A Guide to Publishing Your First Research Manuscript

woman in science laboratory

You have finished your lab work, analyzed your data, and have discussed with your supervisor that you are ready to write a manuscript and publish your work.

Now what?

The publication process may seem overwhelming at first, but keep the below items in mind, ensure you plan your writing well, and you will get it done!

1 Understand Who You Are Writing For

Before you start, you should think about the ideal audience for your work. It can be a scientist in your particular field, it can be a more general scientific audience, clinicians, or other specific audiences.

Once you’ve determined who would be most interested in your work, you get to figure out what journals they most likely read. You might want to look into some metrics to see if a particular journal is read and cited often. You could also choose a journal that publishes many of the articles you used in your references, it likely covers a similar audience as you’d like to target.

Find the journal that matches your work best, and ensure your topic is within the scope of what the journal publishes. Find the journal’s scope and aims at their website.

Once you have a suitable match, it is time for step 2.

2 Know the Journal’s Requirements for Manuscripts

Every journal has its own set of requirements. You can find these on the journal’s website, usually under a tab called “for authors”. 

Important things to consider are:

  • Types of articles the journal publishes (research papers, reviews, short reports, case reports)
  • Sections to include and in which order to include them. For instance, there is quite some variability in where to place the materials and methods section; after the introduction and before the results, or as the last section after the discussion.
  • The length of the paper. Usually given as a maximum word count. Abstracts are typically separate for this and have their own word count
  • The number of references, tables, and figures that are allowed. This is highly variable per journal, but very important to ensure you create your files accordingly
  • Other required journal-specific items, such as clinical statements and synopsis

3 Write and Edit Your Article

Once you have the requirements and your audience sorted out, start writing! Writing and editing will take most of your time. Make sure all work gets checked and edited by multiple co-authors, and ideally you’d want to write this together with someone more experienced with publishing, often the ideal person for this is your supervisor. Plan this phase well and use tools to your benefit.

4 Submit to the Scientific Journal

Don’t be fooled. This is likely going to take a full day. At a minimum. Especially the first time you do this, you are going to run into some issues. 

Every journal/publisher has its own submission system. You will need to create a login and then follow instructions on the screen. 

What often happens is that you need information that you don’t have. So look up what is required before you are ready to submit so you can go after that information. For instance, addresses of co-authors, funding sources, and specific reference codes for those can be information you need but not have available. Sometimes it takes co-authors a while to respond, so the sooner you ask, the better. 

The format of figures and files can be quite a struggle to convert in many of these submission programs. Note the formats and file types for figures and tables that are accepted, and whether you can submit a PDF. Most of the time, this won’t be the case, and the submission menu creates the PDF for you. This is where things can take a while, as small issues can end up giving you a PDF file proof that is incorrect. So, take some time to prepare, and it will be much smoother sailing.

Keep in mind the journal requirements as discussed in point 2, make sure everything is exactly as requested, and carefully read any information in the submission screens to ensure you missed nothing. 

Remember, any file that is not compliant with requirements will be sent back without consideration. You want to prevent that.

And then you wait.

5 Receiving a Response From the Journal

It may take a long time before you hear anything after you have finally hit the submission button. Some journals keep you updated on the status, either by email or in their login menu, while others do not. 

Once you get a response, it can go four ways: 

  • Accepted without revisions. The dream, but unlikely to occur. Good news: you are done. Just wait for the proofs. 
  • Minor revisions: pretty much the dream as well, but you will have to put some effort in. The changes and additions requested by reviewers and editors are usually limited to data analysis or text changes considered minor.
  • Major revisions: still a good chance to get accepted by the journal, but significant changes need to be made based on the reviewer’s and editors’ comments. Major revisions often include additional experiments or a major change in format and content.
  • Rejection: sadly the most common option. If the journal had sent it out to reviewers before rejecting it, it is common to receive the reviewer’s comments. If so, see this as a gift. This is advice to improve your paper before you submit it to another journal.

    Rejection is disappointing and can be extremely frustrating, as the reasoning for it may not always seem fair. Keep in mind that journals receive a lot more submissions than they can ever publish, and the reviews are, in the end, also just opinions. Take from them what you can, find another journal that is a good match, and submit there. You will have to go through the submission process again, so check the journal requirements and adjust your manuscript to their structure, word counts, etc. And start the process again.

6  Responding to the Editor and Reviewers

If you did get the request to make minor or major revisions, you are expected to send a rebuttal or answers to the reviewer’s comments. Usually, this entails copying all comments into a new document and replying to them one by one. 

Some requests or questions you can simply answer with some text. For others, you will have to add text to the manuscript which you should point out in your answer with the exact line and page numbers of where changes are made.

Again, look up journal requirements. Often the editor will send you instructions for revisions. Some journals may ask you to mark all changes in the documents with color, others may ask to highlight those, yet others will require a document with tracked changes. 

Once that is all done, you resubmit the paper. Again, you will use the journal submission system for this, which may require adding all documents again and ensuring they’re in the right format. 

And then you wait again. 

Depending on the comments and the answers, the editor might decide to send it to the reviewers again or to accept or reject it directly.

7 Accepted Manuscript: Checking the Proofs

Woman is editing and writing on a piece of paper

Once your paper is accepted, another team at the journal is going to take over. They will create a proof, the version that will be the actual printed version. This means they will go over the text, make changes, place the figures in the document, and design everything according to the journal’s house style. When they are done, you will receive this document to check. They will usually give you 48 hours for that. This might be a weekend or holiday; if so, email them that you need more time. 

Check all text for correctness, especially numbers. Check all figures and tables for correctness. The journal might also have some queries for you. These are usually marked with a Q and a number at various spots in the document. Queries can be specific questions, any missing information, or simple checks. Ensure you read the details in their email to see how they want you to respond to those. 

Once you have finished this last phase, you are done, and your article will soon appear in the journal for all to read!