How to format your references using the Algorithms for Molecular Biology citation style

This is a short guide how to format citations and the bibliography in a manuscript for Algorithms for Molecular Biology. 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.
EndNoteFind the style here: output styles overview
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
1. Levermann A. Climate economics: make supply chains climate-smart. Nature. 2014;506:27–9.
A journal article with 2 authors
1. Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science. 2014;345:1240–1.
A journal article with 3 authors
1. Yeung LY, Ash JL, Young ED. Isotope geochemistry. Biological signatures in clumped isotopes of O₂. Science. 2015;348:431–4.
A journal article with 7 or more authors
1. Vattré AJ, Abdolrahim N, Kolluri K, Demkowicz MJ. Computational design of patterned interfaces using reduced order models. Sci Rep. 2014;4:6231.

Books and book chapters

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

An authored book
1. Chappell D. The JCT Standard Building Contract 2011. Oxford: John Wiley & Sons; 2014.
An edited book
1. Mohan J. The Logic of Charity: Great Expectations in Hard Times. Breeze B, editor. London: Palgrave Macmillan UK; 2016.
A chapter in an edited book
1. Zondag B, Geurs K. Coupling a Detailed Land-Use Model and a Land-Use and Transport Interaction Model. In: Koomen E, Borsboom-van Beurden J, editors. Land-Use Modelling in Planning Practice. Dordrecht: Springer Netherlands; 2011. p. 79–95.

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 Algorithms for Molecular Biology.

Blog post
1. Luntz S. What Would Happen If You Fell Into a Black Hole? [Internet]. IFLScience. IFLScience; 2014 [cited 2018 Oct 30]. Available from:


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
1. Government Accountability Office. School Finance: State Efforts to Reduce Funding Gaps Between Poor and Wealthy Districts. Washington, DC: U.S. Government Printing Office; 1997 Feb. Report No.: HEHS-97-31.

Theses and dissertations

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

Doctoral dissertation
1. King GD. Public Works Directors’ Perceptions of the Effects of Stakeholders on Environmental Policies in California Cities [Doctoral dissertation]. [Phoenix, AZ]: University of Phoenix; 2010.

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
1. Dudziak ML. Trump and America’s Promise. New York Times. 2016 Jul 23;A19.

In-text citations

References should be cited in the text by sequential numbers in square brackets:

This sentence cites one reference [1].
This sentence cites two references [1,2].
This sentence cites four references [1–4].

About the journal

Full journal titleAlgorithms for Molecular Biology
AbbreviationAlgorithms Mol. Biol.
ISSN (online)1748-7188
ScopeMolecular Biology
Structural Biology
Computational Theory and Mathematics
Applied Mathematics

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