Using reference managers to organize projects and publications: Part 2

Aliyah Weinstein

In Part 1 of this series, I described how a reference manager software can make the process of preparing a manuscript significantly easier. In the second part of this series, I will describe some additional features of reference managers—such as Mendeley, EndNote, and ReadCube—that make them a truly versatile tool for any scientist, whether approaching a publication or not.

A bonus to most reference managers is that not only do they import the article’s metadata (necessary for generating citations), but they also import the article as a PDF when available for free. (If the PDF is not freely accessible but you have it from another source, such as a university journal subscription, you can usually import it manually and link it to the metadata within the reference manager.) This makes reference managers multi-functional programs, as you can also read and annotate articles within the software.

If you often read articles on the computer, reading them within a reference manager as opposed to on a website or a PDF viewer gives you a single, centralized location to store all of your notes and ideas from what you read. Even as someone who prefers to read articles on paper and take notes by hand, I find it extremely useful to work within my reference manager to write information about where I envision citing a particular paper in my future manuscripts. For example, I have notes such as “qPCR primers came from this paper,” and “information on cells related to experiment 2B” saved in the reference manager, so that I can easily find them to cite while writing.

Furthermore, reference managers are just one of many tools you can use to find additional articles relevant to your work. My reference manager sends me a weekly email that lists publications not yet in my library that contain the same keywords as articles I recently downloaded. It also pops up with a link to a suggested article each time I save an article using the web plugin. Not only does this open my eyes to different and relevant research, but because the articles were suggested by my reference manager, it only takes the click of a button to import them, too, into the software. Thus, instead of searching the web, perusing journals each week, and constantly being afraid of missing a relevant article from a smaller journal, I lean on my reference manager to assist me with finding primary literature to read.

While not all reference managers are designed specifically for scientists, some that are have begun to capitalize on the market of making it easier for scientists to share information. Some reference managers now double as scientific social networks, allowing scientists to share articles, form groups around particular projects or research areas, and even search for jobs and funding opportunities! This may be particularly useful for collaborative projects across multiple universities: if all members of the team use the same software, it can facilitate sharing relevant publications and discussing their implications for ongoing work.

Finally, for scientists on the go (as so many of us are), some reference managers have an app in addition to their website and desktop software. This makes it easy to take articles with you on the go, as all of the components sync with one another. It is just important to confirm that your reference manager of choice has an app that is supported by your phone or tablet’s operating system. Whether you are reading during your daily commute to the lab or while flying across the world to a conference, being able to sync your articles and your notes across devices is much easier than lugging around a heavy stack of printed articles.

Reference managers have the potential to transform the way scientists interface with the literature and with one another. Due to the variety of features contained within reference manager software today, each scientist may have a preference based on the functionality of the particular components most important to them. Nonetheless, using a reference manager can facilitate ease of preparing a bibliography, annotating an article, and discussing research with other scientists, among many advantages. Scientists at all levels should consider these benefits when implementing a reference manager into their workflow.

Quartzy is the world’s No. 1 lab management platform. We help scientists easily organize orders, manage inventory, and save money. We’re free and always will be. Visit or reach out at

Interested in writing for The Q? Send us an email!

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

Leave a Reply

Your email address will not be published. Required fields are marked *