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I got my master’s degree in China and had worked for two years as a visiting student in the US. Although my master thesis’s supervisor promised to write me a recommendation letter, my visiting student advisor refused. He is the corresponding author of all my publications. What's more, research experience in his lab was included in my personal statement. He said he would offer me a recommendation letter only if I apply for his lab. When I asked whether he could recommend me for other universities, he did not reply to my email. Is there any possibility that I get an offer without his reference letter? How should I explain this to an admission committee?

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    Does the visiting student advisor make a habit of not giving recommendation letters for students he would like to keep? – Patricia Shanahan Oct 29 '16 at 15:06
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    This isn't an answer, though just to let you know, some people, some advisors, some professors are just jerks. Good luck! – MikeP Oct 29 '16 at 16:59
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    I mean"he did not reply to my email". Sorry for not making myself clear. – Milos Oct 30 '16 at 8:04
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    After you have secured yourself a PhD position elsewhere, please put in a formal complaint about your advisor's shockingly unethical and unprofessional behaviour to the authorities at the university. – Jack Aidley Oct 30 '16 at 20:04
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    Just to emphasize Jack Aidley's point - this is unethical behaviour, and you have every right to be distressed by it. (It should also be a gigantic red flag against applying for that lab - is he going to refuse you a recommendation letter after your PhD unless you do your postdoc with him?) As soon as you have the chance, do consider reporting this appropriately, to both universities, so that this doesn't happen to other students after you. – E.P. Oct 31 '16 at 1:14
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You will need to find another reference.

I recommend not keeping this supervisor up-to-date on your application status.

When asked why his reference was not included, probably you could just say factually and without sounding judgemental that the student advisor offered a reference only under condition that you would work for them, so you sought another reference [pretend that you do not realise what that means - coming from China, you can probably present it, if asked, as if you assume this may be the norm to only give out references under these conditions; of course, this is not true, but I think your best bet is to take the "naive" route].

You also have publications with this student advisor, so that already proves that your work is good enough to pass peer review - a direct reference from them would be nice, but is not anymore vital at this stage.

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    +1 for this, especially the part about not sounding judgemental and just stating it as fact. They will likely assume you're just not familiar with how bad that is, and rest assured, will make their own negative conclusions about it. It's a shame you're in this spot, but best to separate yourself from this person. – Jeff Oct 29 '16 at 16:51
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    It's not "pretend you do not realise how bad this is, because you're international". It's "when presenting bad news like this, it is better to state it coolly without trying to force any conclusion." Maybe that's a shorthand way to think of it but it's a pretty general principle and no slyness is needed. – user18072 Oct 30 '16 at 0:42
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    You gave me so much confidence. As you said, it is better to just state it as fact without making any judgment. – Milos Oct 30 '16 at 1:19
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    Yeah, this sounds like the approach to take. It might be worth stating this in a cover letter, instead of waiting to be asked (which might not happen if the lack of such a recommendation is deemed a critical flaw in the application). – E.P. Oct 30 '16 at 20:53
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    @E.P. That contradicts my and djechlin's suggestion to downplay the judgement on the original referee's refusal (whichever variant - djechlin's or mine - OP wishes to use); it clearly shows that OP considers this a problem. Given that OP has published papers (more than one!) with the supervisor, the actual reference may not be critical. – Captain Emacs Oct 31 '16 at 0:46
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While not illegal, the behavior of your advisor is completely unethical. The behavior is so bad, that it can tarnish the reputation of an entire department. I suggest you attempt to get his position in writing. Make sure you clearly understand that he will recommend you for a position in his lab but no where else. Not recommending someone to a particular program, or even every program, is not unethical. Limiting letters for people to only places where you will benefit is unethical.

Once you have it in writing (or at least a clear understanding), you should approach your department chair asking for a letter of recommendation. Explain that your supervisor is willing to write a letter for his lab, but not for any other labs. Then show him the email. The department chair will also likely feel guilty and read over your papers and write a reasonable letter. More importantly, the department chair can explain why you don't have a letter from your supervisor (i.e., that the chair believes the supervisor is happy with your work, but refuses to write letters because he does not want to lose you). The chair will most likely then have a private discussion with the supervisor about his behavior.

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    This assumes that the atmosphere in the department is generally not toxic. In general, I would assume that, but if OP does not know the precise dynamics behind what transpires, this slightly "aggressive" (not really, but you know what I mean) approach may lead to developments out of their league. – Captain Emacs Oct 31 '16 at 15:49

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