Manuscript Writing

Section-by-Section Guidance

Introduction

Structure as a funnel:

1. Broad context - Establish the field and importance (1-2 paragraphs)
2. Narrow focus - What is known about the specific topic (1-2 paragraphs)
3. Gap statement - What remains unknown or problematic
4. Objective/hypothesis - What this paper addresses and how

Methods

• Enough detail for replication
• Subsections mirror Results sections
• Include: participants/subjects, materials, procedures, analysis
• Statistical methods: specify tests, software, significance thresholds
• Ethics: IRB/IACUC approval statement

Results

• Present findings without interpretation
• Start each subsection with the analysis performed, then the outcome
• Report effect sizes, confidence intervals (not just p-values)
• Reference figures and tables in order
• Use "significant" only for statistical significance

Discussion

Structure:

1. Summary of key findings (1 paragraph)
2. Interpretation in context of prior literature (2-3 paragraphs)
3. Limitations (1 paragraph, honest but not self-defeating)
4. Future directions (1 paragraph)
5. Conclusion (1 paragraph)

Writing Principles

Clarity

• One idea per sentence
• Active voice preferred ("We measured..." not "Measurements were taken...")
• Define abbreviations on first use
• Avoid jargon unless writing for a specialist audience

Precision

• Quantify claims ("increased by 23%" not "significantly increased")
• Cite sources for factual claims
• Distinguish correlation from causation
• Use hedging appropriately ("suggests" vs "proves")

Flow

• Each paragraph: topic sentence, evidence, interpretation
• Transitions between paragraphs connect ideas
• Logical progression within and across sections
• Consistent terminology (don't alternate between synonyms for key concepts)

Citations

• Cite primary sources, not reviews (when possible)
• Recent citations show awareness of current literature
• Cite competing or contradictory findings
• Self-citation should be relevant, not gratuitous

Revision Checklist

After drafting, check:

• Abstract accurately reflects the paper content
• Introduction gap statement matches the study objective
• Methods are sufficient for replication
• Results match Methods (parallel structure)
• Discussion addresses all major findings
• Figures are referenced in text in order
• All abbreviations defined on first use
• References complete and consistently formatted
• Word/page count within journal limits

Additional Resources

• Reference: references/section-templates.md - Templates for each manuscript section
• Reference: references/revision-response.md - How to write point-by-point responses to reviewers