Writing and publishing papers

January 19, 2023

It’s been over a year since I wrote my last blog post. I guess I’ve been busy! I decided it would be nice to start 2023 with a blog post focusing on writing and publishing peer reviewed scientific articles. This has been a blog topic idea ever since I served on a Paper Writing Panel at the virtual Ocean Sciences Meeting back in March 2022. The panel consisted of late stage graduate students and editors of scientific journals. We discussed the sometimes daunting process of submitting a manuscript, providing advice on how to identify a target journal, how to structure a paper, and submission tips. I’ve attempted to summarize what we discussed, including some personal experiences and advice that I’ve learned when submitting papers.

Think in figures

As you are conducting your research or performing experiments, it is helpful to keep a manuscript idea in mind and think about potential figures that will go into the paper. Figures are an important storytelling process of your research and should contain information that allow readers to come to the same conclusions as you have written in your results. Oftentimes, figure ideas can lead to new analyses or experiments, that can ultimately enhance your manuscript. Sketching out figure ideas on paper or a whiteboard can be helpful to conceptualize the main points of your research.

Choose an appropriate journal

Finding an appropriate journal to submit a manuscript to can significantly increase the chances of acceptance and ensure it reaches your desired audience. There are many different academic journals for every type of field of study. To determine which journals are most appropriate for your field, take a look at your references, or the papers you have been reading related to your work. Where have they mostly published? Are there a few that stand out? This would give you a better sense of what journals most scientists in your field choose to publish in and where they are likely reading articles from.

When you find a few journals that might be appropriate for your current research, read the ‘Aims and scope’, which is typically found in the ‘About’ section on the Journal’s website. Each journal describes the objective or purpose of what the journal is trying to accomplish. Writing your paper to align with a journal’s Aim and Scope will improve the chances of having your manuscript accepted for publishing.

Additionally, ask colleagues what journals they recommend. Your advisors and instructors likely have a good sense of what journals are appropriate for what type of research and can point you in the right direction.

There are some journals out there that are considered to be ‘predatory’, meaning they accept articles for publication, along with the author’s fees, without providing the critical editorial or peer review process. Many articles published in predatory journals typically receive no citations over a five-year period (Brainard, 2020). While these journals typically are faster and easier to publish in, they can potentially spread misinformation. See Beall’s List of potential predatory journals and publishers.

Always include a cover letter

Some journals require a cover letter during a manuscript submission, some journals do not. During the Ocean Sciences panel I was involved in, a senior scientist recommended to always include a cover letter. If there is not an option to upload it, email it directly to the editor-in-chief. The cover letter is an opportunity to highlight what makes your research new and important and why it will be of interest to the journal’s readers. It’s important to reference the aims and scope of the journal to demonstrate you have taken the time to consider how your manuscript is a good fit for the journal and how it will help achieve the purposes set out by the journal. This site is a good reference for key points to include and things to avoid, with a downloadable cover letter template.

Consider publication costs

Many students are surprised when they find out how much publishing a manuscript can cost. Most journals require an open access Article Processing Charge (APC) which allows the final version of the published article to be read by everyone, instead of requiring a subscription to read specific articles. These APCs can range from $1,000 to over $10,000 (The Scientist, 2022). Before submitting, it’s important to talk to your supervisor or advisor to see if there is grant money that has allocated funds for publishing. Some universities might have funds set aside for student publications, or sometimes journals have discounts or waivers. I would never recommend paying out of pocket to pay a journal APC.

Read the author guidelines of your target journal

Every journal includes author guidelines that you can download from their website. It is very important to conform your manuscript to these specific guidelines. Some journals have a Word template that can be used, which has the required formatting for the journal. The guidelines will explain how to properly format figures and tables, what sections are required, etc. It is very important to read the author guidelines thoroughly before submitting a manuscript.

Respond to reviewers’ comments positively and constructively

When the journal editor-in-chief receives your manuscript submission, they make the decision to send it on for full peer review. In this case, it is sent to 2-3 reviewers that will read your manuscript and make a decision on if it should be accepted or not. More often than not, reviewers will suggest a list of edits and changes before full acceptance. These changes can be major or minor. Reviewers can also reject the paper, but might still suggest changes. When you, as the author send a revised manuscript back to the journal, it is important to include a detailed explanation where you address every single reviewer comment diligently. I usually copy and paste the reviewer comments in a new document and write out a response to every single comment, even if it is “Thank you for noticing this typo. This change has been made.” It is important to be polite and respectful in your responses. I usually start the reviewer comments document with a paragraph thanking the reviewer for the thoughtful review of this manuscript and how we have restructured or made any major changes to the document per their recommendations. If there is a comment that you and your co-authors do not agree with, you should include a well-argued justification as to why you do not think you should implement their recommendations.

Be involved as a paper reviewer

If you have the opportunity to be involved with a peer review of a manuscript, I highly recommend doing so. If you are a student, ask your advisor to be involved the next time they are asked to review a paper. You can read the submitted manuscript and assist with recommending edits or changes. Experiencing the role of a reviewer will help you understand the process of peer review and provide insight into how to respond to reviewers and work through the reviewing process for your own research.

As you become more of an expert in your field, you’ll likely be asked to review more and more papers. Providing a thorough review of a paper can take a long time, and should not be rushed. Therefore, you might not want to commit to reviewing all of the papers you are asked to. My PhD advisor gave me a good rule of thumb- review at least as many papers as you have submitted in a year. This article suggests giving back at least as much as you consume from the community. Therefore, if you submit one paper and it gets three reviews, you should review three papers. While being a peer reviewer is a lot of work and takes time, it is very important to do to make sure high quality research is being published and read.

Be persistent

Manuscript rejection isn’t a great feeling, but it happens. It actually happens to everyone at some point. It has to me just this past year. While it can be extremely disappointing after months or years of hard work- it is not the end of your manuscript journey. Read all of the reviewer’s feedback, think hard about how the manuscript could be changed to fit the scope of this journal, or if needed, choose another journal to submit to. Be persistent, be patient, and don’t give up. Publishing a paper can take a very long time, and that’s okay. You’ll be so proud of yourself when you finally see that email saying “Your paper has been accepted.” And maybe it’ll inspire you to do it again and again. 🙂