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I am about to do a Ph.D. in applied Mathematics/Theoretical Computer Science. The organization I'm going into is not a university, but a research institute in Europe. I'd like to assess my prospects after the completion of the Ph.D. So I would like to know how my Ph.D. would appear to potential employers. Will I be sidelined because I'm not from an esteemed university in the US, or will the actual contribution or my thesis be what I'm evaluated on? Will the former overshadow the good work I may have done and detract from it?
I thank you for your answers.

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    All the European research institutes I'm familiar with (INRIA, MPI Informatik, IST Austria) have excellent reputations. You'll be fine. – JeffE Dec 14 '13 at 6:40
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    Could you specify the country and the institute? The level is very uneven across the continent. – Doru Constantin Dec 14 '13 at 11:51
  • It is INRIA, France. My concern stems from the fact that it is not a University and hence there'll be trade-offs in some aspects. @JeffE Thanks for the comments. – Arun Dec 14 '13 at 13:10
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    I'll second JeffE: INRIA is excellent. Don't worry about it. – Dnuorg Spu Dec 14 '13 at 14:15
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    INRIA is very large. There is top-notch and rather mediocre people there. However, as an institution, INRIA is well-respected, so nobody is going to sneeze at your PhD from there. – xLeitix Dec 27 '13 at 23:03
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For any job where a PhD is actually necessary, it is the quality of your work that is important (it is you that they want to hire, not your supervisor or institution! ;o). In particular, if you have good papers published in top journals, that ought to count for a lot more than the university where you study, as it is likely your ability to produce top quality journal papers for which you will be hired.

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There are two issues here. The first is the importance of the institute you get your PhD from being a University. This is a non factor as nobody cares about if you get your PhD from a research institute or a university. The second issue is the reputation of the place you get your PhD from. This has some importance, but your supervisor and the quality of the PhD are generally more important.

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Your PhD will be worth exactly as much as the PhDs obtained from other universities. In fact, research institutes have many excellent professors, and they are probably better in terms of the quality of the faculty than many second-tier universities.

However, you will have one serious flaw in your postdoctoral applications; namely, you will have zero teaching experience. Unless you are one of the best in your graduating year, teaching experience is absolutely necessary, and in the US, you need a letter of recommendation addressing your teaching. So in that regard, your prospects are not so good.

But just write a great thesis, and you will be fine.

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