If you have ever moved between disciplines — or even between journals within the same discipline — you already know the frustration. One journal wants numbered superscripts. Another wants author-date pairs in parentheses. A third wants abbreviated journal names in italic, a fourth wants them spelled out in roman type, and a fifth wants them omitted entirely. The DOI goes at the end in one style, as a hyperlink in another, and is formatted as plain text in a third. Every major scientific field has converged on its own citation conventions, and those conventions do not always agree with each other.
This is not arbitrary stubbornness. Each system reflects the reading habits and practical constraints of its community: chemists need compact structures and precise compound identifiers; engineers need numbered references that do not interrupt dense equations; physicists need speed and brevity in preprint culture. Understanding why each system is designed the way it is makes it easier to apply the rules correctly — and to switch between them without losing your mind.
This guide covers the five citation systems most commonly required in STEM writing: ACS (chemistry), IEEE (engineering and computer science), Nature style (multidisciplinary science), AIP (physics), and CSE/CBE (biological sciences).
ACS style is defined by the ACS Style Guide: Effective Communication of Scientific Information (Coghill & Garson, 2006), published by the American Chemical Society. It is required by all ACS journals — including Journal of the American Chemical Society, ACS Nano, and Analytical Chemistry — as well as by many non-ACS chemistry and materials-science outlets that have adopted its conventions.
ACS offers three citation formats and allows journals to select among them: (1) numbered references cited in order of appearance, (2) numbered references cited in alphabetical order, and (3) author-date (name-year) citations similar to APA. The numbered-in-order-of-appearance format is by far the most common in practice.
Journal article:
Whitesides, G. M.; Grzybowski, B. Self-Assembly at All Scales. Science 2002,
295 (5564), 2418–2421. https://doi.org/10.1126/science.1070821
Book:
Clayden, J.; Greeves, N.; Warren, S. Organic Chemistry, 2nd ed.;
Oxford University Press: Oxford, U.K., 2012.
In ACS style, author names use a semicolon as the separator between authors — not a comma. The last author does not take an "and." Journal names are abbreviated using CASSI (the CAS Source Index), and abbreviations are not followed by periods.
Additional details that catch writers off-guard: the year appears immediately after the journal name abbreviation, without a comma; volume numbers are in bold; issue numbers appear in parentheses immediately after the volume; and page ranges use en dashes. When a DOI is available, it is included as a full https://doi.org/ URL at the end of the entry.
IEEE style is governed by the IEEE Reference Guide (IEEE, 2020), published by the Institute of Electrical and Electronics Engineers. It is mandatory for all IEEE publications — including IEEE Transactions on Neural Networks and Learning Systems, IEEE Access, and conference proceedings published through IEEE Xplore — and is also widely used in computer science, electrical engineering, and telecommunications venues that are not formally affiliated with IEEE.
IEEE is a strictly numbered system. References are numbered in square brackets in the order they first appear in the text: [1], [2], [3], and so on. The reference list at the end of the document lists entries in that same numerical order, not alphabetically. This design keeps citation markers compact and unobtrusive in text-heavy or equation-heavy manuscripts.
Journal article:
Y. LeCun, Y. Bengio, and G. Hinton, "Deep learning," Nature, vol. 521,
no. 7553, pp. 436–444, May 2015, doi: 10.1038/nature14539.
Book:
I. Goodfellow, Y. Bengio, and A. Courville, Deep Learning. Cambridge, MA,
USA: MIT Press, 2016.
IEEE uses initials before surnames (e.g., "Y. LeCun"), the opposite of most other styles. Article titles appear in quotation marks, while journal and book titles are italicized. The volume and issue are abbreviated "vol." and "no." in lowercase.
The "doi:" label in IEEE is not a hyperlink prefix — it is a field label, written exactly as doi: 10.xxxx/xxxxx without the https://doi.org/ prefix. Conference paper citations include the conference name, location, and page range, making them notably longer than journal entries. When citing a specific page, IEEE uses "p." for a single page and "pp." for a range.
Nature style is described in the Author guidelines of Nature and Nature-portfolio journals (Nature, 2024). It is used across Nature, Nature Medicine, Nature Methods, Nature Physics, and the broader family of journals published by Springer Nature under the Nature brand. The style is also frequently adopted by high-impact multidisciplinary journals outside the Nature portfolio as a recognizable marker of concise, authoritative scientific writing.
Like IEEE, Nature uses numbered references cited in order of appearance, rendered as superscript numerals in the text. The reference list is ordered numerically. Unlike IEEE, author names use only initials for given names, and journal names are abbreviated without periods.
Journal article:
Banerjee, R., Phan, A., Wang, B., Knobler, C., Furukawa, H., O'Keeffe, M.
& Yaghi, O. M. High-throughput synthesis of zeolitic imidazolate frameworks
and application to CO2 capture. Science 319, 939–943 (2008).
https://doi.org/10.1126/science.1152516
Book:
Watson, J. D. The Double Helix: A Personal Account of the Discovery of the
Structure of DNA (Atheneum, 1968).
In Nature style, the year is enclosed in parentheses at the end of the journal article citation, after the page range — a distinctive inversion of the order found in most other systems. The ampersand "&" is used before the final author name rather than "and," and there is no serial comma before it.
Nature style limits the author list: for papers with more than five authors, journals in the Nature family have historically used "et al." after the fifth author in the reference list, though this varies by title and has evolved toward full author lists in recent years. Always check the specific journal's author guidelines, as they take precedence over general Nature style conventions.
AIP style is defined by the AIP Style Manual and maintained by the American Institute of Physics. It governs journals published by AIP Publishing — including Journal of Applied Physics, The Journal of Chemical Physics, Physics of Fluids, and Applied Physics Letters — as well as many journals of affiliated societies such as the American Physical Society (though APS journals use a closely related but distinct variant).
AIP uses numbered references in order of appearance, rendered as superscript numerals or numerals in square brackets depending on the journal. The system prioritizes brevity: journal names are heavily abbreviated, author given names are reduced to initials, and page ranges often give only the first page.
Journal article:
R. P. Feynman, "There's plenty of room at the bottom," J. Microelectromech.
Syst. 1(1), 60–66 (1992). https://doi.org/10.1109/84.128057
Book:
L. D. Landau and E. M. Lifshitz, Mechanics, 3rd ed. (Butterworth-Heinemann,
Oxford, 1976), pp. 1–170.
AIP style places the year in parentheses at the end of the journal entry, after the page range — the same position as Nature style. However, unlike Nature, AIP gives initials before the surname (like IEEE) rather than after. Volume numbers appear in bold, and the issue number in parentheses follows immediately after the volume with no space.
One practical detail that distinguishes AIP from ACS: while ACS uses the CASSI abbreviation list for journal names, AIP uses its own abbreviation conventions, which do not always agree with CASSI. When in doubt, consult the journal's own reference list in a recently published article — editors expect the abbreviations to match the journal's in-house style, not a general standard.
CSE style is defined by Scientific Style and Format: The CSE Manual for Authors, Editors, and Publishers (Council of Science Editors, 2014), now in its eighth edition. It is the primary standard for biological and life sciences — used in journals such as Cell, Genetics, Journal of Bacteriology, and Molecular Biology of the Cell — and is also adopted in environmental science, agriculture, and public health publishing.
CSE is unusual among STEM styles in offering three fully documented citation systems within a single manual: citation-sequence (numbered in order of appearance, like IEEE and Nature), citation-name (numbered alphabetically), and name-year (author-date, like APA). The choice is made by the journal, not the author.
Journal article (citation-sequence format):
1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al.
Initial sequencing and analysis of the human genome. Nature.
2001;409(6822):860–921. doi:10.1038/35057062
Book (name-year format):
Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K, Walter P. 2015.
Molecular biology of the cell. 6th ed. New York (NY): Garland Science.
In CSE citation-sequence format, author surnames come first, but given names are rendered as initials with no periods and no spaces between them — "Lander ES," not "Lander, E. S." When there are more than ten authors, CSE permits truncation with "et al." after the tenth name.
In the name-year format, the year migrates directly after the author list and before the title — earlier than in most other styles. Journal names in CSE are often given in full (not abbreviated) unless the specific journal instructs otherwise, which distinguishes CSE from AIP and ACS. The DOI is written without the https://doi.org/ prefix, as doi:10.xxxx/xxxxx.
The two fundamental citation philosophies — numbered and author-date — each have strong advocates in STEM.
Numbered systems (IEEE, Nature, AIP, CSE citation-sequence) keep in-text references visually minimal. A paper laden with equations or dense technical prose benefits from a small superscript or bracketed numeral that does not interrupt the reading flow. The cost is that the reader cannot infer anything about the source from the in-text marker alone — they must flip to the reference list to see who wrote it and when.
Author-date systems (ACS name-year, CSE name-year, and styles borrowed from the social sciences) embed authorship and date directly in the text, allowing an informed reader to recognize a landmark study — "(Watson & Crick, 1953)" carries immediate weight — without consulting the list. The cost is that text becomes visually crowded when multiple sources are cited together.
There is no universal winner. Choose the system your target journal requires. If you are writing before selecting a journal — common in thesis writing — choose the system most prevalent in your subfield, or use a tool that lets you switch formats without reformatting every entry by hand.
Every citation system described above now treats the Digital Object Identifier (DOI) as a required or strongly recommended element. The DOI provides a permanent, resolver-independent link to the source: even if a journal changes publishers, moves servers, or reorganizes its URL structure, the DOI continues to resolve correctly.
In STEM specifically, where citation half-life is long and datasets, preprints, and supplementary materials are increasingly cited alongside journal articles, the DOI (or its equivalent for datasets, such as a DataCite DOI) is often the only reliable identifier. CrossRef's database at doi.org can resolve virtually any scholarly DOI, and most reference management tools and citation platforms retrieve full metadata automatically from a DOI — eliminating manual entry errors.
When a DOI does not exist — for books, conference proceedings without DOIs, or technical reports — a stable URL to the publisher's page or institutional repository is the next best option. An unstable URL with no DOI is the weakest form of citation and should be archived via a service such as the Internet Archive's Wayback Machine before submission.
Switching between ACS, IEEE, Nature, AIP, and CSE manually is the kind of work that turns a productive afternoon into an exercise in find-and-replace frustration. Author name order changes. The year moves. Abbreviations differ. The DOI prefix is or is not required. A single reference reformatted incorrectly is enough to draw an editor's attention for the wrong reasons.
DEEPNOTIS supports all of the styles described in this guide. Import your sources once — by DOI, by file, or by manual entry — and export your reference list in whichever format your journal requires. Switching from IEEE to ACS for a different submission takes seconds, not an afternoon. The citation labels feature lets you tag and organize references by topic, chapter, or relevance so that large reference lists remain navigable regardless of which style you are working in.
Whether you are a chemist submitting to JACS, an engineer preparing an IEEE conference paper, or a biologist formatting a Cell manuscript, getting the style right is a submission requirement, not an optional polish. The rules are learnable; the switching costs do not have to be.
American Chemical Society. (2006). ACS style guide: Effective communication of scientific information (3rd ed.). Oxford University Press.
Council of Science Editors. (2014). Scientific style and format: The CSE manual for authors, editors, and publishers (8th ed.). University of Chicago Press.
IEEE. (2020). IEEE reference guide. Institute of Electrical and Electronics Engineers. https://ieeeauthorcenter.ieee.org/wp-content/uploads/IEEE-Reference-Guide.pdf
Nature. (2024). Author guidelines. Springer Nature. https://www.nature.com/nature/for-authors