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Author's Toolkit: A Guide to Manuscript Preparation and more

A guide to dissertation preparation for the Einstein Graduate Programs in the Biomedical Sciences

Citation Management Basics

Bibliographic management software makes it easy to collect and organize references to any type of information, from journal articles to multimedia files. The software also allows students and researchers to insert their citations into papers and format them for publication painlessly.

Citation Manager Tips & Tricks

These suggestions can be applied to most citation management programs.

  • Keep one big database for all of your projects. It will make references easier to find later on.  
  • Use Groups or Folders to organize you references.
  • Add references to your database as soon as you come across them.  This is easy to do with web-based citation managers.  EndNote users can create free EndNote Web accounts, log on  and add references from any computer with Internet access.  Later, synchronize references between EndNote Web and EndNote desktop.
  • Do not limit your database to journal articles only.  Include many material types: websites, meeting abstracts, patents, theses, unpublished works, correspondence, tables and charts, etc.  Might have to type these in by hand (if no Direct Export available), but it will be well worth the effort.)
  • Link full-text PDFs on your hard drive to the corresponding references in your database.  Some programs will let you import PDFs directly in a batch or one by one.
  • Annotate PDFs as a reminder of sections you plan on quoting, paraphrasing, or summarizing.
  • Every citation manager has a Notes field, Research Notes field or several User Defined fields. Copy text from sources you plan to use into these fields.  This will be a good reminder of what you are quoting.
  • As you write, use your citation manager's "insert citation" tool (e.g. Cite-While-You-Write or Write-N-Cite). Keep the citations unformatted or use astyle that includes authors and dates.  When you are finished you can change to your department or publisher's style.
  • Us MS Word's Track Changes and Notes functions to help keep track of article's you are citing.
  • Make sure your references are correct!

Adding quotation and paraphrasing field to EN

Example of Custom Fields for quotes and paraphrasing in EndNote

Highlighting quote on a PDF

Highlighting and annotating a PDF.

10 Tips for Avoiding Accidental Plagiarism

  1. Keep all of your references in one Library.  It will be easier to find them when you need them.
  2. Add references as soon as you come across them.  Don't wait until you are starting to write.
  3. Check for duplicates early & often. 
    2.5. Update your references.  Check to see if epubs or in-process citations have been published.
  4. Import publisher-supplied PDFs directly into your Library.
  5. Use Find Full Text or Attach Files to get PDFs for references already in your Library.  
  6. Annotate PDFs.  Many programs (including EN, Preview for Macs and Adobe Acrobat Pro) will let you highlight text and add notes. 
    6.5. Annotate references in you Library, using the Notes, Research Notes, or User-Defined fields.
  7. Organize with Groups.  References can belong to more than one Group.  It might be helpful to create a separate Group for each section of your manuscript. EndNote creates a temporary, system-generated Group of references being added to a document.  These references can be copied into a regular Group.
  8. Insert citations as you write.  Make it easier to see who you are citing by using an Author/Date style or unformatted citatations while you write. Change to department- or journal-specified style when you are finished writing.
  9. Use your word processor's Comments feature as reminders of passages that must be cited.
  10. Make sure the references you cite are correct!

EndNote Basics and Resources

EndNote is available from the D. Samuel Gottesman Library.

The EndNote Guide will help you

EndNote Resources

Full Text Configuration

OpenURL/Link Resolver:


RefWorks Basics and Resources

RefWorks allows students and researchers to insert their citations into papers and format them for publication painlessly. Access to RefWorks is provided by the D. Samuel Gottesman Library.

The RefWorks Guide will help you

If you experience problems with your RefWorks account, contact

Mendeley Basics and Resources

Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research in your field. Mendeley is a great organization tool for those who have accumulated a large number of PDF files during the research process.

The Mendeley guide will help you

Zotero Basics and Resources

Zotero is a free bibliographic management tool that allows you to store and organize your references. You can add references from library databases, add books with websites like and, and manually add any references, such as websites.

The Zotero guide will help you