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Council of Science Editors (CSE) Citation Style Guide

An overview of the CSE citation style used across the sciences.

Citation–sequence basics

In the citation–sequence system, the references at the end of your work (i.e., your bibliography or works cited) are listed in the order in which they first appear within the text of your work. Within your text, you will use sequential numbers for each citation which will also match the citation's number in the bibliography.

🙂 Advantages of the citation–sequence system:

  • Since in-text citations consist of numbers only, this will save space and only minimally interrupt the flow of your text.
  • Both in-text and end citations follow the standard bibliographic format (see the name–year system for its series of rules).

☹️ Disadvantages of the citation–sequence system:

  • Authors cannot be readily identified from the in-text citations since these appear as numbers.
  • Editing references while working on your manuscript will require renumbering.
In-text citation

The citation–sequence system uses numbers to cite references within the text. Unless a publication's formatting guidelines suggest otherwise, format these numbers in superscript and place them immediately after the cited text and after punctuation marks. If citing multiple references, separate the numbers with commas but no spaces.

Many recent research studies have addressed the molecular mechanism underlying bacterial behavior.3

Bibliography

The citation–sequence system numbers citations in the bibliography by the order in which they appear within the text.

3. Lyon P, Keijzer F, Arendt D, et al. Reframing cognition: Getting down to biological basics. R Soc. 2021;376(1820):20190750. https://doi.org/10.1098/rstb.2019.0750

Example taken from: Nesin SM, Chandrankunnel M. The need for a new perspective on decision-making in bacteria. Commun. Integr. Biol. 2025;18(1):2463926. https://doi.org/10.1080/19420889.2025.2463926

Citation–name basics

In the citation–name system, the references at the end of your work (i.e., your bibliography or works cited) are listed alphabetically by the first author's last name and numbered sequentially. So, reference [1] will be earlier in the alphabet, while reference [27] would be later in the alphabet. Within your text, you will use the number assigned to the reference in the bibliography.

🙂 Advantages of the citation–name system:

  • Since in-text citations consist of numbers only, this will save space and only minimally interrupt the flow of your text.
  • Easy to locate references in the bibliography since they're arranged alphabetically (similar to the name–year system).

☹️ Disadvantages of the citation–name system:

  • Authors cannot be readily identified from the in-text citations since these appear as numbers.
  • Editing references while working on your manuscript will require renumbering.

In-text citation

The citation–name system uses numbers to cite references within the text, just like the citation–sequence system. Unless a publication's formatting guidelines suggest otherwise, format these numbers in superscript and place them immediately after the cited text and after punctuation marks. If citing multiple references, separate the numbers with commas.

Even though the behavior observed is simple, the underlying molecular mechanism is complex, as in the case of chemotaxis in bacteria8 or the case of skilled movement in mammals7.

Bibliography

The citation–sequence system numbers citations alphabetically in the bibliography.

7. Standage DI, Areshenkoff CN, Gale DJ, et al. Whole-brain dynamics of human sensorimotor adaptation. Cereb Cortex. 2023;33(8):4761–4778. https://doi.org/10.1093/cercor/bhac378

8. Wuichet K, Zhulin IB. Origins and diversification of a complex signal transduction system in prokaryotes. Sci Signal. 2010;3(128):ra50. https://doi.org/10.1126/scisignal.2000724

Example taken from: Nesin SM, Chandrankunnel M. The need for a new perspective on decision-making in bacteria. Commun. Integr. Biol. 2025;18(1):2463926. https://doi.org/10.1080/19420889.2025.2463926

Number formatting

Brackets, parentheses, superscripts, or none of the above?

The CSE Manual suggests that numbers should appear in superscript. However, many scientific journals use either parentheses or brackets to enclose numbers. Check with either your instructor (if a student assignment) or journal (if publishing) for their preference.

Many recent research studies have addressed the molecular mechanism underlying bacterial behavior [3].

Many recent research studies have addressed the molecular mechanism underlying bacterial behavior (3).

Many recent research studies have addressed the molecular mechanism underlying bacterial behavior.3

Example taken from: Nesin SM, and Chandrankunnel M. The need for a new perspective on decision-making in bacteria. Communicative & Integrative Biology. 2025;18(1):2463926. https://doi.org/10.1080/19420889.2025.2463926