Skip to content

Reference Managers – The main app for researchers

Boost your research productivity and efficiency with a reference manager

When I was a PhD student, we didn’t have much technology involved in our writing process. It almost feels like I’m some kind of a dinosaur.  For writing my MA thesis I used Word for writing, Stata for carrying out the statistical analysis and Excel for creating tables. Creating correct citations was very difficult and time-consuming. As expected, when I started my PhD, managing all the sources became so difficult, it was almost painful. The amount of research articles needing attention grew every single day. Storing hundreds of texts, remembering them and managing them efficiently became  a very cumbersome task. Thankfully, in my first year of PhD in 2009 the wonderful librarians introduced me to the world of reference managers. I quickly integrated it into my workflow and never looked back.

Yes, As a Masters student, PhD candidate or early career researcher, managing references can be a daunting task. With the vast amount of literature available in your field, it’s challenging to keep track of all the articles, books, and other sources you come across. But our lives changed with the development and spread of reference managers.

Reference managers are software tools that help you collect, organise, and cite your references. They allow  you to create a personal library of sources, store PDFs and other documents, read and annotate them, and automatically generate citations and bibliographies. In this blog post, I will discuss the reasons why reference managers are essential for all academics and researchers (indeed, my condition of supervising students was that they use a reference manager!), the different types of reference managers available, and some practical strategies and tips for effectively using reference managers.

Why Use a Reference Manager?

Manual reference management can be a tedious and time-consuming task. Keeping track of various sources, categorising them, and ensuring that they are correctly cited can be challenging. Reference managers simplify this process, allowing researchers to focus on their research and writing.

Reference managers offer several benefits including:

  • Improved Efficiency and Accuracy: Reference managers allow researchers to quickly organise their sources and ensure they are correctly cited. This saves time and eliminates the risk of human error and plagiarism. No more not being able to find which article information came from. No need to create huge Excell tables with all the information of the articles. 
  • Integration with Word Processing Software: Reference managers often integrate with popular word processing software such as Microsoft Word and Google Docs, making it easy to insert citations and generate bibliographies.
  • Automatic Citation Generation and Formatting: Reference managers generate citations and format bibliographies automatically, saving researchers time and ensuring consistency. You don’t have to know every single dot and comma in a citation style. You just need to understand general guidelines, and the reference managing software will do it all for you. What is more – you can change the citation style of your document within seconds. No more sitting days to change one short article from APA to Vancouver!
  • Collaborative Research Capabilities: Reference managers allow researchers to share their libraries with collaborators and co-authors, making it easy to collaborate on projects and ensure that all team members have access to the same sources. Again, simplicity at your fingertips when  you have co-authors (and it is the majority of our articles these days).
  • Access to Additional Features: Reference managers often include additional features such as note-taking and annotation tools, making it easy to take notes and highlight important passages while reading. You can keep MOST of  your work on literature in one program!

Types of Reference Managers

There are several types of reference managers available, including free and paid options, desktop and web-based solutions, and platforms with varying levels of integration capabilities. The most popular reference managers include Zotero, Mendeley, EndNote, Papers, Citavi, and RefWorks. I am not going to go into details about any of the reference managers, but will summarise some of them. 

First things first, ALL reference managers have a very similar set of applications. They store your resources in a systematic fashion and they empower you to cite your sources easily and consistency without making major mistakes in the style. This is what makes them reference managers. But there are some variations in terms of simplicity of usage, price, form (web or desktop based) and integrations. 

Zotero is a free and open-source reference manager that offers a user-friendly interface and can be used on multiple platforms, including Windows, Mac, and Linux, and has a mobile app. It allows researchers to store and organise PDFs along with their references, and it also has a browser extension that lets them quickly add sources to their library while browsing the web. It works as a desktop version, integrates with Word and Google Docs. Zotero is the software I have been using for the past 10 years. I made the switch, and never regretted it. Only one perhaps weakness I can find: it is not easy to create OWN styles of citing or adjust the existing ones. But at the end of the day, we do need to follow the established conventions and regulations.

Mendeley is another popular reference manager that is free to use. Note though that it belongs to Elsevier (so it’s also integrated to Elsevier’s database), and it could become a freemium or paid app. It has a desktop app that can be used on Windows, Mac, and Linux, as well as a mobile app. Mendeley allows researchers to store and organise PDFs and other documents, and it also has a social networking feature that lets them collaborate with other researchers and discover new literature.

EndNote is a widely used reference manager that is popular in the academic community, as it was the founding father of reference managers so to say. Many universities buy licences for their researchers, but it is quite expensive for single users. It has a desktop app for Windows and Mac and allows researchers to store and organise PDFs, images, and other files along with their references. It also has a free web-based version, though it is less versatile than the desktop one, in my view. 

Papers is a paid reference manager that is designed specifically for Mac users. It has a user-friendly interface and allows researchers to store and organise PDFs and other documents along with their references. Papers also has a browser extension that lets researchers quickly add sources to their library while browsing the web.

RefWorks is a paid web-based reference manager that allows researchers to collect, organise, and cite their sources. It has a user-friendly interface and can be accessed from any device with an internet connection. I have used this for the first 4 years of my reference manager journey. It is good, easy to use and works well. However, it also required subscription (and institutional subscription, so I couldn’t continue using it as a single ussr!), and I decided to switch to a free software to be able to use it irrespectively of University subscription (and changing universities would be a pain, as new licence would require new account and transfer of my literature database every single time).

Other reference managers: Citavi, Paperpile, etc.  I am not going to provide a detailed overview of all the reference managers here. Pretty good comparisons exist elsewhere:

Practical Strategies for Using Reference Managers

As you might understand, reference managers are some of the most powerful tools for any researcher or scholar. I quite honestly can’t even imagine my work without one.  To get the most out of these tools, it is essential to use them effectively. In this section, I will discuss some practical strategies for using reference managers to improve your research workflow.

Organising References by Topic or Project

One of the most basic strategies for using a reference manager effectively is to organise your references by topic or project. Most reference managers allow you to create folders or groups to categorise your references. For example, you could create a folder for each chapter of your dissertation, or you could create folders based on specific topics or research questions.

Organising your references in this way can help you stay focused on specific aspects of your research and ensure that you can easily find the sources you need when you need them. It can also help you avoid the frustration of having to search through a large library of sources to find what you’re looking for. It is also useful to create smaller folders, as you can share them with colleagues, or synchronise them with other programs (Research Rabbit for instance).

Adding Notes and Annotations to References

Another practical strategy for using reference managers is to add notes and annotations to your references. This is particularly useful when you’re reading a long or complex article and want to remember important points or ideas. You can add comments/notes in specific parts of the article, or write-up a summary to use for your writing later on. 

Most reference managers allow you to add notes and annotations to individual references. You can use these notes to summarize key points, highlight important passages, or record your own thoughts and reactions to the source, connect one article to the other.

Using Keywords and Tags to Categorize References

Keywords and tags are another useful tool for organising your references. You can use them to categorise your references in more detail than simply grouping them by topic or project in a folder.

Keywords are words or phrases that describe the content of a source. For example, if you’re researching the effects of climate change on agriculture, you might use keywords like “climate change,” “agriculture,” “crop yields,” and so on.

Tags are similar to keywords but are more flexible. They can be used to categorise references in multiple ways. For example, you might use tags to categorise your sources by author, methodology, geographic location, or any other criteria that are relevant to your research.

I prefer to structure sources in folders by broader topics/projects. Then I add multiple tags on methods, exact indicators analysed, theories if appropriate, etc. So even if I forget what folder I put the source initially, I’ll easily locate it (and similar items) by tags in Zotero.

Setting Up / Adjusting Citation Styles for Different Publications and Journals

One of the most time-consuming aspects of academic writing is formatting citations and bibliographies according to the specific style guidelines of different publications and journals. However, most reference managers have built-in citation style formatting tools that can save you a lot of time and effort.

Before you start writing, it’s a good idea to set up citation styles for the publications and journals you plan to submit your work to. This way, you can ensure that your citations and bibliographies are formatted correctly from the start. Many journals offer templates for their citation style requirements in different reference managers. 

What is even better – you can easily change the referencing style. Just find the style of the new journal you are planning to submit, and apply it.

Backing Up Your Reference Library to Prevent Data Loss

Finally, it’s important to back up your reference library regularly to prevent data loss. Losing your reference library can be a significant setback in your research, so it’s essential to take precautions to prevent this from happening.

Most reference managers have built-in backup and synchronisation features that allow you to store your library in the cloud or on an external hard drive. Make sure to set up these features and back up your library regularly to ensure that you don’t lose any of your valuable research.

Some final tips on using the reference managers:

  • Only use the functions you need. There is no need to really go deep and explore all the functions right away – this could be a waste of time. Learn what you need and start there. You can slowly progress and learn.
  • Make sure to instal regular updates. Glitches and bugs can happen, which can cause some problems with citations, and even bugging and losing some of your text. So, keep up-to-date!
  • It is very important to check every single input when you add a source. Do it right away, and not after you uploaded a dozen of sources. It is much easier to grab the source from a web-page, add it to the manager, then go to all the details and check that all metadata has recorded correctly and how you need it. 
  • I recommend always to save full names of the authors. Some styles use initials, but some might require full names. So, it’s better to be prepared and use the full names. Same goes for the journal names!
  • You can add abstracts to your references in the manager. That’s a very useful feature! You can just keep all your work on literature and citations in one place!
  • If you have enough space and/or can afford extra storage, it is very useful to attach actual pdf’s to the metadata in your reference manager database. This way you don’t need to look for the specific article. Again, it’ll be all in one place. 
  • NB! If you do NOT have the space for synchronising PDF’s, create ONE folder on your computer where you can save ALL your literature, and name the files using the metadata from the reference manager. You can initially attach the file to the source, rename it using metadata (in one click!), and then unattach it, but keep it named correctly and in the same format for all articles.


In conclusion, using a reference manager is an essential tool for any researcher. It streamlines the research process, saves time, and prevents headaches caused by disorganised referencing. I personally cannot imagine my life without a Reference Manager. And I refuse to write and edit my paper without a reference manager. This has become such a basic requirement for academic writing, I can’t even express it enough. 

Reference managers provide various benefits like easy citation and bibliography generation, effective search and filtering, and collaboration with peers. With features like note-taking, annotation, attaching PDF files, and tagging, reference managers can help you organise your references and boost your productivity.

Therefore, if you’re struggling to manage your references, a reference manager can be a game-changer for your research. It will not only make your life easier but also help you present your research in a more organised and professional manner. So, start exploring different options and find a reference manager that suits your needs. Happy referencing!

Spread the word:

Leave a Reply

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