bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

Which reference manager do you use?

So I sent out this tweet yesterday and it produced a bit of a response, so I thought it would be good to get an idea of how people reference when writing papers and grants:

Here is how I do it in Word and Mendeley.

1) Create a new group in Mendeley Desktop


2) Find a paper I want to cite in pubmed


3) Click on the Mendeley Chrome plug-in and save it to my new group


4) Click “insert a citation in Word”:


5) Search and add the citation in the Mendeley pop-up:


6) Change the style to something I want….


7) here choosing “Genome Biology”

8) Add my bibliography by clicking “Insert Bibliography” in Word:



9) Rinse and repeat and I generally add publications iteratively as I write 🙂


In an ideal world this would spurn many other blog posts where people show how they use alternate reference managers 🙂


  1. I do essentially the same as this, except I use Zotero instead of Medndelay

  2. Because I read all my paper through Mendeley as well as using it for reference managing, I don’ t even bother with the bookmarklet/browser plugin – download the PDF, dump it in a watched folder and it is automatically added to your library. The PDFs are sync’d to my iPad for when I want to read them (as well as both my desktop and my laptop) and the reference is present when I want to cite it in Word.

  3. Jonathan Badger

    5th July 2016 at 2:51 pm

    I use “F1000 Workspace” which is a Mendeley-like system for both storing PDFs and managing references (and which also has a Word plug in), but has the advantage of not being owned by Elsevier, if you care about that.

  4. Me too. Plus, I sync the PDFs using a “dropbox like” solution.
    All the computer I use frequently have a ~/Documents/Papers directory, which links to whatever service provider (Dropbox, Spideroak, MEOCloud, etc…) I’m currently using to sync my files across devices.

  5. For about the last year I’ve used Paperpile, which is explicitly designed to work with google docs. Gdocs are vastly superior for collaborative writing (can do simultaneous editing, revision, track changes, comments etc), and a lot of the other tools I’ve tried don’t integrate well (or didn’t a couple of years ago)

  6. Richard Sever

    6th July 2016 at 1:24 pm

    Bear in mind Vitek Tracz has said the business model for F1000 is to sell the company to a big publisher (just like he did BioMedNet and BioMed Central – and as of course did Victor Henning and Jan Reichelt with Mendeley). So the missing word there may be “yet” 😉

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