March 26, 2020

How to format a research article for publication

Select a target journal (or narrow it down to a few)

Maybe helpful tool: "Elsevier Journal Finder". Only use this tool to get ideas, not to decide where your paper should go. 

Search for related topics yourself on PubMed and Google Scholar. Consider the type of study that you are working on (cell function experiments, mRNA-seq, epigenomics array, clinical charts review, etc). Look up the journal's "about" page, impact factor, and recently published research papers to estimate if it is a good fit for your article. 

Journal specific formatting

Search the journal name and "author guidelines" to find information about section names and expected order, word count limits for the abstract, word limits for the whole manuscript, formatting requirements, figure size limits, figure resolutions and file types accepted, etc. For example, here are some journal author guidelines:
(Impact factors updated 9/2024)


If you aren't sure which journal you'll submit to, pick a few journals and read their author guidelines (especially word limits, figure+table limits) and start writing based on the stricter guidelines (lower limits). You can narrow down the journal later.

Microsoft Word formatting

Citation software, continuous line numbering, autocorrect modifications, etc.

  1. Install a references manager and its Word plug-in. Ask your PI or the corresponding author what they prefer and use that. Do this from the start because it is a lot of work to switch all your references later.
    • EndNote - not free, but check if your institution has a license. University of California, Cedars-Sinai Medical Center, and many other academic institutions have licenses.
    • Mendeley - free, but please check with your supervisor before starting to add citations because they likely prefer EndNote
  2. Format article sections as Word headers so that they show up in your Navigation Pane. 
    • This will make your life easier when you are editing!
    • The navigation pane makes jumping from section to section easier
  3. Add continuous line numbering to your document.
    • Required for most journal submissions. 
    • Makes communication among authors easier during the editing process.
  4. Edit the autocorrect dictionary to stop Word from changing your science words, gene symbols, protein names, and specialized abbreviations. Suggestions:
    • Remove hsa-->has (hsa is the 3-letter code for Homo sapien, e.g. hsa-miR-202-3p)
    • Add mRNA-->mRNA
    • Add miRNA-->miRNA
    • Add miR- --> miR-
    • Add lincRNA --> lincRNA
    • Add scRNA-seq --> scRNA-seq
    • Add qPCR --> qPCR
  5. Don't add a header
  6. Do add a footer with page numbering
  7. Be consistent in figure and table references: 
    • "Fig 1", "Fig. 1",  or "Figure 1"
    • "Supplemental Table 1" or "Table S1"
  8. Figures and tables need to be numbered in order of appearance. Don't start discussing Figure 3 before you finish discussing Figure 2.
  9. Acronyms should be spelled out on first appearance and the acronym should follow in parentheses. Examples: National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), first trimester (T1), differentially expressed genes (DEGs). 

Figure formatting


Pay attention to:
  • Number of figures allowed
  • Consistent fonts (don't switch them)
  • Journal font family and font size preferences
  • Figure size in mm, cm, or inches
  • Final resolution

Add references with citation software

Cedars-Sinai and California universities usually use EndNote, so that is what I will focus on below. Cedars-Sinai staff should request EndNote software from the Service Center at myportal.cshs.org. University students should find instructions from their university's library. Libraries often have workshops to train new EndNote users.

Download citations from the journal article's main page or PubMed page. Keep whichever default file format the website recommends, .nbib from PubMed and often .ris from journal websites.

PubMed citation download: (1) click "Cite", (2) click "Download .nbib"


Import each citation file into EndNote with File:Import:File. For citations downloaded from PubMed (.mbib) use import option "Tab Delimited" and leave other setting defaults. For citations downloaded directly from journal websites, it varies but RIS is a common citation filetype and you can select "RIS" from the import options.

Add references to your manuscript using EndNote's Word plugin.

Apply the correct EndNote references style 

Check the author guidelines for the target journal's preferred reference style. Sometimes it is a standard style (e.g. Vancouver) that you can select from EndNote's dropdown menu. If not, download the journal's EndNote style and apply it to the manuscript before submission. I do this formatting as a near-final step. 

Google your journal name and "EndNote style" to find and download the style file from the EndNote.com website. Example EndNote styles:




Follow instructions below to use that style file:

Funding statement

List all grants and funding sources that supported the project. Consult your funding agency's websites for preferred wording. For example, the National Institutes of Health has a webpage called "Communicating and Acknowledging Federal Funding".

Author contributions

Create a section called "Author contributions" and add the list of terms from CRediT (Contributor Roles Taxonomy). For each term, fill in the relevant author initials. Every author should be listed at least once. Authors can be listed in multiple sections. Research projects take years from conception to publication and many people likely contributed to the final work before you joined. To avoid accidentally insulting someone, discuss author contributions with your mentor or supervisor privately before emailing the manuscript draft to all co-authors. 

Pre-submission co-author etiquette

Rule #1: Don't email or submit the manuscript anywhere without your mentor or supervisor's approval. Give them time to review your writing and check the authorship list. 

Rule #2: Tell your co-authors before you submit anything and allow them to review the manuscript before submission. This is not only good etiquette, but also a universal and mandatory journal requirement. Do this when your mentor or supervisor has reviewed the manuscript draft and agreed that it is ready for additional feedback. Tell your co-authors where you plan to submit, what you are submitting, and send them your near-final manuscript so they can provide feedback and corrections. They may not provide any feedback, but you must at least give them the opportunity. 

Rule #3: Check with your co-authors that you have their correct name spelling (including middle initial if desired), degrees, and institutional affiliations. These are difficult or impossible to change after submission. 

If your co-authors are first time authors (such as undergraduate interns), let them know that their publication name does not need to be their legal name. However, for publication history reasons, it does need to be a name that they use consistently so they should think carefully before making their final decision.
  • First and middle names - these can be legal names or names they use day-to-day. Sometimes people have both Anglicized and non-Anglicized names and they prefer one over the other for publication. This is fine. 
  • Middle initials are optional, but let EACH co-author decide that for their own name. Don't omit middle initials without asking them. Personally, my surname is very common so I always include my middle initial for publication. 
  • Surnames - maiden names or married names are okay, whether or not the legal surname was changed. 
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Last updated 1/14/2024
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