Do yourself a favor: learn Markdown – Episode 5. BibTeX interface for PubMed

books on long shelf


A web site to create BibTex entries for bibliography in R Markdown.

R and Markdown

This is a follow-up on 4 “Episodes” in previous posts titled “Do yourself a favor: learn Markdown…”

To add bibliographical information it is necessary to write the information of a paper in the BibTex format. BibTeX-files may contain four different types of entries. The web site offers tools including the Bib2x Online Converter .

The most useful tool I found is from titled:

TeXMed – a BibTeX interface for PubMed

The simple interface allows to query the NIH PubMed database with optional inclusion of the abstract and links.


The web page on my computer still contains that last query I made which was to update an exercise using the built-in R dataset Puromycin. The paper I chose is a review on the effect of this compound, found with a simple web search. With the title of the paper I could then create a formatted entry as I had the title “The science of puromycin: From studies of ribosome function to applications in biotechnology.”

I entered the title in the page. The top panel provided one solution. Once checked the system provided the results in the correct format in the bottom panel.BibTex interface top panel for data entry

The result was shown in the bottom panel:

Exported References will appear here …

trying to export 1 references …

% 32435426 
   Author="Aviner, R. ",
   Title="{{T}he science of puromycin: {F}rom studies of ribosome function to applications in biotechnology}",
   Journal="Comput Struct Biotechnol J",
   Note={[PubMed Central:\href{}{PMC7229235}] [DOI:\href{}{10.1016/j.csbj.2020.04.014}] [PubMed:\href{}{23872350}] }

Then I copied this into a plain text file within RStudio.

For more information see the chapter Bibliographies and citations from the online book R Markdown Cookbook, (Yihui Xie, Christophe Dervieux, Emily Riederer, 2022-09-09)


Credits: portion of photo by Olena Bohovyk on Pexels