How to Use a CSE Citation Generator (9th Edition)

A CSE citation generator turns a DOI into a Council of Science Editors reference in a few seconds, and the punctuation it produces is usually right. What goes wrong is the data underneath: an author's middle initial that the database dropped, a journal name that should be abbreviated, a preprint DOI that resolves to the published paper, and rules that changed when the 9th edition of The CSE Manual came out in 2024. This guide gives you the 9th edition patterns to check against, the steps for generating a CSE reference, and twelve checks to run before your reference list goes in. Every "generated" example below is real output from running a DOI through our own generator's CSE templates, set against the reference the CSE Manual's own quick guide prints for the same article.

Which edition your generator should follow

The current manual is The CSE Manual: Scientific Style and Format for Authors, Editors, and Publishers, 9th edition, published in 2024 by the Council of Science Editors with the University of Chicago Press. Duke University Libraries' CSE guide lists the 9th edition (2024) as current. The 8th edition (2014) was titled Scientific Style and Format, and plenty of library guides, course handouts and older generators still teach its rules.

The difference is not cosmetic. Set the 9th edition quick guide beside the 8th edition quick guide and four changes show up in almost every reference:

If a generated reference shows a city before the publisher, eight authors before "et al.", or doi: at the end, it is running an 8th edition template. The CSL styles behind most free generators (ours included, and Zotero's) were updated to the 9th edition in 2024 and 2025; a Zotero forum thread tracks the numeric style's update and the later fixes to the name-year version.

The three CSE systems, and what a generator gives you

The CSE Manual describes three ways to point from the text to the reference list. The reference entries are nearly identical in all three. The quick guide puts it plainly: they "have essentially the same format in all 3 systems, except for the placement of the date of publication in the name–year system."

• Citation-sequence. Sources get numbers in the order you first cite them, and the reference list runs in that order. A source keeps its first number every time it comes back.
• Citation-name. The reference list is alphabetized by first author's surname first, then numbered. A source by Acosta is 1 and Brown is 2, whatever order they appear in your text.
• Name-year. No numbers. The text gives the author and year in parentheses, and the list is alphabetical, with the year moved up to follow the authors.

Most generators offer citation-sequence and name-year, because those are the two CSE templates in the shared CSL style repository. AllCitations is the same: you can pick CSE citation-sequence or CSE name-year, and there is no separate citation-name option. A section below shows how to get a correct citation-name list from the citation-sequence output.

Which one you use is not your call to make on taste. The manual's own advice is to consult your publisher. For coursework, the assignment sheet or the lab manual decides; if it says only "CSE", ask, because a numbered list and an alphabetical list cannot be swapped late without renumbering every in-text citation.

What a generator can know, and what it cannot

A generator does two jobs. It looks up metadata for the identifier you paste (ours queries OpenAlex for a DOI), then pours that record into a CSL style template. The template handles the parts of CSE that are pure pattern: the period after the author list, the semicolon between date and volume, the colon before the page range, the order of elements. Those come out right nearly every time.

The record is where the trouble starts. Here is the first example in the CSE quick guide, next to what our citation-sequence template produced from the same DOI:

` Generated (citation-sequence, from the DOI): Haasnoot M, Lawrence J, Magnan A. Pathways to coastal retreat. Science. 2021;372(6548):1287–1290. https://doi.org/10.1126/science.abi6594. https://doi.org/10.1126/science.abi6594

CSE Manual quick guide: Haasnoot M, Lawrence J, Magnan AK. Pathways to coastal retreat. Science. 2021;372(6548):1287–1290. https://doi.org/10.1126/science.abi6594 `

Two differences. The third author lost a middle initial, because the database record stores the name without it. And the DOI link printed twice, followed by a period, which the 9th edition rules out ("no punctuation follows the URL"). The element order, the punctuation and the page range are correct. That is the pattern for this whole guide: trust the template, check the record.

The 9th edition formats to check against

You need the target before you can check the output. These patterns come from the CSE Manual's quick guide, which points to Chapter 29 of the 9th edition for the full set of examples.

Journal article

Citation-sequence and citation-name:

Author(s). Article title. Journal title. Date;volume(issue):location. URL

Name-year moves the year to follow the authors and drops it from the volume position:

Author(s). Date. Article title. Journal title. Volume(issue):location. URL

The "location" is usually the page range. For a journal on a continuous publication model it is the article number. Journal titles are abbreviated using the ISSN International Centre's List of Title Word Abbreviations (Appendix 29.1 of the manual), with no periods: Clim Dyn, Cleve Clin J Med. Dalhousie University's CSE 9th edition guide adds the rule a generator template already follows: the last author is joined with a comma, never "and" or an ampersand.

Book

Author(s). Title. Edition. Publisher; year of publication. De Doncker RW, Duco WJP, Veltman A. Advanced electrical drives: analysis, modeling, control. Springer; 2020.

In name-year, the year follows the authors and the publisher ends the entry: De Doncker RW, Duco WJP, Veltman A. 2020. Advanced electrical drives: analysis, modeling, control. Springer.

Website

Author. Title of article. Publisher; date of publication [date updated]. URL

With no author, start with the title. With no publication or update date, add an access date in brackets, as in the quick guide's Google Maps example: [accessed 2022 Jan 3].

In-text references

In citation-sequence and citation-name, the in-text reference is a number, set as a superscript in Dalhousie's description of both systems. In name-year it is the surname and year in parentheses. Two authors are joined with "and" in the text, though a comma separates them in the reference: (Fauci and Lane 2020). Three or more become the first author plus "et al", with no period after "al" in the manual's examples: (Haasnoot et al 2021).

Step by step: generating a CSE reference

1. Choose the system before you add anything. Pick CSE citation-sequence or CSE name-year in the style menu. Switching later reformats every entry, but the in-text references you already typed will not change with it.
2. Search by DOI, not title. A title search can match a preprint, a correction notice, or a later paper with a similar name. Paste the DOI (it starts with "10.") from the article's landing page or PDF.
3. Open the PDF next to the result. You need the byline, the first page and the issue details for the checks below. The PDF is the authority; the metadata record is a copy of it, made by someone else.
4. Run the checks and edit the reference in place. Most fixes are a few characters.
5. Order the list. For citation-sequence, number by first citation in the final draft. For name-year, alphabetize. For citation-name, alphabetize and then number (see below).
6. Insert in-text references last. Once the order is fixed, add the numbers or author-year cues and check each one against the list.

Twelve checks to run on generator output

The first seven are metadata problems that come in with the DOI. The last five come from template settings, from the 9th edition changes, or from the way a source has moved since you found it.

1. Abbreviate the journal title

Every DOI import we ran printed the full journal name. CSE wants the abbreviation, so look up each journal once in the ISSN abbreviation list (Appendix 29.1) and replace it:

Generated: Yohannes AM, Kaplan AG, Hanania NA. ... Cleveland Clinic Journal of Medicine. 2018;85(2 suppl 1):S11–S18. Fixed: Yohannes AM, Kaplan A, Hanania NA. ... Cleve Clin J Med. 2018;85(2 Suppl 1):S11–S18.

The same goes for Climate Dynamics (Clim Dyn) and JAMA Ophthalmology (JAMA Ophthalmol). Single-word titles such as Science and eJHaem stay as they are.

2. Put the article title in sentence case

CSE capitalizes only the first word of an article title, proper nouns and abbreviations. Database records often carry the publisher's Title Case, and the template passes it through:

Generated: Interaction Between the Distribution of Diabetic Retinopathy Lesions and the Association of Optical Coherence Tomography Angiography Scans With Diabetic Retinopathy Severity. Fixed: Interaction between the distribution of diabetic retinopathy lesions and the association of optical coherence tomography angiography scans with diabetic retinopathy severity.

Keep the capitals that belong: COVID-19, HIV, a species' genus name, a place name like Mekong. Book titles follow the same sentence-case rule in the quick guide's examples (Advanced electrical drives: analysis, modeling, control), and so does the word after a colon.

3. Restore missing initials

The database behind a DOI lookup sometimes stores a shortened name. Our imports turned "Magnan AK" into "Magnan A", "Kim KY" into "Kim K", and "Bhaskar ST" into "Bhaskar S". The reverse also happens: the record for the Yohannes article lists "Kaplan AG" where the quick guide prints "Kaplan A". The byline on the article settles it, so copy the initials from there. CSE writes initials with no periods or spaces (Lee SMC), and the quick guide prints Kwang-Yul Kim as Kim KY.

4. Check compound surnames

Surnames with two parts are easy for software to split wrongly. The first author of the vaccine-effectiveness preprint in the quick guide is Jamie Lopez Bernal, cited there as "Lopez Bernal J". Our import produced "Bernal JL", which would also move the entry to B in a name-year list. If an author's surname has two words, a particle, or a hyphen, check the paper and the author's own publications for the form they use.

5. Count the authors under the 9th edition rule

Five authors or fewer: list them all. More than five: the first author, then "et al." This is the 9th edition rule, and it is where generators lag. Our current CSE templates switch to "et al." at five, so a five-author paper comes out truncated:

Generated: Bhaskar S et al. Role of bridging therapy during chimeric antigen receptor T cell therapy. eJHaem. 2021;3(S1):39–45. Fixed: Bhaskar ST, Dholaria BR, Sengsayadeth SM, Savani BN, Oluwole OO. Role of bridging therapy during chimeric antigen receptor T cell therapy. eJHaem. 2022;3(Suppl 1):39–45.

The Liu article on Mekong precipitation has the same problem. Six authors (the Ashraf article) collapsed correctly to "Ashraf M et al." If a generator lists ten authors before "et al.", it is on the 8th edition.

6. Check the year, volume and page range against the PDF

The Bhaskar fix above also changes the year. The record dates the article 2021; the quick guide gives 2022, the year of the supplement it appears in. Use the year printed with the volume and issue. Then check the pages. The record for the Ashraf article has a single page, which the template printed as "1291–1291"; the quick guide has 1291–1297. CSE writes the full second number with an en dash, as in 1287–1290.

7. Fix supplements and article numbers

Supplements are written "Suppl" with a capital S, inside the parentheses: 85(2 Suppl 1):S11–S18 for an issue supplement and 3(Suppl 1):39–45 for a supplement with no issue. Records often store "S1" or "2 suppl 1", which the template prints as is.

Article numbers cause a worse error. Journals on a continuous publication model give each article a number instead of pages, and the CSE location is that number. The Liu article's record has a page count (1–10) where the article number should be, and the journal uses the year as its volume, so the template produced this:

Generated: Liu L et al. Changes in Extreme Precipitation in the Mekong Basin. Advances in Meteorology. 2020;2020:1–10. Fixed: Liu L, Bai P, Liu C, Tian W, Liang K. Changes in extreme precipitation in the Mekong Basin. Adv Meteorol. 2020:8874869. https://doi.org/10.1155/2020/8874869

The article number is usually the last part of the DOI or printed on the PDF's first page.

8. Delete the duplicate DOI and the final period

Our CSE templates currently print the DOI link twice (once from the record's URL field, once from its DOI field) and add a period after the first. The 9th edition wants one DOI-based URL, last, with nothing after it:

Generated: ...2020;383(1):1–4. https://doi.org/10.1056/nejmp1916753. https://doi.org/10.1056/nejmp1916753 Fixed: ...2020;383(1):1–4. https://doi.org/10.1056/NEJMp1916753

DOIs are not case-sensitive, so a lowercased DOI still resolves. Copy the capitalization from the article's own page if you want the reference to match it.

9. Fix the name-year punctuation

Two errors showed up only in our name-year template. The period before the URL is missing (372(6548):1287–1290 https://doi.org/...), and one entry lost a space (eJHaem.3(S1):39–45). Both are one-character fixes, and both are easy to miss in a long list. The template's in-text output also writes "et al." with a period, where the CSE Manual's name-year examples write "Haasnoot et al 2021".

10. Make sure a preprint DOI gives you the preprint

The quick guide's preprint example is a medRxiv preprint by Lopez Bernal and colleagues. When we pasted its DOI (10.1101/2021.05.22.21257658), the lookup returned the later New England Journal of Medicine article on the same study, with a different title, journal, volume and DOI. The lookup database links the preprint to its published version, and the published version is what came back.

Which one you should cite depends on which one you read. If you read the published article, cite it; that is usually the better choice anyway. If you read the preprint (because your course is on the preprint, or the paper changed), build the reference by hand from the quick guide's pattern:

Lopez Bernal J et al. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant [preprint]. medRxiv 2021. https://doi.org/10.1101/2021.05.22.21257658

The [preprint] label and the server name are what separate it from the journal article. For APA papers, our APA 7 generator guide covers the same lookup problem in that style.

11. Update articles that were "ahead of print"

An article cited as published ahead of print has no volume or pages yet. The quick guide's example is a Monthly Weather Review paper "[published online ahead of print 2021 Dec 30]". That paper has since appeared in volume 150, issue 4, pages 753–773, and our import produced a hybrid: the 2021 online year with the 2022 volume. Once an article has an issue, cite the issue version with the issue's year, and drop the "ahead of print" note. Check the journal page before you submit if you cited anything as forthcoming months ago.

12. Rebuild book references from the title page

Book DOIs return the thinnest records. For the quick guide's online-book example, the Oxford Handbook of Clinical Surgery, 5th edition, our import returned two names that are not on the quick guide's editor list (which starts with Agarwal A), set as authors, with no "editors" label, no edition and no publisher:

Generated: McLatchie G, Leaper D. Oxford Handbook of Clinical Surgery. 2021. https://doi.org/10.1093/med/9780198799481.001.0001 Fixed: Agarwal A et al, editors. Oxford handbook of clinical surgery. 5th ed. Oxford University Press; 2022. https://doi.org/10.1093/med/9780198799481.001.0001

For books, search by ISBN if your generator supports it, and then check every element against the title page and its reverse: editors and their role, edition, publisher and year. Leave out the place of publication; the 9th edition dropped it.

Building a citation-name list from citation-sequence output

If your journal or instructor wants citation-name and your generator offers only citation-sequence, the entries themselves need no change: the quick guide says the two systems "are identical except for the order in which the end references are listed." Only the order and numbering differ.

1. Generate every reference in CSE citation-sequence.
2. Sort the list alphabetically by first author's surname. Where one author has several works, the quick guide orders them alphabetically by title.
3. Number the sorted list from 1.
4. Go through the text and give each in-text reference the number of its source in the sorted list. A work by Zielinski that lands at 56 is 56 every time it is cited, wherever it appears.
5. Check that the numbers in the text are no longer in ascending order. In citation-name they should jump around; if they run 1, 2, 3 from the first page, the list is still in citation order.

The same sorting rules apply to a name-year list, with one addition from the quick guide: two works by the same authors in the same year get "a" and "b" after the year, ordered by date of publication when the exact dates are known and by title otherwise. Lee SMC et al. 2020a and 2020b are cited together as (Lee et al 2020a, 2020b).

Special cases a generator will not handle

Organization as author in name-year

The quick guide puts a bracketed abbreviation before the organization's name in the reference and uses the abbreviation in the text:

[ALSG] Advanced Life Support Group. 2020. Acute psychiatric emergencies: a practical approach. Wiley-Blackwell. (ALSG 2020)

A generator will give you the full name in both places. Add the bracketed short form yourself if you cite the organization more than once.

Websites with no author or no date

With no author, the reference starts with the title, and the name-year in-text reference uses the first word or two of the title and an ellipsis: (Health equity . . . 2020). With no date in name-year, write "[date unknown]" in the date position and add the access date. Generators usually fill the author slot with the site name instead, so check that the title has moved to the front.

Personal communication

Letters, emails and conversations do not go in the reference list. The quick guide places them in the running text, as in "(2022 letter from TD Perez to author; unreferenced, see "Notes")", and says permission is usually required and should be acknowledged in an Acknowledgments or Notes section. A generator has no source type for this, which is correct.

Theses, patents and newspaper articles

All three are in the quick guide, and none comes from a DOI lookup reliably. A dissertation takes "[dissertation]" after the title and the university as publisher. A patent lists inventors and the assignee, then the patent number and the full date. A newspaper article takes the full date and, if the story was revised, the updated date in brackets. Build these from the quick guide's patterns, or use the generator's manual entry form and then compare.

Common mistakes and how to avoid them

• Running an 8th edition template. A city before the publisher, ten authors before "et al.", or doi: at the end of a reference all mean the tool or the handout is on the 2014 rules. Check the style name in the menu before you build the list.
• Mixing systems in one paper. Numbered in-text references with an alphabetized list, or author-year cues with a numbered list, is not any of the three CSE systems. Pick one and convert the whole document.
• Keeping the full journal name. No DOI import we ran produced an abbreviation. Abbreviate every journal title, and keep a running list of the ones you use.
• Trusting the record over the PDF. Initials, years, page ranges and supplement numbers all came back wrong in at least one of our test imports. The article's byline and first page win.
• Renumbering after the in-text references are in. In citation-sequence, a source you move earlier in the draft changes every number after it. Settle the order of the text before you number.
• Letting "et al." pick up a period in name-year text. The CSE Manual's name-year examples write "et al" with no period. Some instructors accept either; a consistent list is the point.

Quick-reference table