The ins and outs of submitting and publishing papers: a guide

As a first-time first author, you can run into unexpected hurdles on the way to publishing your journal article. In this post, I’ll take you on a deep dive into the nitty-gritty of submitting, revising, and publishing your manuscript.

1. Check what the journal needs

When I wrote my first paper, I didn’t think about the submission process. I figured I just had to fill out a few details and press submit.

Boy, was I wrong. It took me a week before I finally managed to submit my paper. It was frustrating because I had field trip coming up. So, a tip: make an account with the journal submission system a few weeks before you plan to submit. Go through all the steps of the submission process and check what information is required. A data availability statement? Reviewer recommendations? Author CRediT? Check, check, and check.

By starting a few weeks up front you have some time to collect all required information, and also prepare front matter such as Keywords*, Acknowledgements, and a Running Title. It also allows you to check author information (names and spelling, mailing and email addresses, ORCID id’s, etc.). Tip: send your co-authors a separate email to check if all details are correct, as they tend to get overlooked during feedback rounds. 

The journal will also require specific formatting of the manuscript. Most journals provide a style guide for this, often listed on their website under “Author guidelines”. These guidelines can be a bit confusing and sometimes contradict themselves – although some journals have more lenient formatting guidelines for initial submission. Try to follow them to the best of your ability, but don’t be like me and stress about it for hours.

*Keywords are essential as they help researchers find your work, so choose them carefully.

2. Sell your science

Aside from formatting the manuscript and providing the right details, you also have to sell the science. I don’t mean actually sell – in fact, you’ll probably pay a lot of money to get it published (more on that below). But you do need to convince the editor that handling your manuscript is worth their time (many editors are volunteers, and all reviewers are). There are a few ways to do this.

Start with the title and abstract. According to Elsevier these are the first elements a journal editor sees. A great title captures the content of your work, and a good abstract clearly summarises what you did, why, how, and what you found. Not sure where to start? You can find opinions and advice on good titles and abstracts here and here.

Then, write a compelling cover letter. Many journals request such a letter (or something similar, like a statement of purpose), in which you explain the relevance of the manuscript to the journal. You can find an example of a cover letter here. Your supervisors or co-authors can also help with this.

It also helps to reflect the aims and scope of the journal in the manuscript itself. Maybe it’s very obvious why this is the right journal, and you’ll only need a couple of sentences. However, especially with interdisciplinary work it can take some more text to reflect the journal’s aims and scope.

3. Proofread, proofread, proofread

Once the manuscript is finished and the cover letter written, there is only one thing left to do before submission: proofreading. As boring as it is, it is extremely important, because a manuscript with missing words and odd sentences looks sloppy and can lead to misunderstandings. Proofreading is not my forte, so I usually print out the entire manuscript (and cover letter) and then read the whole thing out loud. It takes me roughly 4 hours, or a bit more for very long manuscripts.

When you submit, the journal submission system usually generates a pdf document of all the files you uploaded. I recommend checking it properly, especially if the original document is not a pdf (e.g. if you submitted a word version). I’ve had figure numbers disappear, which can be quite confusing for the reviewers.

TIP: Make sure you remember which document you submitted, because the editor doesn’t always send it back to you. With my first paper, I spent several hours frantically figuring out which version I submitted. Version10-2; version10-1-final; version10-1-submitted??? It was a small nightmare.

4. Submit and wait

And don’t forget to celebrate! Submitting a paper, especially the first one, is a big deal. Yes, it’s not published yet. But years’ worth of research and writing have culminated into a manuscript so good that your supervisors and co-authors are willing to attach their name and reputation to it. That’s pretty cool!

Now, for the wait. This can range from a few days up to a couple of months. A desk rejection by the editor is quite fast, usually a few days to a few of weeks, while the outcome of a full review process can take anywhere from one to six months (and given the current reviewer shortage, even longer). If your supervisors or co-authors have published in the journal before, they know how long it usually takes.

Tired of waiting? Some journals have a tracker in the submission system that shows the reviewing status (but they are not always clear). Depending on the journal, it’s also okay to ask the editor after ~3 months about the status of your paper.

Note: If you are not the corresponding author, make sure to check in with them, as some journals will only contact the corresponding author.

5. The decision

No matter how long the wait, there will be a moment when you find a decision from the editor in your inbox. The type of decision can differ per journal, editor, and even paper. These are the most common ones:

1. Rejection
   • Desk rejection
     The editor decided that the manuscript in its current format wasn’t suitable for the journal, e.g. due to quality or due to scope. In the latter case, you might be invited to transfer to a sister journal, or revise the manuscript to better reflect the journal aims and scope.
     
     
   • Rejection after peer review
     The peer reviewers did not recommend the manuscript for publication. In this case, you’ll have to find a new journal. It’s wise to address the reviewers’ comments (if they are legit), because (1) they will improve your paper, and (2) you may get the same reviewers again with the next journal.
     
     
2. Revisions
   • Revise and resubmit
     The manuscript in its current format isn’t ready for publication, but if you address the reviewer comments you are welcome to resubmit. Editors may use this option if they feel the required edits take too long for major revisions (although some journals use this strategy with less integrity: to reduce the time between submission and publication, an important metric for scientific journals).
     
     
   • Accepted with major revisions
     The reviewers like your paper, but recommend some revisions. You usually get between 1 and 3 months for this, after which the paper is resubmitted and sent back to the reviewers. Note that some journals only allow one round of revisions.
     
     
   • Accepted with minor revisions
     Minor revisions are less substantial than major revisions. They are usually sent back to the reviewers, but your paper has a good chance of getting published.
     
     
3. Accepted
   It rarely happens that a manuscript is accepted as is, but if it is, congrats! More commonly, the manuscript is accepted after one or more rounds of revision.

6. Revisions

This is a toughie. Who want to read what’s wrong with their work? But it needs to be done, so here we go:

Step 1: Read the comments when you feel ready for it (it’s going to be frustrating).
Step 2: Forget about them for a few days.
Step 3: Assess how much work it will be to address each comment.
Step 4: Revise the manuscript and write a response letter.

The response letter

The response letter is a piece of work. You need to reply to each comment, explain exactly what changes you made, and where the reviewers can find them using line numbers. If you didn’t make any changes, you have to explain why.

To keep track of these changes, you can use a revision table or paste them directly in the letter. For a good example of a revision table and response letter, see here. I usually note the line numbers in both the original manuscript and the revised version. That way the reviewer can easily compare the documents to check the changes I’ve made.

TIP: don’t list the line numbers for your new manuscript until you’re completely done with the edits. Otherwise they’ll change and you will have to do them all over again. It doesn’t take long, but it’s very annoying (I speak from experience).

As much as you can, try to see each of the comments as an opportunity to improve your paper. Most editors and reviewers truly want to help move your paper forward. In case of an unnecessarily difficult reviewer – I sure remember this comment: “Some of the citations you have used are wrong and should cite the authors who first published on certain topics” – I like to imagine they didn’t have any coffee yet when they wrote the review.

7. Acceptance and publication

Paper proofs

Well done! All that hard work is finally accepted. Now it’s only a few more steps to official publication. First, you have to prepare your manuscript for the final submission. Because it’s going into production, it needs to adhere to strict guidelines. These are outlined on the journal website (Author guidelines), and sometimes in the email from the editor. You also need to prepare all figures in a high resolution (usually at least 300 dpi).

Once the manuscript has been typeset by the production office (this can take a few days or a few weeks) you will receive the article proofs. Check them carefully, especially any equations.

A technical tip for PowerPoint users like me: in Windows, PowerPoint doesn’t automatically export at the highest resolution, even if you ask it to. You need to change this setting first.

Article processing fees

At this point, there may be a request to pay publication fees. The total amount depends on the journal and on the licensing agreement. Open access is the gold standard and if you’re in the EU, probably mandatory. Fees can vary widely, from no cost at all to up to €9750 (!) for an open access publication in Nature. If you are not sure which licensing agreement to use, your supervisors or librarian can help. As to who pays: in my case it has always been my institute or university.

What does Early Online mean? 
Some journals provide an Early Online option. This mean that the article is already available but doesn’t have a full citation with volume and page numbers yet (it does have a doi). This early online version can be a pre-proof or the final article. In any case, it’s accepted and available online, so you can share it with others. 

8. Spread the word

Once the article is published, it’s time let the world know about your shiny new paper. This can be really fun, especially if you enjoy science communication. If you don’t love science communication or you’re tired of spending so much time on the topic, here’s a few reasons why you may still want to share the science:

• It can help other scientists – especially in your field – with their own research.
• Your work could be important for policy makers or the general public.
• More scientists read and cite your work, which is great for your scientific track record.
• It shows initiative (also useful for other career paths), and you’ll build transferable skills in science communication.

Of course, sharing the research can add pressure to an already overflowing workload. If you feel that it’s too much, feel free to just leave it be.

There’s loads of ways to share your research, ranging from departmental mailing lists to social media (LinkedIn, ResearchGate, Twitter), and mainstream media. Try to prepare ahead of time, especially if want to generate mainstream media attention. News doesn’t stay news for long. If your institution has a communications department, they can help you with preparing a press release.

9. Celebrate!

Have a beer, drink a coffee, eat some cake. Roll out the red carpet and throw a big party. Whatever you fancy. Because it’s time to celebrate!