How to publish your first scientific paper

I get a lot of email asking me for advice on paper publishing. There’s no way I can make time to read all these drafts, let alone comment on them. But simple silence leaves me feeling guilty for contributing to the exclusivity myth of academia, the fable of the privileged elitists who smugly grin behind the locked doors of the ivory tower. It’s a myth I don’t want to contribute to. And so, as a sequel to my earlier post on “How to write your first scientific paper”, here is how to avoid roadblocks on the highway to publication.

There are many types of scientific articles: comments, notes, proceedings, reviews, books and book chapters, for just to mention the most common ones. They all have their place and use, but in most of the sciences it is the research article that matters most. It’s what we all want, to get our work out there in a respected journal, and it’s what I will focus on.

Before we start. These days you can publish literally any nonsense in a scam journal, usually for a “small fee” (which might only be mentioned at a late stage in the process, oops). Stay clear of such shady business, it will only damage your reputation. Any journal that sends you an unsolicited “call for papers” is a journal to avoid (and a sender to put on the junk list). When in doubt, check Beall’s list of Potential, Probable and Possible Predators.

1. Picking a good topic

There are two ways you can go on a road trip: Find a car or hitchhike. In academic publishing, almost everyone starts out a hitchhiker, coauthoring a work typically with their supervisor. This moves you forward quickly at first, but sooner or later you must prove that you can drive on your own. And one day, you will have to kick your supervisor off the copilot seat. While you can get lucky with any odd idea as topic, there are a few guidelines that will increase your chances of getting published.

1.1 Novelty

For research topics as with cars it holds that a new one will get you farther than an interesting one. If you have a new result, you will almost certainly eventually get it published in a decent journal. But no matter how interesting you think a topic is, the slightest doubt that it’s new will prevent publication.

As a rule of thumb, I therefore recommend you stay far away from everything older than a century. Nothing reeks of crackpottery as badly as a supposedly interesting find in special relativity or classical electrodynamics or the foundations of quantum mechanics.

At first, you will not find it easy to come up with a new topic at the edge of current research. A good way to get ideas is to attend conferences. This will give you an overview on the currently open questions, and an impression where your contribution would be valuable. Every time someone answers a question with “I don’t know,” listen up.

1.2. Modesty

Yes, I know, you really, really want to solve one of the Big Problems. But don’t claim in your first paper that you did, it’s like trying to break a world record first time you run a mile. Except that in science you don’t only have to break the record, you also have to convince others you did.

For the sake of getting published, by all means refer to whatever question it is that inspires you in the introductory paragraph, but aim at a solid small contribution rather than a fluffy big one. Most senior researchers have a grandmotherly tolerance for the exuberance and naiveté of youth, but forgiveness ends at the journal’s front door. As encouraging as they may be in personal conversation, a journal reference serves as quality check for scientific standard, and nobody wants to be the one to blame for not keeping up the standard. So aim low, but aim well.

1.3. Feasibility

Be realistic about what you can achieve and how much time you have. Give your chosen topic a closer look: Do you already know all you need to know to get started, or will you have to work yourself into an entirely or partially new field? Are you familiar with the literature? Do you know the methods? Do you have the equipment? And lastly, but most importantly, do you have the motivation that will keep you going?

Time management is chronically hard, but give it a try and estimate how long you think it will take, if only to laugh later about how wrong you were. Whatever your estimate, multiply it by two. Does it fit in you plans?

2. Getting the research done

Do it.


3. Preparing the manuscript 

Many scientists dislike the process of writing up their results, thinking it only takes time away from real science. They could not be more mistaken. Science is all about the communication of knowledge – a result not shared is a result that doesn’t matter. But how to get started?

3.1. Collect all material

Get an overview on the material that you want your colleagues to know about: calculations, data, tables, figures, code, what have you. Single out the parts you want to publish, collect them in a suitable folder, and convert them into digital form if necessary, ie type off equations, make vector graphics of sketches, render images, and so on.

3.2. Select journals

If you are unsure what journals to choose, have a look at the literature you have used for your research. Most often this will point you towards journals where your topic will fit in. Check the website to see whether they have length restrictions and if so, if these might become problematic. If all looks good, check their author guidelines and download the relevant templates. Read the guidelines. No, I mean, actually read them. The last thing you want is that your manuscript gets returned by an annoyed editor because your image captions are in the wrong place or similar nonsense.

Select the four journals that you like best and order them by preference. Chances are your paper will get rejected at the first, and laying out a path to continue in advance will prevent you from dwelling on your rejection for an indeterminate amount of time.

3.3. Write the paper

For how to structure a scientific paper, see my earlier post.

3.4. Get feedback

Show your paper to several colleagues and ask for feedback, but only do this once you are confident the content will no longer substantially change. The amount of confusion returning to your inbox will reveal which parts of the manuscript are incomprehensible or, heaven forbid, just plainly wrong.

If you don’t have useful contacts, getting feedback might be difficult, and this difficulty increases exponentially with the length of the draft. It dramatically helps to encourage others to actually read your paper if you tell them why it might be useful for their own research. Explaining this requires that you actually know what their research is about.

If you get comments, make sure to address them.

3.5. Pre-publish or not?

Pre-print sharing, for example on the arxiv, is very common in some areas and less common in others. I would generally recommend it if you work in a fast moving field where the publication delay might limit your claim to originality. Pre-print sharing is also a good way to find out whether you offended someone by forgetting to cite them, because they’ll be in your inbox the next morning.

3.6. Submit the paper

The submission process depends very much on the journal you have chosen. Many journals now allow you to submit an arxiv link, which dramatically simplifies matters. However, if you submit source-files, always check the complied pdf “for your approval”. I’ve seen everything from half-empty pages to corrupted figures to pdfs that simply didn’t load.

Some journals allow you to select an editor to whom the manuscript will be sent. It is generally worth checking the list to see if there is someone you know. Or maybe ask a colleague who they have made good or bad experience with. But don’t worry if you don’t know any one of them.

4. Passing peer review

After submission your paper will generally first be screened to make sure it fulfills the journal requirements. This is why it is really important that the topic fits well. If you pass this stage your paper is sent to some of your colleagues (typically two to four) for the dreaded peer review. The reviewers’ task is to read the paper, send back comments on it, and to assign it one of four categories: publish, minor changes, major changes, reject. I have never heard of any paper that was accepted without changes.

In many cases some of the reviewers are picked from your reference list, excluding people you have worked with yourself or who are in the acknowledgements. So stop and think for a moment whether you really want to list all your friends in the acknowledgements. If you have an archenemy who shouldn’t be commenting on your paper, let the editor know about this in advance.

Never submit a paper to several journals at the same time. Also don’t do this if the papers have even partly overlapping content. You might succeed, but trying to boost your publication count by repeating yourself is generally frowned upon and not considered good practice. The exception is conference proceedings, which often summarize longer paper’s content.

When you submit your paper you will be asked to formally accept the ethics code of the journal. If it’s your first submission, take a moment to actually read it. If nothing else, it will make you feel very grown up and sciency.

Some journals ask you to sign a copyright form already with submission. I have no clue what they are thinking. I never sign a copyright form until the revisions are done.

Peer review can be annoying, frustrating, infuriating even. To keep your sanity and to maximize your chance of passing try the following:

4.1. Keep perspective

This isn’t about you personally, it’s about a manuscript you wrote. It is easy to forget, but in the end you, the reviewers, and the editor have the same goal: to advance science with good research. Work towards that common end.

4.2. Stay polite and professional

Unless you feel a reviewer makes truly inappropriate comments, don’t complain to the editor about strong wording – you will only waste your time. Inappropriate comments are everything that refers to your person or affiliation (or absence thereof), any type of ideological arguments, and opinions not backed up by science. All other comments you should go through and address them one by one, in a reply attached to the resubmission and by changes to the manuscript where appropriate. Never ignore a question posed by a referee, it provides a perfect reason to reject your manuscript.

In case a referee finds an actual mistake in your paper, be reasonable about whether you can fix it in the time given until resubmission. If not, it is better to withdraw the submission.

4.3. Revise, revise, revise

Some journals have a maximum number of revisions that they allow after which an editor will make a final decision. If you don’t meet the mark and your paper is eventually rejected, take a moment to mull over the reason of rejection and revise the paper one more time before you submit it to the next journal.

Goto 3.6. Repeat as necessary.

5. Proofs

If all goes well, one day you will receive a note saying that your paper has been accepted for publication and you will soon receive page proofs. Congratulations!

It might feel like a red light five minutes from home when you have to urgently pee, but please read the page proofs carefully. You will never forgive yourself if you don’t correct that sentence which a well-meaning copy editor rearranged to mean the very opposite of what you intended.

6. And then…

… it’s time to update your CV! Take a walk, and then make plans for the next trip.