I am going to submit a manuscript that, if accepted, will be included in my Ph.D. cumulative thesis. The cumulative thesis will be composed of two papers: the first one has already been published in the same journal to which I am going to submit the second one. So, in the best case scenario, I will end up with a PhD thesis having two papers published in the same journal. The papers are somewhat linked but different.

Now, I am writing the cover letter to the editor and wondering if it is a good idea to mention this aspect. Could it be good, bad or irrelevant?

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    Could it be good, bad or irrelevant? — Irrelevant, and none of the editor's business. – JeffE Jun 1 '17 at 17:50
  • @JeffE Can you turn your comment into an answer? – jakebeal Jun 6 '17 at 0:41

It is always important to acknowledge past publication history in any paper or thesis. For example:

  • If any portion of your thesis has been published in any form (such as a technical report, conference paper, working paper, or journal paper), you must acknowledge that prior publication in your thesis.

  • If any portion of a journal submission has been published in any form (such as a technical report, conference paper, working paper, or PhD thesis), you must acknowledge that prior publication in your submission.

In both cases, the later publication must acknowledge the earlier one. Some publication venues impose restrictions or conditions on the later publication of the same result. For example, in many fields of computer science, conference papers can be republished in journals only after the addition of significant new material; in other fields, republishing conference papers in journals is simply impossible. In chemistry, even submitting your PhD thesis to University Microfilms may publication of your thesis research in a journal impossible [source]. Conversely, some publishers require that any thesis that includes results from a published journal paper not only cite that paper but include a copyright notice for the repeated text [same source].

But there is no similar expectation that you acknowledge future publications, because they don't (yet) exist. It's really none of the editor's business what you might put into your PhD thesis—that's entirely between you and your thesis committee.

  • It's worth noting that there are some caveats to this - in particular, some conferences (notably CVPR) insist that you don't cite the technical report or arXiv version of your conference submission. Specifically, they say "Note that a Technical Report (departmental, arXiv.org, etc.) that is put up without any form of direct peer-review is NOT considered a publication and is therefore allowed, but should NOT be cited." – Stuart Golodetz Jun 6 '17 at 22:39
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    @StuartGolodetz Interesting. By a strict reading of CVPR's definitions, a PhD thesis is a prior publication, because it is submitted to peers (the committee) for evaluation and it can be rejected, and therefore thesis chapters cannot be submitted to CVPR after the thesis is accepted. Also, despite what the policy claims, arXiv submissions can be rejected. (I'm an arXiv moderator; I have rejected submissions.) But I'm sure the de facto policy is saner than my literal reading. – JeffE Jun 7 '17 at 4:35
  • I guess I would argue that "peer-reviewed" tends in practice to mean something slightly different from just "reviewed by your peers". From a practical perspective, I'd have thought that it's rare for thesis examiners to peer-review an entire thesis in the same kind of detail that they might review a conference or journal paper, and in that sense I'd be wary about characterising a thesis as peer-reviewed (as far as I know, I don't think others would characterise it as that either). I don't know what CVPR's policy on republishing thesis material is, but I'd be surprised if they prohibited it. – Stuart Golodetz Jun 7 '17 at 17:19

In general it cannot hurt to state in your letter to the editor that you intend for your papers to be inclusions in your thesis. Some journals may even prioritise your paper higher in the review queue because of the time constraints on finishing a thesis.

I would check with the journal regarding any conditions in relation to re-publishing your papers in your thesis. I found this was usually somewhere fairly obvious (easy-to-find) such as in the author instructions or submission guidelines. Some explicitly stated that the author was free to republish in a thesis submission (provided the journal was was cited). Others advised that the author needed to contact the journal to obtain permission. What I found, and what my PhD supervisor thought, is that permission is usually given for a thesis along with instructions how that permission should be included in the thesis (so that thesis examiners know you have followed academic protocol).

I published most of my thesis as peer-reviewed papers in journals. I think I had eight chapters that were published papers, and another that only made it as far as a pre-print at the time of submission, but they were published across three or four different journals. The papers that had a common theme were published in (almost) the same journal. By almost I mean I had one published in the Letters edition of the journal and the others in the main journal.

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