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Could the fact that I publish a working paper in a WP-series at the institution where I am doing my PhD jeopardise my chance to have it accepted in a peer-review journal? Since I know it might depend on editor/journal, I specify I was leaning towards Energy Policy (Elsevier).

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The 'Guide for Authors' states the following:

[...] Submission of an article implies that the work described has not been published previously (except in the form of an abstract, a published lecture or academic thesis, see 'Multiple, redundant or concurrent publication' for more information) [...]

[...] Please note that preprints can be shared anywhere at any time, in line with Elsevier's sharing policy. Sharing your preprints e.g. on a preprint server will not count as prior publication (see 'Multiple, redundant or concurrent publication' for more information). [...]

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Additionally, the page 'Multiple, redundant or concurrent publication' states:

[...] Multiple, redundant or concurrent publication: An author should not in general publish manuscripts describing essentially the same research in more than one journal or primary publication. Elsevier does not view the following uses of a work as prior publication: publication in the form of an abstract; publication as an academic thesis; publication as an electronic preprint. [...]

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To answer your question, you should clearly define what the WP-series really is. Is it just a collection of pre-prints or is it a primary publication? That's how you will get the answer you need.

In case of doubt, contact the Editor in advance.

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