How to format your references using the Pathogens citation style

This is a short guide how to format citations and the bibliography in a manuscript for Pathogens. 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
Teske, A. Oceans. Cryptic links in the ocean. Science 2010, 330, 1326–1327.
A journal article with 2 authors
Leek, J.T.; Peng, R.D. Statistics: P values are just the tip of the iceberg. Nature 2015, 520, 612.
A journal article with 3 authors
Barkeshli, M.; Berg, E.; Kivelson, S. Coherent transmutation of electrons into fractionalized anyons. Science 2014, 346, 722–725.
A journal article with 4 or more authors
Acosta, I.F.; Laparra, H.; Romero, S.P.; Schmelz, E.; Hamberg, M.; Mottinger, J.P.; Moreno, M.A.; Dellaporta, S.L. tasselseed1 is a lipoxygenase affecting jasmonic acid signaling in sex determination of maize. Science 2009, 323, 262–265.

Books and book chapters

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

An authored book
Le Ruyet, D.; Pischella, M. Digital Communications 1; John Wiley & Sons, Inc.: Hoboken, NJ, 2015; ISBN 9781119232421.
An edited book
Paleomicrobiology: Past Human Infections; Raoult, D., Drancourt, M., Eds.; Springer: Berlin, Heidelberg, 2008; ISBN 9783540758549.
A chapter in an edited book
Keeble, A.H.; Maté, M.J.; Kleanthous, C. HNH Endonucleases. In Homing Endonucleases and Inteins; Belfort, M., Wood, D.W., Stoddard, B.L., Derbyshire, V., Eds.; Nucleic Acids and Molecular Biology; Springer: Berlin, Heidelberg, 2005; pp. 49–65 ISBN 9783540251064.

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 Pathogens.

Blog post
Andrews, R. Watch This Guy Simulate How “Human Skin” Reacts To Being Electrocuted Available online: (accessed on Oct 30, 2018).


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 Question Concerning Whether Funds Available Under Career Education Incentive Act Were Illegally Rescinded; U.S. Government Printing Office: Washington, DC, 1980;

Theses and dissertations

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

Doctoral dissertation
Laffitte, L. A Comparison of Pull-Out and Co-Teaching Models on the Reading Performance of Third through Fifth Grade Elementary Students with a Diagnosed Specific Learning Disability in Reading. Doctoral dissertation, Pepperdine University: Malibu, CA, 2012.

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
Shear, M.D.; Erlanger, S. Trump Condemns ‘Deeply Troubling’ Leaks on Attack After Complaints in Britain. New York Times 2017, A12.

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 titlePathogens
ISSN (online)2076-0817

Other styles