Citation Managers to Compile Literature


When you are diving into the scientific literature, it is important to accumulating work that has been done in the field you are planning on researching in. It takes a fair bit of time, but having the knowledge of what has been done and what still needs to be done in a particular field of research is what will ultimately drive the research you are doing currently and for years to come.

Once you start acquiring papers, being able to compile literature into a place that allows you to easily organize, parse, find, and cite work are critical to understanding and producing valuable work. Luckily, modern day science has a number of tools at our disposal to make documenting and writing up research much easier.

We have all had to write those stupid “works cited” pages  for past class projects. Typically, one might spend 30 minutes finding 5 papers that support your claims, followed by an hour and a half on churning out MLA citations, only to get docked points for improper formatting. And now, depending on what journal you submit to, everyone has their own citation and reference formats. When you see papers with more than 40 citations, it’s pretty baffling to think that anyone would consider typing al of this out by hand anymore.

We have it way better today. A number of citation managers exist that more or less automate the in-text citation and works cited generation process. Furthermore, citation managers offer a way to organize and group articles according to field or project, keep papers and supplementary materials together, highlight and annotate papers, and so much more. Here, I will talk about some of the citation managers I have used, as well as some other options you may want to pursue.



EndNote, which was originally developed by Thompson-Reuters but is now offered by Clarivate Analytics, is my go-to manager that I have been using for several years now. It is one of the top citation manager used by numerous academics across the globe. Back in undergrad, I paid $60 for a student license. Today, I can confidently say that it is worth significantly more than I paid for it.

Endnote organizes a collection of articles and citations as “libraries.” When you download a paper from any journal, you can simply drag and drop PDF articles directly into your Endnote Library and it will populate all of the information fields for that article (about 73% of the time… more later). It super simple and fairly straightforward to get the hang of.

Endnote also has a built-in PDF viewer, with the ability to highlight and annotate text in the PDF. Additionally, you can build groups related to different fields of research and sort your articles into custom groups to make them easier to find. You can also organize your libraries by dates of publication, author names, dates added to your library, journal title, and much more. There’s a built-in rating system if you are into that. It has a clunky but effective search feature. It’s powerful, and there’s a reason it’s so widely used.

One of the most useful things that I like about Endnote it how easy it is to send article from one library to another. Imagine you are working with a colleague to write a paper, and you have a bunch of citations in your library that you want to share with them. Rather than sharing your whole library (mine has over 1000 articles at this point… not feasible) you can just select groups of articles to send to a new library and share that library it with your colleague. You can actively collaborate on libraries over something like Dropbox, Google Drive, OneDrive, Box, or whatever you prefer. Additionally, if you want to send a colleague a paper or citation from your library, there is an email button in the Endnote GUI that automatically opens a new message and attaches the article PDF to an email (I use this feature almost daily).

The key thing that makes Endnote so great is it’s integration into Microsoft Word and PowerPoint. Endnote has its own tab of functions that lets to make in-text citations as you write, and it works incredibly well. As you are writing and citing, Endnote automatically populates and sorts your Works Cited at the end of the document. You can also easily change the citation format from one journal to another in three clicks. Every journal provider has a formatting file that can be imported into Endnote, which makes writing up and formatting manuscripts that much easier. This functionality is what has kept me using Endnote for so long. You don’t need to stay up late working on that works cited page all night anymore. Endnote pretty much does it for you. All you have to worry about is finding the papers and figuring out if the in-text citation comes before or after the period. (Citation format checking would be an awesome feature to add)

It is also worth mentioning that Endnote can search PubMed, Google Scholar and Web of Science directly in the application, which makes adding publications to your library even easier. However, if any papers are behind any sort of pay wall, it does not work well. I have steer clear of this method of searching for reasons I will discuss in a later post: Tips for Literature Searches.

Endnote also has an online library, which is accessible from any internet browser as well as their iPhone/iPad app. While it give you some built in data backup, you are only able to have one online library, which makes it difficult if you want to share online library items with colleagues when writing manuscripts. Additionally, syncing between online and offline libraries is not terribly smooth. The iPhone/iPad app is really good. You can download your papers for reading and markup offline (in fight, on car trips), it’s really handy. That said, the lack of Android support is infuriating to me, even after years of existence. I really hope Clarivate gets an Android app out at some point.
Endnote has a number of quirks. For example, articles from some journals (particularly with pre-2000 papers) do not populate the information fields in Endnote when you drag in the PDF files. When this happens, the publisher often has an ‘export citation’ option that lets you export a file you can open in endnote with all of the information fields. From there, you can drag your PDF onto the listed article and it will attach to the listing. It’s some extra steps, and it’s a minor inconvenience, but it’s not a game-changer. To be fair, this problem is not exclusive to Endnote. I have noticed with some conference proceedings papers, Endnote has a tendency to put the conference chairs as co-authors on the papers, which took me a while to catch on to. It’s easy enough to go in and delete, but it’s still a huge pain. Coupled with the online library situation and the lack of android support, there are plenty of improvements that can make. Nonetheless, the core functionality of Endnote has not changed over the last several years. I’m pretty used to Endnote the way it is now, but by today’s tech standards, the lack of updates is poor form for a software product like this. That said, I’m still running Endnote x7, they are on x8 now. Things may have changed, but Endnote x8 does not have favorable reviews so far.

While it is the pricier option, I would definitely recommend Endnote to anyone who is in the market for a quality, legacy-tested citation manager. You can buy it from Clarivate or Amazon, but I would check to see if your institution offers a discount through their software exchange first.



Currently run by Elsevier, Mendeley was originally released in 2008 and has grown by leaps and bounds over the last decade. It is rooted in cloud-based technology, which has many benefits over standalone applications as I will get to shortly.

Mendeley has much of the same functionalities as EndNote, and even improves on many of the issues noted above. The desktop application is clean, and it updates directly and automatically to you cloud Mendeley library very smoothly. It has Android and iOS support, which are huge points in my book. It does a pretty good job at populating information directly from PDF files, but still runs into similar issues as Endnote with older papers.  Additionally, to the benefit of many students, Mendeley is free. The cost comes with some drawbacks, but nonetheless it is an attractive perk for the financially-strapped students among us.

Mendeley has a fairly well-refined social profile setting, which enables you to collaborate with other users fairly easily (so does Endnote, but it’s pretty crumby and disappearing soon). You can link your profile with your Scopus and ORCID iD profiles to link all of your papers to your Mendeley profile in a streamlined fashion. Collaborating on a Mendeley library is extremely simple compared to Endnote. You can make a Shared Group in Mendeley and drag the papers you have in your library into your shared groups. This makes writing papers from the same Mendeley library much easier, especially when coupled with the new Office 365 tools that let you collaborate on documents simultaneously with others. This is one of the many things that makes Mendeley’s cloud-based approach to citation management work so well.

Other benefit of Mendeley being cloud-based is that it brings along a number of useful features, as well as room for improving on features without constantly downloading updates. It’s easy to stay up to date, and many new features can be implemented independent of the standalone applications. For example, based on the items you have in your library, Mendeley have implemented machine learning techniques (after all, who isn’t anymore) to draw up recommended papers that you may have missed in your literature search. I have actually found a handful of papers with this feature, which I really appreciate.

Additionally, journals are now implementing Mendeley support into their websites. This means you can export directly to your Mendeley library with the click of a button. Endnote has a similar feature, but it does not work nearly as well as Mendeley’s does. Mendeley is optimized to perform on the web, where Endnote is not. This give Mendeley the upper hand.

The biggest drawback to Mendeley is its lack of online cloud storage. Free accounts get 2GB of storage, while there are individual and institutional options for more space. If you are fortunate to be at an institution that has Mendeley, you are all set. If your institution does not have Mendeley, then you are going to have trouble accessing all of your papers from the cloud if you overshoot your 2GB allowance. This may or may not be an important feature for you, but I will let you decide.

I will be honest, I have not used Mendeley as extensively as Endnote because I am so rooted in Endnote at the moment. But I have used it on occasion to work on collaborative papers, and as of writing this I’m working on migrating my library over to use it more frequently. I like what Mendeley is doing and how it is constantly improving. With their marketing tactics and growth as of late, I’m convinced Mendeley is going to be the future of citation management over the course of the next few years. Unless Endnote really changes outdated approach to the citation manager market, I’m willing to hedge a bet that Endnote will lose a huge chunk of it’s market share over the next few years.

Other Managers

There are a number of other managers available for free. I am not directly familiar with them, but I will do my best to give them some time.


Zotero is an open-source reference manager developed at George Mason University. It integrates with MS Office, LibreOffice and OpenOffice fairly well from what I can find. There was some reverse-engineering lawsuits between GMU and then Thomson-Reuters over Zotero’s software usage relative to Endnote… which looks bad at face value. Despite potential infringement, if Zotero is anything like Endnote, I’m sure you will not be disappointed. Have you used Zotero? What do you like about it? Leave a comment or tweet me your experiences with Zotero.


BibTeX was designed to interface with LaTeX. For those unfamiliar with LaTeX, it’s a document writing software that is extremely popular in the fundamental science community, namely physics and computer science. That said, in my experience, it’s complicated to use, but produces beautiful manuscripts. If you are of the mindset of a computer programmer, then you’ll likely enjoy using LaTeX and BibTeX. The LaTeX equation editor is still far superior to anything I have tried. That said, BibTeX is designed to integrate well with LaTeX. If you are an avid power-user of LaTeX, you probably have not read this far into the article and are likely already using BibTeX to some extent. Nonetheless, BibTeX deserves a fair mention here since it is fairly popular.

Basic RGB

RefWorks is another cloud-based reference manager offered by ProQuest, but I personally do not know many people who use it. I’ve run into a handful of people at conferences talking about it, and I see a lot of the RefWorks emblems when I am downloading papers, but I have yet to try it myself. Do you use RefWorks? How do you like it? Does it compare to Endnote of Mendeley? Leave a comment below or tweet me and let me know.


There are dozens of reference managers you can use (see Wikipedia). The ones I have listed here are those that I have personal experience with or have come across in conversation with colleagues. This is by no means an exclusive list. But in my opinion, if you are in the market for a citation manager, use the manager that everyone in your lab uses. But if you can, make your way to Mendeley when you have the chance. It’s drawbacks are sharply offset by the pricepoint and functionality.

What reference managers do you like? Are there any features of Endnote or Mendeley that I missed that make your life much easier? Leave me a comment here or tweet me and I’ll keep a running list.

[Disclaimer: I’m not a market expert. Don’t ever take my half-assed speculations as market advice]


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