When I do research, I often write papers in LaTeX (in most cases) and Microsoft Word. My question is how to manage hundreds or even thousands of papers efficiently and effectively? I know several possible solutions:

  1. Use Endnote. This solution is specially suitable for Microsoft Word. If you use Word, Endnote is No. 1 option. However, it is not good for LaTeX. Because I use LaTeX most of the time, I don't use it.

  2. Use a .bib file manager, such as Jabref. This solution is good for LaTeX users. I use this method so far. The problem is that most of these software tools, including Jabref, are not very mature and not very user-friendly.

  3. Use Refworks. Refworks is a great tool based on the cloud and server. However, it is only good for "managing" references, but the most common scenario is inserting and managing reference during writing paper. Thus, Refworks is not useful if you write paper in LaTeX or Word. By the way, Refworks also offers a Microsoft Word plug-in but it is not stable compared to Endnote. Refworks also supports exporting in BibTeX format but we need to insert reference and manage them during our research life. Exporting is not a good option.

According to my experience, so far the bib tool (such as jabref) is the best option.

Does anyone have any better ideas?

migrated from stackoverflow.com Sep 23 '11 at 15:42

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  • 2
    See this question for two of the most popular choices. Bibliography tools that are compatible with biblatex and biber BiBDesk on the Mac can export a formatted bibliography in RTF, so although it won't handle automatic citations in Word, for the occasional Word file, it makes life a lot simpler. Make citations manually, but use BiBDesk itself to produce the bibliography. Unfortunately I don't think JabRef can do this. – Alan Munn Sep 23 '11 at 15:51
  • Have you tried RefTeX? – N.N. Nov 19 '11 at 9:46

I would have to recommend you give Mendeley a try. It's free, runs on Win/Linux/Mac. You can use both MS Word/OpenOffice and also generate bibtex files from your library quite easily. It seems to be a two-in-one fit solution for your question. Quick edit: FYI I'm a Community Liaison at Mendeley and also PhD candidate in Bioinformatics.

  • 1
    Is Mendeley-desktop compatible with biber? – nutty about natty Apr 1 '13 at 19:47
  • 3
    "free" only till a limit, once you have a large enough collection you will use up all your free storage space and end up having to pay, that is how they charge you. – chutsu Dec 26 '15 at 15:52
  • @chutsu You can keep as many PDFs as you like locally in your PC, or in the cloud through Dropbox or Google Drive – becko Mar 18 '16 at 14:08

Thank for all of you providing so many exciting tools. However, several months passed, I'll share my experience and my simple conclusion.

I found that there is no PERFECT tool so far which can deal all kinds of reference formats(latex/word) on all OS (win/linux/mac) platforms. And some tools are ugly and some are expensive.

My case is sometimes I work on win/ms word, sometimes I work on Mac/linux/latex or win/latex.

Thus, I decide: Use Endnotes for windows/Word case (Endnote is not bad and it can import/export rich formats and work perfectly with MS word. In win/word case, it is BEST); Also, I use Jabref for latex case on win/mac platforms. Jabref supports all OS platforms. Besides the basic reference management functions, it can find duplicate items and even can display "correct" author names! For example. JabRef can display "Tom and Jack" or "John et al." in the database! This feature is killing feature if you are confusing so many different confusing middle/first/last names from authors from different countries! Jabref is also supporting you fix some bib items manually because, as you know, some bibtex item downloaded from ACM/IEEE are not perfect and contain messy strings.

so far, my solution works perfect for me.

The Mendeley and other fashion tools are beautiful than Jabref. However, they are "common" reference tools and their features are not killing features for me. "Displaying authors names intelligently" kick a lot of tools out.

Also, the "cloud storage" feature is also not very useful for me. If you really need, dropbox, icloud and other tools have solved this problem perfectly. I hate to register another account for this one.

Refworks is also popular. But I think it is not useful for me. As I mentioned, the "cloud storage" is not very urgent for me. And it supports hundreds of bibliography formats, what the hell is that feature? any modern researcher needs to copy the those reference with formats manually ? I think the most cases is that writing academic paper is more "design" or "programming" rather than "writing" or "editing". The use-case is that we use tools to make the bibliography issue as automatic as possible.

So far, endnotes/jabref+word/latex+win/mac/linux make my academic writing more like programming, I just focus on the research itself and never spend time on the labor working.

What's more, a lot of ref manager tools claim that they are good at managing or searching PDF files and abstracts.... I think in the "Google" era, the folder and some built-in searching functions is not needed anymore. I just throw all PDF files into a folder without any "management"(but I name them with good file names using titles), thus, either I can find the paper PDF quickly just based on my fresh brain memory or just Google it for those old papers.


The answer does of course depend on the OS (I guess it's windows) you're using and your specific situation, but in general I'd try to avoid Endnote if possible. While it's still widely used and considered THE STANDARD by many, it's incredibly buggy and hasn't seen any substantial updates for a long time. The only thing stable about Endnote is the update cycle – a $100 update every year. Endnote's styles editor is the same as it was ten years ago and about all of its unique selling points (connection files, available style files) are paralleled or surpassed by its competition. Of course, if you have to use it because your collaborators do, that's something elese.

The perfect tool for all worlds does not exist yet, since it really depends on your individual needs. But there are several bibliographic apps which can work with Word and export BibTeX. Actually, most bibliographic apps I know do BibTeX export, though the quality varies greatly (even Endnote can export BibTeX in theory, unfortunatley, its export template is seriously broken). Mendeley has already been mentioned, Citavi (Windows-only) and Zotero (cross platform, open source and free) are other possibilities. On the Mac side you have Bookends and Sente.



I would like to put docear on the list. It combines the functionality of Jabref with the possibility to draw graphs of freeplane. Give it a try! I really liked it.


Zotero with the nice addon "Better BibTeX" [https://zotplus.github.io/zotero-better-bibtex/] is a great combination. You may or may not need JabRef here, ... All you need to do is read an interesting article, add to Zotero and Better BibTeX snychs with your linked bib file. Any changes done in Zotero will be automagically effected on the linked bib file.There is a high degree of customization.

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