Word manuscripts · reference formatting

Reference Hygiene for Busy Authors

Reading time ~6 minutes · Published September 13, 2025

Editing a Word manuscript with a reference list open; a DOI and page range highlighted
Premise: Clean references reduce desk rejections, copy-editing queries, and production delays. This quick guide focuses on the four fixes that save the most time in Word manuscripts—capitalization, page ranges, DOIs, and duplicates—with fast workflows for EndNote, Zotero, Mendeley, and Word’s built-in References tools.
Contents

1) Capitalization that sticks

Problem: Title-casing and sentence-casing are often applied automatically, which downcases proper nouns, acronyms, and gene or product names.

Fix (Word, plain list): Use Home → Change Case for bulk conversion, then restore protected terms manually. Avoid ALL CAPS in titles; keep acronyms uppercase.

Fix (Zotero/EndNote/Mendeley): Store titles in sentence case and rely on the output style to apply case rules. Add protected words (e.g., CRISPR, SARS-CoV-2, ICU) to your manager’s exceptions list when available. In EndNote, adjust the style’s “Change Case” rules; in Zotero, prefer sentence-case input and correct case at cite time if a style forces downcasing.

2) Page ranges and article numbers

Problem: Hyphens are not en dashes; many styles expect an en dash (–) in numeric ranges. Article numbers must not be expanded into fake ranges.

Fix (Word Find/Replace with wildcards):

Find:    ([0-9])([-–])([0-9])    (check “Use wildcards”)
Replace: \1^=\3                   (^= inserts an en dash in Word)

Tip: Keep article numbers as given (e.g., e123456) in the pages slot if the journal style requires it; do not add ranges.

3) DOIs: consistent field, consistent display

Goal: One format throughout. Either plain DOI (e.g., 10.1038/s41586-025-01234-5) or a URL (https://doi.org/10.1038/s41586-025-01234-5) depending on the target journal.

Word bulk normalisation (plain list):

To force URL form:
Find:    (<|\\s)10.([0-9]{4,})[^\\s]+
Replace: https://doi.org/\2   (run carefully; review each)

Managers: In EndNote/Zotero/Mendeley, keep the DOI in its dedicated field. Toggle URL/DOI printing via the output style. Avoid placing DOIs in Notes.

4) Duplicates: detect, merge, keep one canonical entry

Problem: Imports from multiple databases produce near-duplicates (same DOI, slightly different titles or author lists).

Fix: De-duplicate in the manager before finalising the Word document. Prefer the entry that has a DOI, full author names, correct accents, and complete metadata. Use one consistent key or record as the source of truth.

Quick workflows

EndNote

  • Find Duplicates → merge by DOI/title; keep the record with complete metadata.
  • Style Editor → ensure case and DOI/URL rules match the journal.
  • In Word: use the EndNote tab to “Update Citations and Bibliography,” then “Convert to Plain Text” only at the end.

Zotero

  • Duplicate Items → merge to a master record; confirm DOI.
  • Select journal CSL style (APA/AMA/Vancouver/IEEE). Toggle DOI/URL as required.
  • Refresh from the Zotero Word plugin; unlink citations only just before submission (creates a static bibliography).

Mendeley

  • Tools → Check for Duplicates; merge best metadata.
  • Pick the correct journal style; ensure DOI/URL rules match policy.
  • Update bibliography in Word; only “Remove Field Codes” at the final pass.

Word (built-in References)

  • Manage Sources → de-duplicate; ensure each source has a consistent Tag.
  • Choose a style close to target (e.g., APA). If journal requires AMA/Vancouver/IEEE, use a manager or format manually.
  • When the journal demands plain text, use Paste Special → Unformatted Text or “Convert to Plain Text.”

Before/After: one reference, four fixes

Before (static list in Word)

SMITH A, LEE B. A crispr based assay for sars-cov-2 detection in ICU settings.
Clinical Methods. 2025;12(3):101-109. DOI: https://doi.org/10.1038/S41586-025-01234-5

After (clean, journal-ready)

Smith A, Lee B. A CRISPR-based assay for SARS-CoV-2 detection in ICU settings.
Clin Methods. 2025;12(3):101–109. doi:10.1038/s41586-025-01234-5
  • Capitalization: Restored proper nouns and acronyms; removed all-caps.
  • Pages: En dash (–) in the range.
  • DOI: Consistent lowercase, no duplicate “DOI:” label if the style prints one.
  • Abbrev: Journal abbreviation applied (per style) rather than full title.

Journal-style mini-checklist

Need help with a Word manuscript? I will return a tracked-changes edit of the entire document plus a reference-list normalisation pass: capitalization, page ranges, DOI policy, de-duplication, journal style, figure/table callout checks, and cross-reference integrity. Make my references submission-ready
Localization note (JP/KR/CN): I adapt punctuation spacing, dash conventions, and title capitalization to local journal norms while preserving author voice.