statement is your chance to address it directly. It will be noticed, so it is better to explain it than to avoid drawing attention to it.

Reference letters are most helpful from people who know you well. It is better to ask a lecturer you TAed for than to ask a National Academy member down the hall that you met only a couple times. Brass tacks are more helpful than vague platitudes to those evaluating your application.

How does graduate student financial support work?

When a prospective student applies to a Biology PhD program, they will often hear that support (including tuition, stipend, and benefits) is guranteed for a given interval of time, e.g. five years, as long as you stay in good academic standing. It is important to realize that this doesn’t usually mean that you just got a five year free ride from the University. What it means is that someone is guaranteeing financial support for your PhD in case external support isn’t obtained, but there is an expectation that every effort will be made to get external support. The university and department often provide a fixed amount of support (a year or two) to all students. The faculty advisor is expected to pay for the rest out of external grants, or you as the student will serve as a teaching assistant in more courses to help cover the cost.

The details of grad student funding vary widely from school to school. Although these details are often not explained when a student is exploring different programs or deciding whether to accept an offer, it is important to ask about them. For example — “I see the PhD program gurantees five years of support. How does this support usually break down?” Understanding this breakdown will help answer many critical questions about your PhD- how many classes will you be expected to be a teaching assistant in, what happens if external funds are not obtained, are external funds already in place?

The fact that your funding as a student comes from multiple sources makes it very important to seek external funding you may be eligible for. This is great for your own professional development, can give you more flexibility in your PhD work, and defer costs that can be put toward other expenses (such as your lab or fieldwork). I highly recommend that all eligible PhD applicants (criteria include being a US citizen) apply for the NSF Graduate Research Fellowship Program in the same application cycle as they apply to PhD programs. The deadline is usually in October. Other potential external funding includes the Fulbright Foundation.

How do I apply to a Biology PhD program?

Most applications to PhD programs are due sometime between November and January. Ideally you would start thinking about the application process much earlier. The preceding March or April is a good timeframe.

The first step is to identify prospective advisors and departments. After reviewing the scientific literature and browsing lab and department web sites, you will start reaching out to potential advisors. Your letters to them should be short (a paragraph) and specific. Do not write a letter that could have been copied and pasted to anyone in the field —there is a good chance that it will be ignored along with the dozens of other emails that have been broadcast to a large number of professors with little previous evaluation of fit.

Brevity is important for a few reasons. There will be plenty of chances to follow up with more detail later if the initial contact is promising. Lengthy emails tend to bury some of the most important points and dilute rather than showcase your strongest points. Academics all spend more time than they would like on e-mail, in large part because they have to sift through so many long-winded emails that could have made the same point in a much shorter note. A short email signals that you understand this and are a clear and effective communicator.

The best way to make your initial contact email specific is to refer to the primary literature. For example, “I am interested in the work your lab published on X in papers A,B,C.”

If the initial contact is promising (the advisor hopes to take students, and is actively pursuing work in the area you want to study), then it is good to have a larger conversation about what a PhD project in the lab would be like. A skype call are a great way to do this. Be clear on what is really important to you. If you are excited to join a particular lab because you are really excited about the field work they do, you want to be sure that there are plans for that field work to continue. Also provide examples of the things that get you most excited about the work you want to do. Be sure to provide enough detail for faculty to get a sense of how much you know about the questions, methods, and system they work on. One really helpful way to do this is to discuss hypothetical PhD projects to illustrate your goals and interest. These aren’t binding agreements for a specific project, just a chance to test drive some ideas.

Many professors have appointments in multiple departments. By sure to ask prospective advisors which department you should apply to. The decision about which department to apply to can have important implications for research focus, graduate student community, and funding. If the professor can take students from multiple departments, they will likely have a strong opinion very early in the process about which would be the best fit for your needs. They may assume you are coming in through a particular department and not bring this up, which can lead to very unfortunate misunderstandings about the application process.

The application materials really are helpful for evaluating prospective PhD students — that is why we ask for them. Pre-application conversations are a way for you (the applicant) to decide whether to apply to the program, and for the prospective advisor to frame your application when it arrives. A prospective advisor may be inclined to delay most correspondence until after the application is in hand. Don’t take this as a cold shoulder or lack of interest, it is just that it can be difficult to evaluate the candidates until all the applications for the year are in hand. Professors often have a series of shorter conversations with a larger number of students before applications are submitted, and then more in depth conversations after the applications are in hand.

Many departments invite finalists or accepted students for a campus visit in January or February. This is a very good chance to get to know each other better before making a 5+ year commitment.

One other important point — almost every year a student contacts me that can’t apply to a program they are interested in because they miss a test or application deadline. This is one of the reasons it is so important to identify prospective departments and labs very early on. It gives you plenty of time to identify and meet all application requirements.

How do you prepare for entering grad school?

There are usually long delays between deciding to apply to PhD programs, getting accepted, and starting your studies. You may have other commitments that keep you fully busy during this time, which is fine. But if you have some time to start preparing for your PhD research it is great to get a head start.

The main advice I give students who have some time on their hands before entering grad school is to read the literature in their field of study and to develop their computational skills. The reason is that they are both important no matter what you go on to do in Biology, and they can both be done with no more than a computer and an internet connection. Both will allow you to hit the ground running. The book I co-authored with Steve Haddock, Practical computing for Biologists, is in part targeted at students in this exact phase of their studies.

I wasn’t accepted to my PhD program of choice. Should I take that as a statement about my worth as a scientist?

No. There are two very different things that are evaluated during grad student admissions — the general strength of the candidate, and the current fit of the candidate to the lab and department. Very strong candidates often aren’t accepted because the fit isn’t right at the time. It may be, for example, that someone with very similar interests and strengths to you was accepted in the previous year, and this year the lab is looking to grow in a new way. It could also be that you are a great candidate and a great fit for the lab, but funding isn’t available to support the work. Also, the number of students that each department can accept is usually set by the graduate school. It may be that the number of graduate students the faculty would like exceeds the number of slots that are allocated, and not all faculty can make an offer to their top choice.

Prepare to be surprised.

Sometimes prospective students that have a very specific idea of the best way that graduate school could work out, and see any other path as something short of ideal. No matter how much work you put into selecting and applying to PhD programs, though, there will still be many things you don’t initially anticipate about your five years of training. While there can be an overemphasis on the ways that things can go wrong in unexpected ways, there are so many ways that things can go right in unexpected ways. You may be focused on getting into what someone has told you is a “top” lab in your field, only to visit and find you just don’t like it and instead really click with a potential advisor somewhere else that wasn’t initially high on your list.

Key takeaways

  • Biology PhD training isn’t just for people who want to become professors — it is excellent training for a wide range future goals that address big, difficult problems.
  • PhD programs will evaluate both your prospects as a PhD student and your fit with the department and lab research goals. Even if you are an exceptional student, you may still not be accepted if the fit isn’t right.
  • Evaluating fit is a two-way street. Applying to a PhD program isn’t just a chance for them to evaluate you, it is a chance for you to evaluate them. In this way it is a collaborative process.
  • Prospective advisors and departments are very interested in what you have to bring to the community. Don’t underestimate what you have to offer, and get specific about your talent and experience. The more concrete your description of yourself is, the more helpful it is.



Casey Dunn

Evolutionary biologist at Yale University. The views expressed are mine alone and do not necessarily reflect the views of Yale University.