Classes in grad school, or just research in general usually involve reading a TON of readings, conference articles, journal articles, and other papers. And there will come the time where you will ask yourself “What paper said that Virtual Reality’s ideal for architectural applications? Did I read it for my research, or in class? I need that claim!”

The inspiration to this post arose directly from writing for my qualifier exam, where I wrote a conference style paper. There were so many sources, so many papers, and I needed a good procedure to handle it all.

Here are some tips and procedures I use to manage the overload of papers, citations, and notes accompanying papers:

  • Learn and actively use a citation management program.Here’s some recommendations:
    • Mendeley: A great general citation management program. You can do notes in the paper too, but they are not searchable.
    • BibTeX: A standard code-like document where document citations. I love this because I use LaTeX. Additionally, BibTeX is a standard that will die much later than other company-dependent software, so BibTeX citations will most likely still be readable 20 years later.
    • RefWorks: I tried it when my university had a license for it, and I used it for really easy conversion of citations to BibTeX.
    • EndNote: Tried it, but at the time, I didn’t use one of their main features: their Word plugin.
  • Keep all the papers you read in your classes/lab. What if the course website goes down and you need that paper 2 years later? At least keep a list of references for all the papers that were discussed.
  • If you’re asked to do a review/summary/critique for a specific paper, connect the paper to your review. I connect it through Mendeley’s note feature.
  • Find a way to take notes on PDFs such that it’s re-findable.You need the following features:
    • Highlighting
    • Annotation
    • Be able to search and re-find your own annotations.
  • I can give a few recommendations, depending on your platform of choice:
  • Windows:
    • Nitro PDF: for all my in-pdf annotations, highlighting, and notes. Such notes and in-pdf annotations are also compatible with Mendeley’s & Adobe’s search feature.
    • Mendeley’s note feature: For paper reviews, or notes that apply to the entire pdf only.
  • Mac: Milk
  • Keep your notes organized. Some people have a blog just for their class or research notes, others have notebooks for research ideas, classes, etc.

My personal workflow for now when I find a paper is:

  1. Import the citation to Mendeley.
  2. Download the paper pdf, and make sure it’s connected to Mendeley.
  3. Open Nitro PDF and load the paper pdf. Annotate the pdf.
  4. Search and re-find for later use in Nitro’s search feature and/or Mendeley’s search feature.
  5. Export the citation to BibTeX if I need it for a paper.

If you have any other suggestions, please let me know! Thanks!


  1. Hadn’t heard of Mendeley. I was using zotero for a while but it got complicated going between computers so now I use for research papers and delicious for articles.

    1. Author

      Thanks for responding. Can you annotate research papers with citeulike though? Like, highlight a paragraph, write a note about a specific paragraph, and search for it later?

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