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I'm currently a postdoc and I'm planning to apply for faculty positions soon. However, I'm pretty sure that my current supervisor wants me to stay on for another year. When applying for a job, I'm usually required to state 3 referees. Am I expected to state my current supervisor as one of the referees? Is it going to weaken my application if he's not among the 3? Due to the mentioned conflict of interest, I would rather state other people I've been working with...

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For how long have you been in this postdoc position? It may affect whether you or the advisor is viewed as the "bad guy" here. –  eykanal Dec 7 '12 at 20:08
Unless there's a contract (and leaving early is violating it), a supervisor doesn't "own" the postdoc. Maybe they have joint projects they are working on, and maybe the supervisor would like to get something to get to completion, but it's not clear that this discussion has happened: the "pretty sure" is a bit of a warning sign. While this doesn't help with your question, I wonder if you've spent enough time talking to your supervisor about what your plans: maybe this question will be moot. –  Suresh Dec 7 '12 at 20:49
+1 for Ask your supervisor. If she's willing to write you a reference letter, great! If you don't have a contract to stay, but she isn't willing to write you a reference letter, ask why. She might just think you're not ready (in which case you should take her advice seriously), or she might just pull the "loyalty" card (in which case RUN!) –  JeffE Dec 7 '12 at 21:25
@eykanal: 2 years so far. –  Gandalf Dec 8 '12 at 4:16
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If you need to list references, you will almost certainly be expected to list your current boss—in this case, your advisor—as a potential reference. At the very least, if you do not, there is a non-insignificant chance that at some point in the interview process you'll be asked at will ask why he wasn't listed. You should have as good of an answer as possible ready.

Note that stating "I'm ready to move on, but he wanted me to stay on" may raise flags for a potential employer, as they could wonder whether this reflects a lack of loyalty on your part.

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I personally think that if any academic is questioning "loyalty" then you should stay well away from them. Academia should not be about building little empires at the expense of your postdocs/grad students (though it often is). As JeffE mentions in his comment (paraphrasing) if they "pull the "loyalty" card ... RUN!" –  Luke Mathieson Dec 8 '12 at 1:17
@eykanal: The person in question is a post-doc. Postdoctoral appointments are typically two to three years. Nobody should raise a stink if a postdoc says "I want to do something new" beyond the first two years. –  aeismail Dec 8 '12 at 9:26
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