Paper Writing and Reference Management Tips

Here are my suggested tips for working with references when writing papers and a thesis. If you are working with me you must use this system. This is good news for you, though, because I already have already done extensive searches and tedious reference entry for papers on some topics and using my work will actually save you time.

I have found the following to be the best strategy: 

Use Word  

I used to use latex, but today I feel Word is the best choice, particularly for the type of papers that I'm usually writing. Those I work with need to use Word because it has excellent "track changes" options that make collaborative editing go smoothly. Latex has some nice properties, but overall at this point I feel Word wins out.  

Use Endnote

I have found Endnote to be a good citation manager. Endnote is also the de facto standard among academics who do not use Latex/bibtex. Endnote is substantially better than using Bibtex because Endnote can connect with the electronic databases and save you a huge amount of typing. You can also use it to store your personal notes on papers you read and abstracts downloaded from the web. Endnote is free to students/staff at Northeastern, and recently they (finally) added the ability to share a small library with a group. To get started, download Endnote from your myNEU software page. Install and update until you are on the most recent version. Then, read the manual so you are using Endnote properly before adding references. Learn how to insert citations into a Word document.

Send a note to me to request access to the shared library I have setup: mHealthGroup. Once I add you, you will be able to do File -> Open Shared Library. You will then be able to look at and use the shared library, and when you make changes they will sync with the master library. The good news is that when you fix a problem, you have fixed it for everyone. The bad news is that you need to be careful not to add junk to the library or undo changes others have done. So, when in doubt about whether you should make a change, ask. 

Use Endnote "Smart Groups"

Within the mHealthGroup library are several thousand papers. To narrow this down to those you care about, setup a "Smart Group." You can search Labels, Abstracts, and Titles for keywords. In Endnote, those papers will then be clustered in one virtual folder. We will setup Smart Groups for general areas of interest of people in the research group.

Add papers to Endnote

When you find a paper that you think is interesting enough to cite in your work, or that you think others in the mHealth research group might be interested in, add it to Endnote. The best way to do this is via a direct electronic link that downloads an Endnote reference format, complete with abstract. This saves typing and minimizes typos. However, you will always need to make some manual modifications to the entry as follows:

Label field

Ideally, all papers will have "Label" tags. This facilitates easily finding papers that cluster together and also setting up Smart Groups. You can enter multiple labels for a paper, one per line, in the "Label" field. Some of these labels are special and can be used for sorting.

Try to be consistent in how you enter labels, using camelcase. You want labels to be distinctive so that if you search for them, you get the labeled papers and only the labeled papers.

Common labels are:

Other labels are similar.

PDF archive

Our goal when we add a paper to the Endnote library is to also add the PDF, which can be shared with a small group of us. These days many papers are available electronically, either directly from the web or from the electronic databases the library gives you access to. When you find a paper, download the paper and save it to your desktop. Go to the paper entry in Endnote and attach the PDF. Endnote will then save a copy of the paper saved with the following naming convention: [First author last name]-[Year]-[First part of title].pdf. The paper is saved buried in the Endnote directory structure, but you can always easily find it on your computer just by searching for [First author last name]*.pdf (or by using Endnote itself). You can delete the copy on your desktop.

Anytime you email the paper to anyone in the group, please use the Endnote-named PDF.

Anyone with access to the mHealthGroup library will also be able to find and grab the PDF, just with the paper reference.


Make sure after you make changes to the mHealthGroup library that you allow the program to sync. It sometimes takes it quite a while of staying active in the background before it will finish.


It is very easy to introduce duplicate entries into Endnote that are the same reference with slightly different information. Should you see this, you should merge the two entries manually. Unfortunately the automatic duplicate detector is not very good.

To avoid duplicates, always check before you add references if they already exist in the library.

Last updated: 4/6/2005