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
Hatten, M.E. New directions in neuronal migration. Science 2002, 297, 1660–1663.
A journal article with 2 authors
Chen, J.; Kriegstein, A.R. A GABAergic projection from the zona incerta to cortex promotes cortical neuron development. Science 2015, 350, 554–558.
A journal article with 3 authors
Altabet, M.A.; Higginson, M.J.; Murray, D.W. The effect of millennial-scale changes in Arabian Sea denitrification on atmospheric CO2. Nature 2002, 415, 159–162.
A journal article with 4 or more authors
Ouyang, Z.; Takáts, Z.; Blake, T.A.; Gologan, B.; Guymon, A.J.; Wiseman, J.M.; Oliver, J.C.; Davisson, V.J.; Cooks, R.G. Preparing protein microarrays by soft-landing of mass-selected ions. Science 2003, 301, 1351–1354.

Books and book chapters

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

An authored book
Center for Chemical Process Safety Guidelines for Safe and Reliable Instrumented Protective Systems; John Wiley & Sons, Inc.: Hoboken, NJ, 2007; ISBN 9780470924921.
An edited book
Virtual Realities: International Dagstuhl Seminar, Dagstuhl Castle, Germany, June 9-14, 2013, Revised Selected Papers; Brunnett, G., Coquillart, S., van Liere, R., Welch, G., Váša, L., Eds.; Lecture Notes in Computer Science; Springer International Publishing: Cham, 2015; Vol. 8844; ISBN 9783319170428.
A chapter in an edited book
Andrianoelina, O.; Rakotondraoelina, H.; Ramamonjisoa, L.; Maley, J.; Danthu, P.; Bouvet, J.-M. Genetic diversity of Dalbergia monticola (Fabaceae) an endangered tree species in the fragmented oriental forest of Madagascar. In Forest Diversity and Management; Hawksworth, D.L., Bull, A.T., Eds.; Topics in Biodiversity and Conservation; Springer Netherlands: Dordrecht, 2006; pp. 49–68 ISBN 9781402052071.

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
Davis, J. Global Coral Bleaching Event Declared (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 Office of Education Contracts With Consultants, Experts, and Consulting Organizations; U.S. Government Printing Office: Washington, DC, 1975;

Theses and dissertations

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

Doctoral dissertation
Green, E.I. Caregiver wellness: An inquiry of health risks among frontline direct caregivers of the elderly and disabled. Doctoral dissertation, Capella University: Minneapolis, MN, 2009.

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
Kenigsberg, B. Imperfections. New York Times 2017, C9.

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

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