journal publishing - what happens between submission and publication?

you’ve written your first paper, you’ve selected a journal to submit it to (using the advice offered in the august 2012 issue of microbiology today) and now you’re ready to send it through the peer-review process. if you haven’t done this before it can be daunting and there are mistakes that can be made that can either slow down the process or, worse still, result in the receipt of a rejection letter. karen rowlett, managing editor of the international journal of systematic and evolutionary microbiology, gives karen mcgregor some insight into what you should expect during the process from submission to publication.

what is your number one tip for authors?

read and stick to the instructions for authors of the journal you are submitting your paper to – it seems obvious, but it is not always done. if you submit a manuscript in a format that doesn’t strictly conform to the instructions laid down by the journal it is likely that your paper will be returned to you, delaying the whole process. equally important is to make sure that the contact details for the corresponding author are correct – particularly the email address. there are a number of steps during the process where you will need to be contacted so make sure you use an email address that will be monitored regularly and will be active throughout the process (if you are coming to the end of your phd don’t use your university email address if there is a chance that that account will be closed in a few months’ time).

what should go in the covering letter?

a covering letter is a useful way of introducing your research to the journal editor. remember, editors may handle hundreds of papers a year and may not be fully up to date in every area – this is why they rely on specialist reviewers. if you explain the relevance of your research (and possibly include references to other recently published papers or papers in press), you will give the editor a better idea of the significance of your findings.

if there is a good reason why you would like a quick decision on your paper, for example, to fulfil the requirements for a phd defence, let the editor know in your covering letter. they may not be able to expedite review, but if they are aware of the deadline they may be able to help.

how can the author identify appropriate editors/reviewers to suggest?

most journal submission systems will ask you to suggest an editor and potential reviewers for your paper. the journal website will list the names of the editorial board for the journal and may give some guidance on the types of paper that each editor handles. you may also have the option to exclude individual editors from handling your paper; think carefully about this and only exclude editors if there is a very good reason for doing so, e.g. they are in direct competition with your laboratory.

reviewers should have an understanding of the scientific concepts in your paper. if you have completed a literature review or attended relevant conferences, you may be able to identify appropriate reviewers easily. talk to your supervisor or other members of your department if you need additional suggestions. ‘jane’ (journal/author name estimator, www.biosemantics.org/jane/) allows you to input the abstract or title of your paper to identify authors that publish similar work. don’t suggest inappropriate reviewers – dr jo blogs who works in the lab next door may have a very good opinion of your work but would not be a suitable reviewer. in general, reviewers should not work at your institution.

how should the author respond to reviewers’ comments?

make sure that you prepare a response to all of the reviewers’ comments. if you do not agree with a comment, give a clear reason why you think that the change is not necessary, don’t just ignore it. when you upload your point-by-point response to reviewers with your revised manuscript, it can help the editor if you create a separate version of your manuscript with the main changes highlighted or in a different coloured font; this makes it easy for them to check that all the required changes have been made.

keep a note of the revision deadlines imposed by the journal editor. if you know that conducting extra experiments within this time frame will be difficult, let the editor know well in advance and they may extend the deadline for revision.

if the paper is rejected what are the author’s options?

rejection is a reality of the process and some journals, particularly high-impact ones, have very high rejection rates. rejection may not necessarily mean that your paper is not of good quality, it may just mean that it is not appropriate for that journal. sometimes editors will reject a paper but encourage resubmission once particular problems have been addressed.
some large publishers operate ‘cascade journals’. your rejection letter may suggest submission to an alternative journal within the same publishing group. the second-tier journal will have a lower impact factor but may still be a suitable home for your paper. if you decide to pass the submission to the next journal in the ‘cascade’, you won’t need to reformat your paper and the reviewers’ comments may go with it to the next editor. this could lead to a quicker decision than starting the submission process again with a new journal. however, you should think about whether the second-tier journal is actually the best place for your paper; could it be improved and submitted elsewhere?

what happens after the paper is accepted?

receiving an acceptance letter is by no means the end of the process. in the acceptance letter, the editor may suggest some further minor changes; if so, make sure that you do these quickly.
after acceptance, your paper will be prepared for publication by the journal’s editorial team. depending on the type of journal, this may involve some copy-editing and reformatting of your manuscript. the editorial team may need to contact you at this stage if they have any queries relating to your manuscript such as missing references, and inconsistencies between results in the text and tables or figures. you may also be asked to submit the source files for any images if the versions that were submitted for review are not suitable for final print or online publication.

once your paper has been converted to journal format, you will be sent a proof of the typeset paper. check the deadline for returning the proof – it could be only a few days as journals often have very rigid production schedules. look at the proof very carefully – this will be your last chance to check that the text is correct and to put right any minor mistakes (but it is not the time to make extensive changes!). as you will be very familiar with your paper by now it can be very easy to overlook mistakes, so why not get a colleague to check it too? mark the proof up very clearly (there is no need to use ‘proper’ proof correction symbols as long as your instructions are clear). if you need to insert several lines of text or a reference, type this out in an email so that there is no possibility of misread handwriting.

you, and your fellow authors, are likely to be asked to sign a copyright form or a license to publish. read any copyright agreements carefully and make sure that they do not conflict with the policies of your institution or funder. if your funder or institution has a policy that published research should be open access, you may have to arrange to make a payment to the publisher at this stage.

once that is done, you can sit back and look forward to seeing your name in print – or get started on your next paper and go through the publication process all over again!

if your paper has already been rejected by one journal, make sure that you reformat the manuscript according to the style of the next journal. if you don’t do this, the paper will be returned to you and it may also be obvious to the editors that the paper has been submitted elsewhere first (particularly if you forget to change your covering letter!). editors don’t like to think that their journal might be a second choice.