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In terms of judging a doctoral program--and possibly also relevant for postdoc-ships(?)--which is the more important consideration, who your advisor is or the institution at which you study?

Obviously both are important, but when it comes down to it, which should weigh more heavily?

For example:

Professor Alpha is a premiere name in the field, but he's set up at Southern State University, an otherwise middling school. Perhaps he's there because he's a big fish in a small pond and gets carte blanche and limitless resources to do what he wants. His graduate students are thus treated similarly.

On the other hand, Professor Beta is a new, unproven professor at Top University, a world-renowned, leading institution. He personally may not have the resources and freedom as Professor Alpha, but he's at an institution whose name carries weight. Therefore the school certainly has the capacity for the same, if not more, resources, but access for Professor Beta's grad students will be more limited as they must be shared with other professors' groups.

Assuming all else is equally appealing (funding, location, research topics, etc), which offer do you choose, or which program would you hold in higher regard?

(The situation doesn't have to be so stark as like Harvard vs. Middle-Of-Nowhere University, but it makes the point clearer.)

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    I assume you're asking mainly about the experimental sciences, but let me point out anyway that in mathematics many students enter a Ph.D. program without yet having a clear idea of what subfield of mathematics they will specialize in. In such a case, the weight obviously shifts toward the institution. – Andreas Blass May 3 '15 at 23:57
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    Another important consideration is, even within the same university, whether you want an older, more-established, advisor or a younger, more-to-prove one. Both have their pros and cons. – Patrick Sanan Nov 6 '16 at 22:35
  • I think the answer to this question varies a lot between the US and most European countries. In Europe, the distance between top and bottom universities is not so steep (in particular when compared within the same country) and it is possible for a middle tier university to have a top-class group in a particular (sub)field. I would say that in (most of) Europe the group (or PI) should carry more weight. Possible not-so-clear-cut cases can be Cambridge, Oxford, ETH Zurich, etc. – Miguel Nov 6 '16 at 23:57
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Obviously one needs a competent advisor with whom one is compatible. But assuming that both professors qualify, I think what matters most is the quality of the students who will be your peers. You need to surround yourself with students who, from day 1, expect nothing less of themselves than to produce novel scientific research of the highest caliber, present it at top meetings, publish it in top journals, and forth. Ultimately you will learn more from your peers than from your advisor. A sufficiently talented and ambitious cohort will hold the bar high for you and push you to excel whereas a sufficiently talentless and unambitious cohort will help you make excuses for your own failures to reach your potential.

In my experience, top schools with top graduate programs have the sorts of students you want to surround yourself with. Second tier regional programs may, but I have yet to see it.

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    How can one asses the quality of PhD students?. Check their publication record? – Keine Apr 29 '15 at 8:23
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    In many STEM fields in the US, prospective PhD students visit as part of the admissions process. This is the best opportunity to assess the quality of the PhD students. Meet them. Talk with them. Get a sense of departmental culture. Figure out whether they are publishing, and where. Etc. – Corvus Apr 29 '15 at 14:14
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    As the OP almost 2 years later, I can confirm that this was easily the best advice. Good advisers are important, but you heavily rely on and collaborate with your peers. High quality and collaborative students is a big thing – marcman Jan 13 '17 at 5:20
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    Delighted to hear that, @marcman! – Corvus Jan 28 '17 at 4:39
  • @marcman One might call the core of academia a social constructivist approach to building knowledge. Peers are who you co-construct with; you bring your own unique perspective, and they their own. Together, you build entirely new ideas, processes, etc. If you consider your advisor just another peer (but perhaps with more experience), you may just find that your plural peers provide more room for growth, and thus to be more important :) – Chris Cirefice Feb 9 '17 at 22:39
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I personally think that your rapport with your supervisor is of primary importance, and I personally didn't care to choose my PhD by university when I got the opportunity. (Assuming that both your options are offering what you want from a PhD in terms of subject and skill sets.)

As a final year student in biomedical sciences, what I have mostly found is the following:

Money

Your supervisor should be able to fund you, and your experiments fully. You should not come to a situation where you are choosing the second best option (especially in biology) because of the lack of funds. This will ruin the quality of your thesis.

Go-to guy

You should have a supervisor or a post doc in the lab who will be able to help you when you initially start out to answer your stupid questions. There will be many, and you'll need to find some one in the lab who is friendly enough, and patient enough to answer them. You'll know them when you see them. And of course, the other members of the lab do make a difference. See what they are like.

Higher up or lower down?

You should need to ask yourself, how high up the totem pole you want your supervisor. Remember, the higher up they are (especially professors) the lesser you are likely to meet them on a regular basis, and most probably have lost touch with bench experience. On the other hand, profs have better connections and their recommendation carry weight.

The argument for university preference goes like this: If your prof doesn't have his own lab, and relies on community equipment, then you must go to a university which has the money to spend. Otherwise the choice of university is mostly trivial.

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Here are some additions to the other answers.

First, since I don't know how you've made your assessments of A & B, a couple of things you should look into if you haven't already:

  1. Look up what kinds of jobs the former students of Professor Alpha got. If almost all of them got truly great jobs, then working with him seems like a safe (though not necessarily the better) choice. If not, maybe you should reconsider his pull in the field. (But if not, one factor is that his students may not be as strong on average as those at a better university--still this is bad for you as in Corvus's answer.)
  2. Check to see if Professor Beta was hired as an assistant professor or associate professor. At many top departments, it's really hard to get tenure, but they hire more established people they are sure of at the associate leve. So if Beta was highered as an associate professor, then it's safe to say Beta is "proven."
  3. If you have professors in this field, ask them for their opinion.

In addition, the other answers don't seem to address your job prospects after getting your degree at one of these universities. For your question, "which university would you hold in higher regard?", if I were reviewing an application for a job application without specific knowledge of the professors, I would hold the higher ranked university in higher regard. If you're looking for a research job, and you have a positive answer to point 1 above, then it shouldn't be a problem as enough people in your area will know how good Professor Alpha and his students are. But if you're applying for more teaching-oriented positions, or positions in industry, then graduating from Better Name University can help you. (It's not just the name, but other factors as well: more contact with more talented people, etc. See this related question.)

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A very small answer, in addition to other good observations: I do claim that a particular analogy is relevant. Namely, would you want to have good parents but live in an unpleasant town, or bad parents but live in a nice town (if one imagines that "nice town" can truly make sense if one has bad parents).

Yes, if your penchant is for complete commodification of the whole process, then the parental/familial thing can be scoffed-at. But I'd recommend against going too far in that attitude.

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The most important thing is your adviser. Obviously you're not looking for a label, you want to do some valuable stuff in your PhD period. The professor in middle-of-nowhere university has the vision that's needed and can make you the researcher you need to be.

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