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I am a postdoc working in one university till 1. July. I am leaving for another university after that. During my stay at my current work, I wrote a paper as a first author for a conference that will kick off in September.

Which affiliation should I use? Taking into account that the conference travel will be covered by the new employer, however, the paper is written at my current university.

By reading this article, it looks like using the two affiliations is one approach. But I'm not quite sure if the new employer will be happy with this.

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    Both should be fine! Your employer should be able to understand that. – The Guy May 8 '18 at 11:03
  • How about asking your new employer? – Dirk May 8 '18 at 11:04
  • Thanks @scaaahu, however, my case is with conferences and funding the travel. so it is a bit different. – Mohammad Zahrawy May 8 '18 at 11:08
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    You may want to take a look at the answer of the linked question. Generally, we mark dups because of the answers will answer the question, not exactly because the question is the same. Also, there are quite a few questions about the affiliation. You may want to look at the linked questions, or related questions. I picked the linked duplicate because it's a general question. However, your field may have different conventions. If so, please specify it. Thanks. – scaaahu May 8 '18 at 11:17
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You are conflating funding sources with affiliations when they should be discussed separately.

The affiliations tell you where the work was performed. The work was performed at the old institution, so it must be listed as an affiliation, and should be the primary affiliation. If you have done work on the presentation at the new institution—for instance, used your research time to prepare the presentation and rehearse it in front of colleagues—then you can list the new institute as an additional affiliation. It should be listed as a "current address" in any event.

As for the funding issue, since they're providing the resources for you to travel, it can be acknowledged when listing anybody else who sponsored the research alongside those other sources.

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I don't think there's any need for judgement in this case. At the time of publication, you are going to hold a position at your new employer. Therefore, your current affiliation should be your new employer.

The work was performed at your old employer and not your new employer. Therefore you must put your old employer on the paper to disclose this.

The way to do this actually depends on the journal/conference. Some put your new employer on the top with a "work was performed at old employer" footnote, and some swap it, so the footnote reads "now at new employer". Find previous articles and copy them.

The affiliations in papers are necessary for the integrity of publications. For example, people need to contact you if they have any questions or concerns about the paper. If misconduct is detected, the institution where the work was performed holds some responsibility.

The travel is paid for by your new employer. Therefore, they are entitled a funding credit along with other funders.

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