Whether you’re writing a manuscript or doing a literature review, you will have to cite and reference your sources. In the past, researchers had to keep track of their references by hand – it’s hard to imagine what a nightmare that was! Thankfully, today there are various options for citation managers to keep track of references and make the entire process more efficient and less stressful. In this article, we’ll cover four of the most commonly used citation managers used in academia – EndNote, Mendeley, RefWorks, and Zotero.

Common features

Endnote Basic, Mendeley, RefWorks, and Zotero are great citation managers that all include some of the essential features that you need (and want) for referencing your work:

  • Basic version is fully functional and free
  • Integration with Microsoft Word
  • Cite while you write
  • Option to change citation styles to match different journals
  • Citation library can be synched from anywhere
  • Import from databases
  • Create groups and shared libraries for collaboration
  • Compatible on Windows and Mac

Differences between citation managers

There are a few subtle differences between these citation managers, and we’ve highlighted them in the chart below:

EndNote Basic




  • Ability to search external databases
  • A large number of output styles
  • Paid desktop version can attach PDFs and full-text search PDF
  • Export travelling library for easy collaboration
  • Can attach PDFs Automatically extract citation information from PDFs
  • Full-text search in PDF
  • Annotate PDF
  • PDF full-text search-ability
  • Works with Linux Integration with social networking to see what others in your field are reading
  • Can attach PDFs
  • Automatically extract citation information from PDFs
  • Full-text search in PDF
  • Works with Google Docs
  • Works with Linux
  • Can scrape webpage for citation information
  • Ability to save snapshots of webpages in citation library and annotate them
  • Ability to search external databases
  • A large number of output styles
  • Can attach PDFs
  • Full-text search in PDF
  • Works with Google Docs

We think that many of the differences between these managers are minor and are not deal-breakers when it comes to choosing which one is best. The pricing for their respective paid versions, which include more support and features, is also fair. The choice of which citation manager you want to use will really depend on your personal preference. However, in collaborative projects, where authors from different institutions are working together, you will have to use the same citation manager that other people are using.

Citation Managers are not Perfect

Citation managers are there to help make referencing sources easier, but they are not perfect. You still have to carefully check your citations and references for common mistakes:

  1. Missing information for authors, date, volume, issue, and page numbers on journals
  2. Inconsistent or incorrect abbreviations for journals
  3. Duplicate references, which are very common in large review papers with various different authors
  4. Inconsistent capitalization of titles and journal names

To get started, we suggest that you use the same citation manager that your collaborators are already using or use the one that has the most support from your institution. For us, that’s EndNote (paid version) and Mendeley. However, it’s always good to be able to quickly adapt and learn to use new citation managers as needed.


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The Sengi team is led by Dr. Brad Hall, a vision scientist and expert medical writer. A regular peer reviewer for several medical and ophthalmology journals, Dr. Hall has authored a multitude of articles personally, is a successful grant writer, medical writer, and master of the art of simplifying data and statistical analysis. Since launching in 2015, Sengi has provided medical writing and biostatistics analysis expertise to SMBs and researchers around the world that lacked the necessary means to share their scientific breakthroughs outside of the lab. Sengi’s work has enabled these companies to put advanced technology into the hands of those who need them most.