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I submitted my PhD thesis and went to work in a company where my PhD supervisor co-founded. I submitted part of my thesis work to a conference, and it got accepted. Now my supervisor asked me to affiliate the paper with the new institution. Is it alright if I do this? The thesis work was mostly done at the university, although under the supervision of the same person.

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    Not a laywer, but I doubt there are any legal issues. Different fields treat affiliations differently, so the norms will depend on the field you wrote your thesis in. Commented May 21, 2023 at 11:05
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    In computer sciences, I have always seen authors use their current affiliation. Sometimes, a footnote indicates that most work was done at institution X, but that's it.
    – Clément
    Commented May 21, 2023 at 12:44
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    In mathematics, it is not uncommon to see an acknowledgement somewhere in a paper to the effect of "this is part of a dissertation submitted to Univ. X. ... ." If an affiliation is listed, it is almost always the current one. Commented May 21, 2023 at 18:29

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Answer by @ZeroTheHero is fine, but I don't think you need to be that explicit about the details, or at least it's not the norm. Having multiple affiliations is not a rare thing, and you can simply write both of the institutions in your affiliation(s) without any additional comments.

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The simple way is to use dual affiliations.

Zero the Hero
Department of [then]
current address: [company now]

It makes it clear the work was done and supported by an institution different from the one you currently work at.

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