How to format your references using the Bioinformatics citation style

This is a short guide how to format citations and the bibliography in a manuscript for Bioinformatics. For a complete guide how to prepare your manuscript refer to the journal's instructions to authors.

Using reference management software

Typically you don't format your citations and bibliography by hand. The easiest way is to use a reference manager:

PaperpileThe citation style is built in and you can choose it in Settings > Citation Style or Paperpile > Citation Style in Google Docs.
EndNoteDownload the output style file
Mendeley, Zotero, Papers, and othersThe style is either built in or you can download a CSL file that is supported by most references management programs.
BibTeXBibTeX syles are usually part of a LaTeX template. Check the instructions to authors if the publisher offers a LaTeX template for this journal.

Journal articles

Those examples are references to articles in scholarly journals and how they are supposed to appear in your bibliography.

Not all journals organize their published articles in volumes and issues, so these fields are optional. Some electronic journals do not provide a page range, but instead list an article identifier. In a case like this it's safe to use the article identifier instead of the page range.

A journal article with 1 author
Smith,C. (2004) Getting up speed. Nature, 428, 229.
A journal article with 2 authors
Finkelstein,I. and Piasetzky,E. (2003) Comment on ‘14C dates from Tel Rehov: Iron-Age chronology, pharaohs, and Hebrew kings’. Science, 302, 568; author reply 568.
A journal article with 3 authors
Aldaye,F.A. et al. (2008) Assembling materials with DNA as the guide. Science, 321, 1795–1799.
A journal article with 3 or more authors
Zaric,S. et al. (2004) Optical signatures of the Aharonov-Bohm phase in single-walled carbon nanotubes. Science, 304, 1129–1131.

Books and book chapters

Here are examples of references for authored and edited books as well as book chapters.

An authored book
Taylor,F.J. (2011) Digital Filters John Wiley & Sons, Inc., Hoboken, NJ.
An edited book
Mamou,J. and Oelze,M.L. eds. (2013) Quantitative Ultrasound in Soft Tissues Springer Netherlands, Dordrecht.
A chapter in an edited book
Yoshiyama,K. and Sakurai,A. (2012) Manifold-Regularized Minimax Probability Machine. In, Schwenker,F. and Trentin,E. (eds), Partially Supervised Learning: First IAPR TC3 Workshop, PSL 2011, Ulm, Germany, September 15-16, 2011, Revised Selected Papers, Lecture Notes in Computer Science. Springer, Berlin, Heidelberg, pp. 42–51.

Web sites

Sometimes references to web sites should appear directly in the text rather than in the bibliography. Refer to the Instructions to authors for Bioinformatics.

Blog post
Andrew,E. (2013) New Invisibility Cloak Completely Conceals Objects. IFLScience.


This example shows the general structure used for government reports, technical reports, and scientific reports. If you can't locate the report number then it might be better to cite the report as a book. For reports it is usually not individual people that are credited as authors, but a governmental department or agency like "U. S. Food and Drug Administration" or "National Cancer Institute".

Government report
Government Accountability Office (1986) Efforts To Comply With P.L. 94-142 and Selected Youth Services Administration Management Functions U.S. Government Printing Office, Washington, DC.

Theses and dissertations

Theses including Ph.D. dissertations, Master's theses or Bachelor theses follow the basic format outlined below.

Doctoral dissertation
Smith,T. (2012) Outsider leadership transitions: A phenomenological study of Army Reserve General Officers.

News paper articles

Unlike scholarly journals, news papers do not usually have a volume and issue number. Instead, the full date and page number is required for a correct reference.

New York Times article
Williams,J. (2016) Waiting for the Mail. New York Times, BR4.

In-text citations

References should be cited in the text by name and year in parentheses:

This sentence cites one reference (Smith, 2004).
This sentence cites two references (Smith, 2004; Finkelstein and Piasetzky, 2003).

Here are examples of in-text citations with multiple authors:

  • Two authors: (Finkelstein and Piasetzky, 2003)
  • Three or more authors: (Zaric et al., 2004)

About the journal

Full journal titleBioinformatics
AbbreviationComput. Appl. Biosci.
ISSN (print)1367-4803
ISSN (online)1460-2059
Molecular Biology
Computational Theory and Mathematics
Computer Science Applications
Computational Mathematics
Statistics and Probability

Other styles