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Imaging that I am a student from College A and cross-registered in Institute B. I am a college kid so I receive very little care from the professors from my own school, and I do not have an official supervisor. Most of the works are done in the library and computer lab of B, and I discussed my ideas very often with professors in B. However, I do not have department affiliation with B. My formal status in B is something like "exch. stud." I guess it means exchange student.

What should I list as my academic affiliations in scientific publishing?

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    You can use both. When we have exchange students publishing stuff, they list both places. – Gimelist Feb 11 '18 at 7:29
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I would expect you to list both affiliations. This is very common at all levels of research.

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