Using reference managers to organize projects and publications: Part 1

aliyah-headshot Aliyah Weinstein

Reading primary literature is a crucial component of being a scientist. Especially at the early stages of a project, but even throughout, keeping up-to-date on the newest advances in your field can help direct your project by ensuring that you are answering novel questions and using the latest techniques. Toward the end of a project, these papers become important for a different reason: as references in the publication you prepare describing the work. Over the course of a project that may take years, the number of relevant publications may reach the hundreds! So how to stay organized when sorting through what you’ve read in order to cite the most relevant of the articles in your manuscript? Reference managers make the process significantly less stressful.

Quartzy users already know the utility of having software to help manage lab inventory, and can think of managing their references in the same way. Whether you are a reference manager pro looking for tips on how to make the most of your software, or are new to the idea and wondering why some people swear by them, this article will get you up to speed.

Imagine this scenario: Not only is your project completed, but the manuscript is written up. As you haven’t yet selected which journal to submit to, you prepared the manuscript in the common format of Materials and Methods before the Results section. Only then do you think to look at the author guidelines for the two journals you have narrowed down to, and notice that both require the Materials and Methods to be placed at the end! If you had used a reference manager for inserting your citations, this fix would be as easy as copying and pasting the Materials and Methods further down in the document, and clicking “refresh” to update your citation numbers and bibliography. Unfortunately, because the references in this manuscript were inserted manually, you instead spend two hours renumbering all 50+ references and re-ordering the bibliography—and repeat this a few weeks later when it becomes necessary to add additional references in the discussion section based on reviewer comments.

Reference managers serve a few important roles. First, they ensure consistency in formatting throughout a manuscript. In most software, it is possible to program the exact citation style requested by a journal, meaning all of your references will automatically be formatted to match the journal specifications. Next, a reference manager will catch if you cite the same article multiple times throughout a manuscript, avoiding double-citing and making sure that the reference number corresponds to the article’s first mention. Finally, reference managers save time. Instead of inserting references, confirming their numbering, and typing a bibliography all manually, reference managers allow these steps to be completed with the press of a few buttons, and updated just as easily. The time this saves throughout the entire publication process—from manuscript preparation through revisions and proofing—easily amounts to many hours.

To make the citation process as seamless as possible, it’s best to choose a reference manager software at the beginning of a project’s design, before you’ve even begun to delve into the literature. There are many software options available—such as Mendeley, EndNote, and ReadCube—all with their own pros and cons.

Once you’ve chosen a software, you can and should install its web browser plugin, which will allow you to import articles you find online into the software. These plugins are typically designed to automatically identify the article’s metadata, meaning information such as the article’s title, author list, journal information, publication date, abstract, and keywords are saved. If you do this each time you find an article relevant to your research (literally as simple as clicking a button!), all the information necessary to generate a bibliography from the citations in your manuscript will be stored in the reference manager. You will save not only time, but ultimately a lot of anxiety at the end of the road by making this small adjustment to your workflow when reading articles throughout the process.

Here, I’ve described how reference managers make adding citations to your publication a breeze, and how to optimize their use for this purpose. In Part 2 of this series, I will discuss additional features of reference managers that make them useful for many other purposes.

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Aliyah W.

Aliyah W.

Aliyah is a PhD candidate at the University of Pittsburgh, where she studies cancer immunology. She is also an advocate for science communication. You can find her on Twitter @desabsurdites and on her blog at