Manuscript Writing

Title Construction

Strong titles follow these patterns:

Declarative (states the finding):

• "Gene X regulates metabolic pathway Y in species Z"
• Best for clear, significant results

Descriptive (states the topic):

• "Regulation of metabolic pathway Y in species Z"
• Best when results are complex or exploratory

Question (poses the research question):

• "Does gene X regulate metabolic pathway Y?"
• Use sparingly; can seem uncertain

Title Checklist

• Contains key terms for searchability
• Avoids abbreviations (except universally known ones)
• No colons unless necessary for subtitles
• Specific enough to distinguish from similar papers
• Accurate representation of content

Section-by-Section Guidance

Introduction

Goal: Move from broad context to specific research question.

Structure (funnel shape):

1. Opening hook - Why does this topic matter?
2. Background - What do we already know?
3. Gap - What remains unknown?
4. Objective - What does this study address?
5. Approach - How did you address it? (brief)

Common mistakes:

• Too much background, too little gap identification
• Burying the research question
• Citing exhaustively rather than selectively
• No clear statement of objectives

Methods

Goal: Enable replication.

Key principles:

• Describe what you did, not why
• Use past tense throughout
• Include enough detail for replication
• Cite established protocols rather than re-describing

Standard subsections:

• Study design/overview
• Participants/samples
• Data collection/procedures
• Data analysis
• Ethics statement (if applicable)

Results

Goal: Report findings without interpretation.

Key principles:

• Lead with most important findings
• State results, then reference supporting figure/table
• Report effect sizes, not just significance
• Present results systematically (by hypothesis, by variable, etc.)

Structure each paragraph:

1. Topic sentence stating the result
2. Supporting statistics
3. Reference to figure or table

Discussion

Goal: Interpret findings and place in context.

Structure:

1. Summary - Restate key findings (1-2 sentences)
2. Interpretation - What do results mean?
3. Context - How do they fit existing literature?
4. Implications - Why do they matter?
5. Limitations - What are the caveats?
6. Future directions - What comes next?
7. Conclusion - Final take-home message

Common mistakes:

• Repeating results without interpretation
• Overstating conclusions
• Ignoring contradictory literature
• Limitations section that undermines the entire study

Abstract Types

See ABSTRACT_TEMPLATES.md for templates.

Structured abstract (with headings):

• Background/Introduction
• Methods
• Results
• Conclusions

Unstructured abstract (single paragraph):

• Same content, flowing prose
• Typically follows same order

Key Transitions

See SECTION_TRANSITIONS.md for phrases to move between sections.

Quality Checks

Before submission, verify each section:

• Title - Searchable, accurate, appropriate length
• Abstract - Stands alone, within word limit, no citations
• Introduction - Clear gap and objectives
• Methods - Replicable, complete, properly cited
• Results - Systematic, properly referenced figures/tables
• Discussion - Interprets (not repeats), acknowledges limitations

Related Files

• IMRAD_STRUCTURE.md - Detailed checklists for each section
• ABSTRACT_TEMPLATES.md - Templates with word budgets
• SECTION_TRANSITIONS.md - Transition phrases