Regex-Based Manuscript Error Detection: A Comprehensive Checklist for Academic Writing

Why Use Regex for Manuscript Editing?

Manual proofreading is essential but time-consuming and error-prone. Regular expressions (regex) offer a powerful complementary approach to catch systematic errors that human eyes often miss—double spaces, repeated words, inconsistent formatting, and punctuation mistakes.

This comprehensive guide provides regex patterns for detecting common manuscript errors, organized by category. Each pattern includes examples and usage notes to help you implement automated quality checks in your writing workflow.

Tools you can use: VS Code, Sublime Text, Notepad++, Python scripts, or command-line tools like grep and sed.

Repetition Issues

Repeated words are among the most common manuscript errors, often introduced during editing and revision.

Usage Example

In VS Code, open Find (Ctrl + F), enable regex mode (Alt + R), and search for \b(\w+)\s+\1\b to highlight all repeated words.

False positives to watch for: Scientific terms like "chi-chi square" or proper names like "New New York" (fictional location).

Pro tip: Use case-insensitive search for the first pass, then case-sensitive to catch subtle errors like "The the."

Spacing Issues

Spacing errors are invisible to casual reading but look unprofessional and can cause LaTeX compilation issues.

Common Workflow

Problem: Your manuscript has inconsistent spacing from multiple editing rounds.

Solution:

1. Press Ctrl + H (Find and Replace)
2. Enable regex: Alt + R
3. Find: \s{2,}
4. Replace: (single space)
5. Review matches and replace all

For LaTeX users: Be careful with intentional double spaces after periods in older styles, though modern practice recommends single spaces.

Punctuation Errors

Systematic punctuation errors are easily caught with regex patterns.

Ellipsis Standardization

Find: \.\.\.
Replace: … (single Unicode ellipsis character)

Or for three-dot style:
Replace: . . . (spaces between dots)

Journal style check: Some journals prefer \ldots in LaTeX. Check your target journal's author guidelines.

Quotation Mark Issues

Convert straight quotes to smart (curly) quotes or standardize quotation styles.

Smart Quote Conversion

For double quotes:
Find: "([^"]+)"
Replace: "$1" or "$1" (depending on style)

Note: Many journals require straight quotes in manuscripts. Check guidelines before converting.

Number and Unit Formatting

Scientific manuscripts require consistent number and unit formatting.

Temperature Formatting

Find: (\d+)\s*degrees?\s*C\b
Replace: $1°C

Result: "25 degrees C" → "25°C"

LaTeX equivalent: Use \SI{25}{\celsius} with siunitx package for best practice.

Unit Spacing

Find: (\d+)(mm|cm|m|km|mg|g|kg|mL|L|ms|s|min|h)\b
Replace: $1 $2

Example: "5mm" → "5 mm"

Important: Review matches carefully—some contexts might use different conventions (e.g., "5mm" in figure dimensions).

Common Word Errors

Catch frequently confused words and articles.

Context-Dependent Checking

Pattern: \bit's\b

This finds all instances of "it's" (contraction for "it is"), which in scientific writing should often be "its" (possessive).

How to verify:

1. Find all instances with regex
2. Manually check each one
3. Replace where "it is" doesn't make sense

Example:
"The model and it's parameters" → "The model and its parameters"
"It's important to note" → Keep as is (means "It is")

Mathematical and LaTeX Formatting

Special patterns for LaTeX manuscripts.

Convert Sections to Unnumbered

Find: \\section\{([^}]+)\}
Replace: \\section*{$1}

Result: All sections become unnumbered.

Use case: Converting to appendix format or supplementary materials.

Find Math Mode Issues

Pattern: (?<!\\)\$[^$]*[^$\\]\$(?!\$)

This finds potential math mode errors where special characters might need escaping.

Reference and Citation Formatting

Ensure proper citation formatting throughout your manuscript.

Standardize DOI Format

Find: DOI:\s*
Replace: doi:

Or for modern format:
Find: doi:\s*(\S+)
Replace: https://doi.org/$1

Example: "doi:10.1234/example" → "https://doi.org/10.1234/example"

Collapse Consecutive Citations

Find: \[(\d+)\]\s*\[(\d+)\]
Replace: [$1,$2] or [$1-$2] (depending on style)

Before: "[1] [2] [3]"
After: "[1-3]" or "[1,2,3]"

Figure and Table References

Maintain consistency in figure and table references.

Capitalize References

Find: \bfigure\s+(\d+)
Replace: Figure $1

Find: \btable\s+(\d+)
Replace: Table $1

Add Non-Breaking Space in LaTeX

Find: (Figure|Table|Section|Equation)\s+\\ref
Replace: $1~\\ref

Result: Prevents line breaks between "Figure" and its number.

Line Break and Special Character Issues

Platform-specific and special character problems.

Standardize Line Endings

Convert Windows to Unix:
Find: \r\n
Replace: \n

Remove excessive line breaks:
Find: \n{3,}
Replace: \n\n

Fix Multiplication Signs

Find: (\d+)\s*x\s*(\d+)
Replace: $1 × $2

Result: "5 x 3" → "5 × 3"

LaTeX alternative: Use $5 \times 3$ for proper mathematical notation.

Parentheses and Bracket Errors

Check for matching and spacing issues.

Advanced: Find Unmatched Brackets

This is complex in pure regex, but a simple check:

Find: \([^\)]*\[ (opening bracket inside parentheses without closing)

Better approach: Use your editor's bracket matching feature or a dedicated tool like grep -P with recursive patterns.

URL and Email Formatting

Ensure proper URL and email formatting.

Find All URLs

Pattern: https?://[^\s]+

Use case: Verify all URLs are accessible before submission.

Pro tip: Export matches to a list, then use a script to check if each URL returns HTTP 200.

Abbreviation Formatting

Standardize abbreviation styles.

Standardize Latin Abbreviations

Find: \bi\.e\.(?!,)
Replace: i.e.,

Find: \be\.g\.(?!,)
Replace: e.g.,

Result: Ensures comma follows these abbreviations per Chicago Manual of Style.

Note: Some journals prefer "i.e." without comma—check your target journal's style guide.

Implementing Regex Checks

Method 1: VS Code Bulk Find

1. Open Command Palette: Ctrl + Shift + P
2. Type "Find in Files"
3. Enable regex: Click .* icon or press Alt + R
4. Paste pattern in search box
5. Review all matches across your project
6. Use Replace in Files for batch corrections

Method 2: Python Script

import re

def check_manuscript(filename):
    with open(filename, 'r', encoding='utf-8') as f:
        content = f.read()

    # Check for repeated words
    repeated = re.findall(r'\b(\w+)\s+\1\b', content, re.IGNORECASE)
    if repeated:
        print(f"Found repeated words: {set(repeated)}")

    # Check for double spaces
    double_spaces = len(re.findall(r'\s{2,}', content))
    if double_spaces:
        print(f"Found {double_spaces} instances of multiple spaces")

    # Add more checks as needed

# Usage
check_manuscript('manuscript.tex')

Method 3: Command Line (Linux/Mac)

# Find repeated words
grep -n -E '\b(\w+)\s+\1\b' manuscript.tex

# Find double spaces
grep -n -E '\s{2,}' manuscript.tex

# Count occurrences
grep -c -E 'pattern' manuscript.tex

Method 4: Automated Pre-Submission Check

Create a shell script check-manuscript.sh:

#!/bin/bash

FILE=$1
ERRORS=0

echo "Checking manuscript: $FILE"
echo "================================"

# Check for repeated words
if grep -E '\b(\w+)\s+\1\b' "$FILE" > /dev/null; then
    echo "❌ Found repeated words"
    grep -n -E '\b(\w+)\s+\1\b' "$FILE"
    ERRORS=$((ERRORS + 1))
else
    echo "✓ No repeated words"
fi

# Check for double spaces
if grep -E '\s{2,}' "$FILE" > /dev/null; then
    echo "❌ Found double spaces"
    ERRORS=$((ERRORS + 1))
else
    echo "✓ No double spaces"
fi

# Check for space before punctuation
if grep -E '\s+[.,;:!?]' "$FILE" > /dev/null; then
    echo "❌ Found space before punctuation"
    ERRORS=$((ERRORS + 1))
else
    echo "✓ No space before punctuation"
fi

echo "================================"
echo "Total error categories: $ERRORS"

if [ $ERRORS -eq 0 ]; then
    echo "✓ All checks passed!"
    exit 0
else
    echo "❌ Please review and fix errors"
    exit 1
fi

Usage:

chmod +x check-manuscript.sh
./check-manuscript.sh manuscript.tex

Complete Checklist

Here's a prioritized checklist for manuscript review:

High Priority (Always Check)

• Repeated words: \b(\w+)\s+\1\b
• Double spaces: \s{2,}
• Space before punctuation: \s+([.,;:!?)])
• Missing space after punctuation: ([.,;:!?])([A-Za-z])
• Trailing spaces: \s+$
• Lowercase figure/table references: \bfigure\s+\d+, \btable\s+\d+

Medium Priority (Common Errors)

• Missing space after comma: ,([A-Za-z0-9])
• Number-unit spacing: (\d+)([a-zA-Z]{1,3})\b
• Double punctuation: ([.,;:!?])\1+
• Incorrect "it's" usage: \bit's\b
• Missing space after citation: \[\d+\]([A-Za-z])
• DOI formatting: DOI:\s*, doi:\s+

Low Priority (Style and Consistency)

• Multiple line breaks: \n{3,}
• Tab characters: \t
• Ellipsis standardization: \.\.\.
• Em-dash formatting: --
• Degree notation: (\d+)\s*degrees?\s*C\b
• Latin abbreviations: \bi\.e\.(?!,), \be\.g\.(?!,)

LaTeX-Specific

• Missing tilde before ref: (Figure|Table|Section)\s+\\ref
• Math mode issues: \b[A-Za-z]_\{?\d+\}?
• Comment spacing: %\s+
• Section formatting: \\section\{([^}]+)\}

Best Practices

1. Test on Sample Text First

Before running replacements on your entire manuscript, test patterns on a small section or dummy file. Regex can make unexpected matches.

2. Review Before Replace All

Always click through matches before using "Replace All." Some matches might be intentional (e.g., "New New York" in fiction).

3. Use Version Control

Before bulk replacements:

git commit -m "Before regex cleanup"
# Run your regex replacements
git diff  # Review changes
git commit -m "After regex cleanup"

This lets you revert if something goes wrong.

4. Create a Personal Regex Library

Save commonly used patterns in a text file for quick reference:

# My Manuscript Regex Patterns
Repeated words: \b(\w+)\s+\1\b
Double spaces: \s{2,}
Missing space after period: \.([A-Z])
# ... etc

5. Combine with Manual Review

Regex catches systematic errors but can't replace human judgment. Always:

• Read your manuscript thoroughly
• Use grammar checkers like Grammarly or LanguageTool
• Have colleagues review your work
• Check against journal style guides

6. Be Journal-Aware

Different journals have different requirements:

• American vs. British spelling
• Serial comma preferences
• Citation format (numbered vs. author-year)
• Figure/table caption placement

Adapt your regex checks accordingly.

Common Pitfalls

Pitfall 1: Over-Eager Matching

Problem: \ba\s+[aeiou] matches "a united" (where "a" is correct because "united" starts with "yoo" sound)

Solution: Review matches manually; not all vowels start with vowel sounds.

Pitfall 2: Breaking LaTeX Commands

Problem: Replacing -- with — breaks \texttt{--flag} or \verb|--|

Solution: Use negative lookbehind: (?<!\\texttt\{)--(?!\})

Or: Manually review all replacements in code blocks.

Pitfall 3: False Positives in References

Problem: Finding "repeated words" in bibliography entries like "Smith, J. J."

Solution: Exclude bibliography section from checks, or use more specific patterns.

Pitfall 4: Different Encodings

Problem: Regex works in VS Code but fails in terminal

Solution: Ensure UTF-8 encoding everywhere:

file -bi manuscript.tex  # Check encoding
iconv -f ISO-8859-1 -t UTF-8 manuscript.tex > manuscript_utf8.tex

Advanced Regex Techniques

Lookaheads and Lookbehinds

Positive Lookahead: Match pattern only if followed by something

\b(Figure)(?=\s+\d+)  # Match "Figure" only before a number

Negative Lookahead: Match pattern only if NOT followed by something

\be\.g\.(?!,)  # Match "e.g." only if not followed by comma

Positive Lookbehind: Match pattern only if preceded by something

(?<=\d)\s+(?=mm)  # Match space between number and "mm"

Negative Lookbehind: Match pattern only if NOT preceded by something

(?<!\\)\$  # Match $ only if not preceded by backslash (LaTeX)

Non-Capturing Groups

Use (?:...) when you need grouping but don't want to capture:

(?:Dr|Mr|Mrs|Ms)\.?\s+([A-Z][a-z]+)
# Matches title + name, captures only the name

Named Capture Groups

For readability in complex patterns:

\b(?<year>\d{4})-(?<month>\d{2})-(?<day>\d{2})\b
# Captures date components with meaningful names

Multiline Mode

Enable with flag m or (?m):

(?m)^\s+  # Matches leading spaces at start of each line

Troubleshooting

Issue: Pattern Works Online but Not in My Editor

Cause: Different regex flavors (PCRE, ECMAScript, Python, etc.)

Solution:

• VS Code uses JavaScript regex (ECMAScript)
• Python uses its own flavor
• Check your tool's regex documentation

Example: \K (keep) works in PCRE but not JavaScript

Issue: Too Many False Positives

Cause: Pattern is too general

Solution: Add context with lookarounds

# Too general
\bthe\s+the\b

# More specific (not in comments)
(?<!%).*\bthe\s+the\b

Issue: Pattern Doesn't Match Across Lines

Cause: . doesn't match newlines by default

Solution: Use [\s\S] or enable DOTALL mode

# Match paragraph with specific text
(?s)\\begin\{abstract\}.*?specific.*?\\end\{abstract\}

Issue: Replacement Breaks Formatting

Cause: Captured groups not preserved correctly

Solution: Use numbered backreferences ($1, $2) or named ones

# Find
(\d+)\s+(mm|cm|m)

# Replace
$1 $2  # Preserves both captures

Integration with Writing Workflow

Stage 1: During Writing

Light checks only to avoid interrupting flow:

• Double spaces (as you type)
• Obvious typos

Tool: Enable "show invisibles" in your editor to see extra spaces.

Stage 2: Section Complete

After finishing a section, run:

• Repeated words check
• Punctuation spacing
• Reference formatting

Frequency: After each major section or daily writing session.

Stage 3: Full Draft Complete

Comprehensive check before sharing with co-authors:

• All high-priority patterns
• Medium-priority patterns
• Style consistency checks

Tool: Run automated script or manual search through all patterns.

Stage 4: Pre-Submission

Final polish before journal submission:

• All checklist items
• Journal-specific formatting
• Reference and citation verification
• Figure/table reference consistency

Best practice: Create a submission checklist document tracking all checks.

Real-World Example Workflow

Scenario: 30-Page Research Paper, Pre-Submission

Step 1: Setup (5 minutes)

# Create working copy
cp manuscript.tex manuscript_before_cleanup.tex

# Initialize git if not already
git init
git add .
git commit -m "Before regex cleanup"

Step 2: High-Priority Checks (15 minutes)

In VS Code:

1. Find repeated words: \b(\w+)\s+\1\b

   • Review: 8 instances found
   • Fixed: 6 were errors, 2 were intentional ("Cha-Cha" dancing, "Wagga Wagga" place name)

2. Find double spaces: \s{2,}

   • Found: 47 instances
   • Replace all with single space

3. Fix capitalization: \bfigure\s+(\d+) → Figure $1

   • Found: 23 instances
   • Replace all

Step 3: Medium-Priority Checks (10 minutes)

4. Number-unit spacing: (\d+)(mm|cm|m|kg|g|mg)\b → $1 $2

   • Found: 15 instances
   • Manually reviewed each (some were in figure filenames—excluded those)
   • Replaced: 12 instances

5. Citation spacing: \[\d+\]([A-Za-z]) → [$1] $2

   • Found: 5 instances
   • Replace all

Step 4: LaTeX-Specific (10 minutes)

6. Non-breaking spaces: (Figure|Table)\s+\\ref → $1~\\ref

   • Found: 31 instances
   • Replace all

7. Clean up comments: %\s\s+ → %

   • Found: 12 instances
   • Replace all

Step 5: Verification (5 minutes)

# Compile to check for errors
pdflatex manuscript.tex

# Check git diff
git diff manuscript.tex

# Commit changes
git add manuscript.tex
git commit -m "Regex cleanup: spacing, punctuation, references"

Total time: 45 minutes
Issues found: 145+ formatting errors
Errors prevented: Potentially embarrassing submission issues

Additional Resources

Regex Testing Tools:

• Regex101 - Interactive regex tester with explanation
• RegExr - Visual regex learning tool
• RegexBuddy - Desktop regex development tool

Learning Resources:

• Regular-Expressions.info - Comprehensive tutorial
• RegexOne - Interactive lessons
• Mastering Regular Expressions - O'Reilly book

LaTeX-Specific:

• LaTeX Stack Exchange - Q&A for LaTeX issues
• Overleaf Guides - LaTeX tutorials and best practices

Editor Documentation:

• VS Code Regex
• Sublime Text Regex
• Python re Module

Downloadable Resources

Create these helper files for your workflow:

1. Quick Reference Card

Save as regex-manuscript-checks.txt:

=== MANUSCRIPT REGEX QUICK REFERENCE ===

HIGH PRIORITY:
Repeated words:           \b(\w+)\s+\1\b
Double spaces:            \s{2,}
Space before punct:       \s+([.,;:!?)])
Missing space after:      ([.,;:!?])([A-Za-z])
Trailing spaces:          \s+$

CITATIONS:
Missing space after:      \[\d+\]([A-Za-z])
DOI formatting:           DOI:\s*
                         doi:\s+

FIGURES/TABLES:
Lowercase references:     \bfigure\s+\d+
                         \btable\s+\d+

LATEX:
Missing tilde:           (Figure|Table)\s+\\ref
Math outside mode:       \b[A-Za-z]_\{?\d+\}?

=== END REFERENCE ===

2. VS Code Snippets

Add to your VS Code settings:

{
  "Regex Checks": {
    "prefix": "regex-check",
    "body": [
      "// Repeated words: \\b(\\w+)\\s+\\1\\b",
      "// Double spaces: \\s{2,}",
      "// Space before punctuation: \\s+([.,;:!?)])",
      "// Missing space after punctuation: ([.,;:!?])([A-Za-z])"
    ],
    "description": "Common regex patterns for manuscript checking"
  }
}

Regular expressions transform manuscript editing from tedious manual proofreading into systematic quality control. While regex can't replace human judgment, it excels at catching repetitive, systematic errors that are easy to miss but embarrassing in publication.

The key is building a personal library of patterns tailored to your writing style and common errors. Start with high-priority checks (repeated words, spacing issues), then gradually expand your toolkit as you identify additional patterns in your work.

Remember:

1. Always test patterns on sample text first
2. Review matches before bulk replacements
3. Use version control to enable safe experimentation
4. Combine regex with traditional proofreading
5. Adapt patterns to journal-specific requirements

Investment vs. Return: Setting up regex checks takes 1-2 hours initially but saves hours on every subsequent manuscript. For researchers submitting multiple papers yearly, this efficiency gain compounds significantly.

Share your patterns: What manuscript errors do you catch most often? What regex patterns have you found most useful? Share your experiences in the comments!

Happy writing and error-free submissions! 🔍📝

Last updated: December 25, 2025