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This guide covers how to cite sources in CSE format, the citation style used in biology, the natural sciences and much of scientific publishing.
The CSE Manual is a paid publication, so this page does not claim to reproduce it. Instead, every example below comes from one of three free, named sources, and each rule says which:
- CSE's own Scientific Style and Format Citation Quick Guide, published by the Council of Science Editors. It states that its numerous specific examples come from chapter 29 of the 8th edition.
- Duke University Libraries' CSE guide, written against the 9th edition.
- Penn State University Libraries' CSE guide, also written against the 9th edition.
Where those sources disagree — and on one point they do — this page says so rather than picking a winner.
What is the CSE Citation Format?
The Council of Science Editors (CSE) style is used by researchers in biology, ecology, environmental science and other natural sciences. Dalhousie University Libraries' citation style guide records the history: the style "originated in the 1960s, when it was known as the Council of Biology Editors (CBE) style," intended for editors of peer-reviewed biology journals; "In 2000, the organization became known as the Council of Science Editors (CSE). The style then became known as the CSE style."
The current standard is The CSE Manual: Scientific Style and Format for Authors, Editors, and Publishers, 9th edition, published 3 May 2024 (ISBN 9780226683942) — the details Duke's guide records in its catalogue entry.
Quick Overview: CSE Citation Format
CSE offers three documentation systems. Confirm with your instructor or target journal which one to use.
- Citation-Sequence: sources are numbered in the order they first appear in your text; the reference list follows the same numerical order.
- Citation-Name: the reference list is alphabetized by author, then numbered; those numbers are used in the text regardless of the order in which sources appear.
- Name-Year: parenthetical citations with author surnames and the year; the reference list is alphabetical and puts the year straight after the author names.
CSE's quick guide notes that the end references have "essentially the same format in all three systems, except for the placement of the date of publication in the name–year system."
Conventions common to all three, as Penn State's guide summarises them: "no commas are used to offset the author's last name from his or her initials, no space separates the first and middle initial, and periods do not, in general, follow initials." Journal titles are abbreviated without periods — Am J Vet Res, not Am. J. Vet. Res. — using the ISSN International Centre's List of Title Word Abbreviations.
What changed in the 9th edition
Penn State's 9th-edition guide records two changes that matter for almost every reference:
"Access dates are no longer required unless the citation lacks publication, copyright, or modification date."
"Publisher location is no longer required (often irrelevant and can be confusing when publishers have multiple locations)."
Duke's 9th-edition examples follow that: books are given as Springer Nature; 2022, with no city. CSE's own free quick guide still shows the 8th-edition form with a place — New York (NY): Springer; 2000 — because it was written for that edition. If your instructor or journal specifies the 9th edition, drop the place.
In-Text Citations in CSE
Citation-Sequence System
Number sources in the order they first appear. Duke's guide: "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
For consecutive references use a dash: ⁵⁻⁷. For non-consecutive references use commas: ²,⁴,⁸.
Duke notes that although the manual prefers superscripts, many journals use parentheses or brackets — [3] or (3) — so check your instructions.
Citation-Name System
The numbers come from the alphabetized reference list, so they do not follow the order of appearance (Duke's example):
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.
Name-Year System
Many recent research studies have addressed the molecular mechanism underlying bacterial behavior (Lyon et al. 2021).
Duke's rule for this system: "the last names of up to 2 authors and the year of publication of the document, enclosed in parentheses. For works with 2 authors, separate the names by 'and.' If a work has 3 or more authors, list the first author name followed by 'et al.'" CSE's own quick guide agrees: two authors are joined by a comma in the end reference but by "and" in the in-text reference, and for three to ten authors the in-text reference gives only the first, followed by "et al."
Reference List Format
Journal Articles
Citation-sequence / citation-name format, per CSE's quick guide: Author(s). Article title. Journal title. Date;volume(issue):location.
Duke's 9th-edition example:
- Picó Y, Barceló D. Analysis and prevention of microplastics pollution in water: Current perspectives and future directions. ACS Omega. 2019;4(4):6709-6719. https://doi.org/10.1021/acsomega.9b00222
Name-year format — the same reference with the year moved:
Picó Y, Barceló D. 2019. Analysis and prevention of microplastics pollution in water: Current perspectives and future directions. ACS Omega. 4(4):6709-6719. https://doi.org/10.1021/acsomega.9b00222
How many authors before "et al."? The sources disagree. CSE's own quick guide, written for the 8th edition, says: "For articles with more than 10 authors, list the first 10 followed by 'et al.'" Duke's and Penn State's 9th-edition guides both say more than five: Penn State's wording is "when there are 2-5 authors, all should be named in the reference. If there are more than 5 authors, list the first author followed by 'et al'". If your instructor names an edition, follow that edition's rule; otherwise ask, and be consistent.
A six-author article, on the 9th-edition rule (Duke's example):
- 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
Volume with no issue, from CSE's quick guide:
- Laskowski DA. Physical and chemical properties of pyrethroids. Rev Environ Contam Toxicol. 2002;174:49–170.
Books
9th-edition format, per Duke: Author, organization, or editor name. Book title. Edition. Publisher; Year.
Single author:
- Rathinamoorthy R, Balasaraswathi SR. Microfiber pollution. Springer Nature; 2022.
Edited volume:
- Karapanagioti H, Kalavrouziotis IK, editors. Microplastics in water and wastewater. IWA Publishing; 2019.
Chapter in an edited book — note In:, editors. and p with no period before the page range:
- Tunalı M, Yenigün O. Effects of microplastics on freshwater and marine microalgae. In: Karapanagioti H, Kalavrouziotis IK, editors. Microplastics in water and wastewater. IWA Publishing; 2019. p 170-181.
Online book, with the DOI as a full URL:
- Crate SA, Nuttall M, editors. Anthropology and climate change: From actions to transformations. 2nd ed. Routledge; 2016. https://doi.org/10.4324/9781315530338
Organizational author, where a division is named in descending hierarchy:
- National Academy of Sciences, Institute of Medicine. Science, evolution, and creationism. National Academies Press; 2008.
Websites
Duke's 9th-edition format: Author name. Title of article/webpage. Publisher; publication date [date updated]. URL
- Green infrastructure and extreme weather. U.S. Environmental Protection Agency; 2015 Oct 1 [updated 2025 Feb 14]. https://www.epa.gov/green-infrastructure/green-infrastructure-and-extreme-weather
A newsletter item with no personal byline, built to the same pattern (we checked the page and it carries no named author, so the reference opens with the title):
- Positive emotions and your health: developing a brighter outlook. NIH News in Health, National Institutes of Health; 2015 Aug. https://newsinhealth.nih.gov/2015/08/positive-emotions-your-health
Remember the 9th-edition change: an access date is needed only when the page gives no publication, copyright or modification date.
Dissertations and Theses
Duke's format: Author name. Title [dissertation or master's thesis]. Publisher; Year. URL. "Thesis" is master's-level work; "dissertation" is doctoral.
- Juang JY. Investigating biosphere-atmosphere interactions from leaf to atmospheric boundary layer scales [dissertation]. Duke University; 2007. https://hdl.handle.net/10161/171
- Tosiano MA. The social context of environmental exposures: An application to swine CAFO air effluent and pregnancy outcomes in North Carolina [master's thesis]. Duke University; 2012. https://hdl.handle.net/10161/5439
CSE Citation Examples by Source Type
Conference Papers
Duke's format puts the paper, then the proceedings, then the conference itself — number, name, dates, place:
- Machowski L, Marwala T. Nano version control and the repo as the next data structure in computer science and artificial intelligence [conference paper]. In: Conference proceedings: 2021 Ethics and Explainability for Responsible Data Science (EE-RDS). 1st Ethics and Explainability for Responsible Data Science; 2021 Oct 27–28; Johannesburg, South Africa. IEEE; 2022. p 1–7. https://doi.org/10.1109/EE-RDS53766.2021.9708575
For an unpublished poster or paper, CSE's quick guide replaces In: with "Paper presented at" or "Poster session presented at":
- Antani S, Long LR, Thoma GR, Lee DJ. Anatomical shape representation in spine x-ray images. Paper presented at: VIIP 2003. Proceedings of the 3rd IASTED International Conference on Visualization, Imaging and Image Processing; 2003 Sep 8–10; Benalmadena, Spain.
Technical Reports
Duke's format distinguishes the organization that did the research from the one that funded it, and includes report and contract numbers:
- Page E, Harney JM. Health hazard evaluation report. National Institute for Occupational Safety and Health; 2001. Report No.: HETA2000-0139-2824. https://www.cdc.gov/niosh/hhe/reports/pdfs/2000-0139-2824.pdf
Preprints
Give the repository and its identifier, and make clear the work is a preprint:
- Medina M, Chang YT, Rahmani H, Fuentes D, Barad BA, Grotjahn DA. Surface morphometrics reveals local membrane thickness variation in organellar subcompartments [preprint]. bioRxiv; 2025 May 1. https://doi.org/10.1101/2025.04.30.651574
Blogs
CSE's quick guide format: Author's name. Title of post [descriptive word]. Title of blog. Date of publication. [accessed date]. URL. Duke's 9th-edition example:
- Williams S. Behind the paper: Neuronal activity can drive cerebrospinal fluid flow in the human brain [blog post]. PLOS Biologue. 2023 Nov 22. https://biologue.plos.org/2023/11/22/behind-the-paper-neuronal-activity-can-drive-cerebrospinal-fluid-flow-in-the-human-brain/
Common CSE Mistakes to Avoid
- Forgetting journal abbreviations. CSE abbreviates journal titles. Duke points to the ISSN International Centre's List of Title Word Abbreviations, the NLM Journal Catalog and the CAS Source Index (CASSI) as the free places to look one up, because the underlying standard (ISO 4) is paywalled.
- Including periods in author initials. Write "Morrison JK", not "Morrison J.K." or "Morrison, J. K."
- Using "and" or "&" between authors. Duke: "Do not use & or 'and' before the last author." Separate all authors with commas.
- Inconsistent system use. Stick to one of the three systems throughout a paper.
- Adding an access date to everything. On the 9th-edition rule, an access date is for sources with no publication, copyright or modification date — not for every URL.
- Keeping the city of publication. The 9th edition dropped it. Generators and older guides still add it.
CSE Citation Tools
Reference managers such as Zotero and Mendeley include CSE style templates. For quick verification, CSE publishes its Citation Quick Guide free on its own site; it is drawn from the 8th edition, so cross-check anything affected by the 9th-edition changes above against a current university guide.
Sources Checked
- Council of Science Editors. Scientific Style and Format Citation Quick Guide. https://www.scientificstyleandformat.org/Tools/SSF-Citation-Quick-Guide.html
- Council of Science Editors. The CSE Manual: Scientific Style and Format for Authors, Editors, and Publishers. 9th ed. 2024. ISBN 9780226683942. (Paywalled; edition, date and ISBN taken from Duke's catalogue entry.)
- Duke University Libraries. Council of Science Editors (CSE) Citation Style Guide. https://guides.library.duke.edu/cse
- Penn State University Libraries. CSE. https://guides.libraries.psu.edu/CSE
- Dalhousie University Libraries. CSE 8th edition — Citation Style Guide. https://dal.ca.libguides.com/CitationStyleGuide/CSE
- The DOIs in the examples were confirmed against Crossref:
10.1021/acsomega.9b00222,10.1093/cercor/bhac378,10.4324/9781315530338,10.1101/2025.04.30.651574,10.1109/EE-RDS53766.2021.9708575. The two Duke thesis handles, the EPA page and the PLOS Biologue post were confirmed to resolve. The NIH News in Health item was read through an Internet Archive snapshot, because newsinhealth.nih.gov refuses automated requests; the CDC report PDF and CSE's own quick guide likewise block HEAD requests but serve their content on a normal GET.
