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I am a graduate student considering submitting a paper either to Bioinformatics as a typical refereed journal article or to Bioinformatics as a refereed conference proceeding. A webpage providing information about submitting as a refereed conference proceeding (https://www.iscb.org/ismb2018-submit/proceedings) states the following:

"Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal with an electronic version distributed to conference delegates. The proceedings will be available online approximately one month prior to the conference opening."

and

"Publication of the proceedings as an online part of the Bioinformatics journal will result in fully citable articles, indexed by Medline and ISI. See the conference proceedings for https://academic.oup.com/bioinformatics/article/33/14/i1/3953992 for an example of online-only publication by Oxford University Press."

As a graduate student preparing for a career in academia, I am unsure whether I should submit my work as a typical refereed journal article or a refereed conference proceeding. I generally feel that conference proceedings have less impact, but in this case, I would also be able to present my work orally at the conference.

Moreover, I am unsure how I would handle such a conference proceeding publication on my CV in an honest manner. Could it still be included as a "refereed journal article" on my CV or would it need to go as something else like a "refereed conference proceeding". I am unclear as the statement "Accepted papers will be published as conference proceedings in an open access, online-only, section of a regular issue of the Bioinformatics journal" seems to imply it can be considered a regular refereed journal article.

I would be grateful to hear any advice on this subject matter!

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After the passage you quote it says

ISMB 2018 provides authors of accepted papers an oral presentation to provide an oral summary of their work. All presentations should be no longer than 20 minutes including 3-4 minutes for discussion.

It seems like this organization has both a regular journal and a conference. If you submit as a journal article it would be a peer-reviewed journal article. If you submit as a conference paper it would be a peer-reviewed conference presentation.

In my field (computer science) these would likely be viewed as being the same in terms of prestige, but this is not true in most fields. Your advisor would be a good resource for feeling out how people in your field view conference papers vs journal papers.

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    In my field is often possible to do both. The publication shouldn't be right replica of course. It can be not straightforward but timing of events and content of the papers make it possible. Sometimes I skip proceedings. It should be field independent otherwise conference would be deserted. – Alchimista Jan 30 '18 at 12:50

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