paper-writer

Paper Writer Skill

Full-pipeline academic paper writing assistant. From literature search to submission-ready manuscript.

Overview

This skill manages the entire paper writing workflow:

[Discovery] → Literature Search → Outline → Tables/Figures → Draft → Humanize → References → Quality Review → [Adversarial Review] → Pre-Submission → [Revision] → [Post-Acceptance] → [Rejection → Resubmission]

Each paper is a project directory containing structured Markdown files for every section, a literature matrix, and quality checklists.

AI-for-Science Operating Model

This skill is not only a manuscript factory (write → format → submit). It is a research engine that wraps the writing pipeline in a discovery loop and names the two things only a human can supply. Before doing anything else, read ~/.claude/skills/paper-writer/references/ai-for-science-model.md — it defines:

The two human-sovereign inputs. 💡 IDEA (what is worth asking, what it means, what is ethical) and 📊 DATA (real, IRB-approved, never machine-originated). AI proposes and executes everything else at full power; the human owns exactly these two gates. AI must never originate a data point, participant, or result.
The loop. Phase −1 Discovery (hypothesis → novelty → design → pre-registration lock) feeds the existing pipeline; Phase 6.5 Adversarial Review red-teams the central claim before any journal sees it. A red-team KILL sends the project back to Discovery — that is the system working.
The three integrity guardrails that make AI-accelerated research more rigorous, not less: pre-registration (anti-HARKing), novelty check (anti-reinvention/inflation), adversarial self-review (anti-slop). Each prevents a documented frontier failure mode.
The autonomy dial (Manual / Co-pilot / Autopilot). Hard rule for clinical work: the 💡 IDEA gate, the 📊 DATA gate, and the pre-registration lock are never autopilot.

The rest of this document is the execution detail. When a phase touches a sovereign gate, stop and get the human; everywhere else, run at full power.

Supported Paper Types

Type	Structure	Reporting Guideline	Notes
Original Article	Full IMRAD	STROBE / CONSORT	Default
Case Report	Intro / Case / Discussion	CARE	Separate templates
Review Article	Thematic sections	-	Flexible structure
Letter / Short Communication	Condensed IMRAD	Same as original	Word limit focus
Systematic Review	PRISMA-compliant	PRISMA 2020	With PRISMA checklist
Study Protocol	SPIRIT-compliant	SPIRIT 2025	For trial registration papers

Workflow

Phase −1: Discovery (the research engine)

This phase is what separates a research engine from a manuscript factory. The rest of the skill assumes the research question and the data already exist. Phase −1 produces them — a novelty-checked, powered, pre-registered study plan — before Project Init. Read ~/.claude/skills/paper-writer/references/ai-for-science-model.md first for the operating model.

Phase −1 is re-enterable — enter at the first guardrail not yet passed. It is not all-or-nothing: a study that already has a sharpened question (but no novelty check, power, or pre-registration) enters mid-chain, not at the forge. Route by the Phase −1 entry matrix:

What the user arrives with	Enter at	How
(a) A raw clinical observation	−1.1 Forge	Run `templates/research-question.md` in Mode A (forge a question from the spark), then continue −1.2 → −1.3 → −1.4 in order.
(b) An existing question / advanced protocol, pre-data	−1.2 Novelty	Run `templates/research-question.md` in Mode B (resume/refine — back-fill PECO, single Attack pass, FINER) first, then −1.2 novelty, then −1.3 design as an AUDIT of the existing protocol (not a fresh draft — check it against `templates/study-design.md`, fix gaps), then −1.4 prereg, then run `references/adversarial-review.md` in design-stage mode (§0, pre-data) BEFORE the pre-registration lock so cheap design fixes land before freezing.
(c) Question + design + data all locked	Skip to Phase 0	Pure writing-up. Still confirm the 💡 IDEA and 📊 DATA gates are human-owned and that a pre-registration exists or is consciously waived (and disclosed as such).

−1.2 novelty is the mandatory minimum entry for any unpublished study — novelty cannot be assumed from the fact that a protocol is already being written. Only path (c) (already locked + data in hand) may skip it.

Start the project's accountability ledger now: create log/human-loop-ledger.md from ~/.claude/skills/paper-writer/templates/human-loop-ledger.md and declare the autonomy mode (Manual / Co-pilot / Autopilot). Record every gate decision in it from here on.

Step −1.1: Forge the research question (💡 IDEA gate)

Read ~/.claude/skills/paper-writer/templates/research-question.md. From the user's clinical observation, generate 5–15 candidate questions, debate and rank them by FINER, evolve the top 2–3 — then stop and have the human select. AI never auto-selects the question. Output: one sharpened research question with its PICO.

Step −1.2: Novelty check (guardrail: anti-reinvention)

Read ~/.claude/skills/paper-writer/references/novelty-check.md. Run a live-literature sweep on the selected question using the real literature tools (PubMed MCP, OpenAlex, Europe PMC, Semantic Scholar — see Phase 1 plumbing). Classify the gap: genuinely novel / incremental / already-answered / contested. An already-answered question is killed here at near-zero cost. Do not inflate novelty — that is the Sakana v2 failure mode.

Step −1.3: Design the study & power it

Read ~/.claude/skills/paper-writer/templates/study-design.md. Choose the design, operationalize every PICO element into a measured variable, define the single primary outcome, map confounders with a DAG, and run a sample-size/power calculation (justify the effect size from the novelty-check literature, not from hope). Check feasibility against the clinic's real volume. This design becomes both the pre-registration and, later, the Methods section.

Step −1.4: Pre-register & lock (guardrail: anti-HARKing)

Read ~/.claude/skills/paper-writer/templates/preregistration.md. Freeze the hypotheses and the primary analysis plan (OSF / UMIN-CTR / jRCT / PROSPERO) before the 📊 DATA gate. After the lock: pre-registered analyses are confirmatory; everything else is exploratory and labeled as such. This is the integrity backbone for publishing under your own name. For retrospective data, register before examining outcome data and disclose the data's pre-existence honestly.

The 📊 DATA gate: only after the plan is locked does the human supply real, IRB-approved data. AI never originates data. Proceed to Phase 0.

Phase 0: Project Initialization

When the user invokes this skill, ask for:

Working title (can change later)
Paper type (Original Article / Case Report / Review / Letter / Systematic Review)
Target journal (optional but recommended)
Language (English / Japanese / Both)
Research question in one sentence
Key data available (what Tables/Figures already exist?)

Step 0.1: Capture Journal Requirements

If a target journal is specified, look up and document:

Word limits: total manuscript, abstract, each section (if specified)
Citation style: Vancouver, APA, NLM, or other
Required sections: some journals require separate Conclusion, others don't
Abstract format: structured or unstructured, word limit
Figure/Table limits: maximum number allowed
Reporting guideline: which checklist the journal requires
Special requirements: cover page format, line numbering, etc.
AI disclosure: whether the journal requires AI usage disclosure, and where (Methods, Acknowledgments, or dedicated section). See references/ai-disclosure.md.
Keywords: number required, MeSH preferred or free-text. See references/keywords-guide.md.
Graphical abstract: required or optional. See templates/graphical-abstract.md.

Use WebSearch to look up the journal's "Instructions for Authors" page.

Record all requirements in the README.md under a "Journal Requirements" section.

Step 0.2: Select Reporting Guideline

Based on paper type and study design, select the appropriate reporting guideline:

Study Type	Guideline	Reference
Randomized Controlled Trial	CONSORT 2025	`references/reporting-guidelines-full.md`
Observational study (cohort, case-control, cross-sectional)	STROBE	`references/reporting-guidelines-full.md`
Systematic review / meta-analysis	PRISMA 2020	`references/reporting-guidelines-full.md`
Case report	CARE	`references/reporting-guidelines-full.md`
Diagnostic accuracy study	STARD 2015	`references/reporting-guidelines-full.md`
Quality improvement study	SQUIRE 2.0	`references/reporting-guidelines-full.md`
Study protocol (clinical trial)	SPIRIT 2025	`references/reporting-guidelines-full.md`
Prediction model (incl. AI/ML)	TRIPOD+AI 2024	`references/reporting-guidelines-full.md`
Animal research	ARRIVE 2.0	`references/reporting-guidelines-full.md`
Health economics	CHEERS 2022	`references/reporting-guidelines-full.md`

Read ~/.claude/skills/paper-writer/references/reporting-guidelines.md (summary) or references/reporting-guidelines-full.md (comprehensive) and note the key checklist items for the selected guideline. These items will be checked throughout the writing process.

Step 0.3: Create Project Directory

For Original Article / Review / Letter / Systematic Review:

{project-dir}/
├── README.md                        # Project dashboard (status, timeline, links)
│
├── 00_literature/                   # Phase 1: Literature
│   ├── search-strategy.md           #   Search terms, databases, dates
│   ├── literature-matrix.md         #   Structured comparison table
│   └── key-papers/                  #   Notes on important papers (1 file per paper)
│
├── 01_outline.md                    # Phase 2: Paper skeleton
│
├── sections/                        # Phase 3: Manuscript sections (writing order)
│   ├── 02_methods.md
│   ├── 03_results.md
│   ├── 04_introduction.md
│   ├── 05_discussion.md
│   ├── 06_conclusion.md
│   ├── 07_abstract.md
│   └── 08_title.md
│
├── tables/                          # Tables (numbered: table1_baseline.md, ...)
├── figures/                         # Figures + captions (fig1_caption.md, ...)
├── supplements/                     # Supplementary materials
│   ├── supplementary-tables/        #   e.g., tableS1_sensitivity.md
│   ├── supplementary-figures/       #   e.g., figS1_subgroup.md
│   └── appendices/                  #   Additional methods, datasets, etc.
│
├── data/                            # Research data (see templates/data-management.md)
│   ├── raw/                         #   Original data (READ-ONLY, gitignored)
│   ├── processed/                   #   Cleaned, de-identified data
│   ├── analysis/                    #   Statistical output, scripts
│   └── data-dictionary.md           #   Variable definitions
│
├── ethics/                          # Ethics & regulatory
│   ├── irb-approval.md              #   IRB approval details, number, dates
│   ├── informed-consent.md          #   Consent process documentation
│   ├── protocol.md                  #   Study protocol (SPIRIT if applicable)
│   └── registration.md              #   Trial/study registration (UMIN, ClinicalTrials.gov)
│
├── submissions/                     # Submission history (1 subfolder per attempt)
│   └── v1_{journal}/                #   e.g., v1_bmj/
│       ├── compiled-manuscript.md   #     Full compiled manuscript snapshot
│       ├── cover-letter.md          #     Cover letter
│       ├── title-page.md            #     Title page
│       ├── declarations.md          #     Ethics, COI, funding, AI disclosure
│       ├── highlights.md            #     Key points (if required)
│       ├── graphical-abstract.md    #     Graphical abstract (if required)
│       └── submission-log.md        #     Date, portal, manuscript #, status
│
├── revisions/                       # Revision rounds (Phase 8)
│   └── r1/                          #   Round 1
│       ├── reviewer-comments.md     #     Original reviewer comments
│       ├── response-letter.md       #     Point-by-point response
│       ├── revision-cover-letter.md #     Revision cover letter
│       ├── diff-summary.md          #     Changes made (section, line, change)
│       └── compiled-manuscript.md   #     Revised manuscript snapshot
│
├── coauthor-review/                 # Co-author feedback tracking
│   ├── review-tracker.md            #   Who reviewed, when, status
│   └── feedback/                    #   Individual feedback files
│
├── correspondence/                  # Editor & reviewer communication log
│   └── YYYY-MM-DD_{subject}.md      #   e.g., 2026-03-05_decision-letter.md
│
├── references/                      # Reference management
│   └── 09_references.md             #   Formatted reference list
│
├── checklists/                      # Quality control
│   ├── section-quality.md           #   Per-section quality scores
│   ├── submission-ready.md          #   Pre-submission checklist
│   ├── reporting-guideline.md       #   CONSORT/STROBE/etc. item tracking
│   ├── gate-state.md                #   Stage-gate iteration state
│   └── feedback-*.md                #   Auto-generated gate feedback
│
└── log/                             # Decision & progress log
    ├── decisions.md                 #   Key decisions with rationale
    ├── meetings.md                  #   Meeting notes (co-authors, supervisor)
    └── timeline.md                  #   Milestone targets & actual dates

For Case Report:

{project-dir}/
├── README.md                        # Project dashboard
│
├── 00_literature/
│   ├── search-strategy.md
│   ├── literature-matrix.md
│   └── key-papers/
│
├── 01_outline.md
│
├── sections/
│   ├── 02_case.md                   # Case presentation (CARE structure)
│   ├── 03_introduction.md           # Introduction (why reportable)
│   ├── 04_discussion.md
│   ├── 05_abstract.md               # Abstract (CARE format)
│   └── 06_title.md                  # Title (must contain "case report")
│
├── tables/
├── figures/
├── supplements/
│   ├── supplementary-tables/
│   ├── supplementary-figures/
│   └── appendices/
│
├── data/
│   ├── raw/
│   ├── processed/
│   ├── analysis/
│   └── data-dictionary.md
│
├── ethics/
│   ├── irb-approval.md
│   ├── informed-consent.md          # Patient consent for publication
│   └── patient-perspective.md       # Patient's perspective (CARE item)
│
├── submissions/
│   └── v1_{journal}/
│       ├── compiled-manuscript.md
│       ├── cover-letter.md
│       ├── title-page.md
│       ├── declarations.md
│       └── submission-log.md
│
├── revisions/
│   └── r1/
│       ├── reviewer-comments.md
│       ├── response-letter.md
│       ├── diff-summary.md
│       └── compiled-manuscript.md
│
├── coauthor-review/
│   ├── review-tracker.md
│   └── feedback/
│
├── correspondence/
│   └── YYYY-MM-DD_{subject}.md
│
├── references/
│   └── 07_references.md
│
├── checklists/
│   ├── section-quality.md
│   ├── submission-ready.md
│   ├── reporting-guideline.md
│   ├── gate-state.md
│   └── feedback-*.md
│
└── log/
    ├── decisions.md
    ├── meetings.md
    └── timeline.md

Read ~/.claude/skills/paper-writer/templates/project-init.md with the Read tool and use it to generate README.md. For Case Reports, use project-init-case.md instead.

File numbering follows the recommended writing order, not the reading order. This is intentional.

Step 0.4: Organize Research Data

If the user has existing research data (clinical records, CSV files, statistical output, etc.):

Create data/raw/, data/processed/, data/analysis/ directories
Read ~/.claude/skills/paper-writer/templates/data-management.md for the full template
Ask the user to place raw data files in data/raw/ — these files are READ-ONLY from this point
Create data/raw/README.md documenting the data source, extraction date, and IRB information
Create data/data-dictionary.md listing all variables with types, ranges, and labels
Confirm de-identification status — if not yet de-identified, create a processing plan in data/processed/README.md

Security rules:

NEVER commit patient-identifiable data to git
Add data/raw/*.csv, data/raw/*.xlsx etc. to .gitignore if the repository is shared
Always confirm IRB approval number before proceeding with data analysis

Data flow: raw/ (never modify) → processed/ (clean, de-identify) → analysis/ (statistical output) → tables/ and figures/ (manuscript-ready)

Step 0.5: Data Analysis

If the user has quantitative data ready for analysis, Claude Code can execute Python scripts directly. Read ~/.claude/skills/paper-writer/templates/analysis-workflow.md for the full workflow.

Available analysis scripts:

Script	Purpose	Key Output
`scripts/table1.py`	Table 1 (baseline characteristics)	Markdown table with N, %, mean±SD, P values
`scripts/analysis-template.py`	Statistical analyses	Descriptive stats, t-test, logistic regression, survival
`scripts/forest-plot.py`	Forest plot (meta-analysis)	PNG + SVG

Workflow:

Inspect data: Load data/processed/cohort_final.csv, check shape, dtypes, missing values
Table 1: Run scripts/table1.py to generate baseline characteristics table → tables/table1.md
Primary analysis: Choose analysis type based on study design:
- Cross-sectional / case-control → logistic regression (OR with 95% CI)
- Cohort with time-to-event → survival analysis (Kaplan-Meier, log-rank)
- Continuous outcome → linear regression
- Group comparison → t-test / Mann-Whitney U
Subgroup & sensitivity analyses: By sex, age group, disease severity, etc.
Generate figures: Box plots, KM curves, forest plots, ROC curves
Link to manuscript: Map analysis output to Results section paragraphs

Analysis output directory: All results go to data/analysis/. Figures for the manuscript go to figures/.

Required Python packages: Install the utility-script dependencies from the skill root:

pip install -r ~/.claude/skills/paper-writer/requirements.txt

Statistical reporting requirements (before writing Results):

Effect sizes with 95% confidence intervals
P values to 3 decimal places (P < 0.001 for very small)
Statistical test names specified
Software and version documented
Two-sided tests (unless justified)
Multiple comparison correction (if >1 primary outcome)
Missing data handling described

See references/statistical-reporting-full.md for detailed SAMPL guidelines and templates/analysis-workflow.md for step-by-step commands.

Phase 1: Literature Search & Organization

Step 1.1: Define Search Strategy

Create 00_literature/search-strategy.md with:

Databases: PubMed, Google Scholar (always available); Scopus, CiNii (if user has institutional access)
Search terms: MeSH terms + free-text keywords
Inclusion/exclusion criteria for papers
Date range

How to search — use REAL literature tools, not plain web search.

This skill runs in an environment with a real PubMed MCP and research APIs. These return structured, verifiable records (PMID, DOI, authors, abstract) — use them as the primary path. Plain WebSearch is a fallback, not the default.

Primary: PubMed MCP (biomedical, authoritative). Build the query with references/pubmed-query-builder.md, then:

mcp__claude_ai_PubMed__search_articles — run the MeSH + free-text query
mcp__claude_ai_PubMed__get_article_metadata — pull structured metadata per PMID
mcp__claude_ai_PubMed__find_related_articles — snowball from a key seed paper
mcp__claude_ai_PubMed__lookup_article_by_citation — resolve a citation to a PMID/DOI
mcp__claude_ai_PubMed__get_full_text_article — fetch full text where available

Supplementary APIs (broader coverage; fetch via WebFetch / firecrawl_scrape / tavily_search):

OpenAlex — https://api.openalex.org/works?search=... (filter by year, cited_by_count)
Europe PMC — https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=...&format=json (full text, preprints)
Semantic Scholar — https://api.semanticscholar.org/graph/v1/paper/search?query=... (citation graph, influential-citation counts)
Cochrane / PROSPERO / Epistemonikos — check for existing or in-progress systematic reviews

Why this matters: structured-record retrieval means every paper carries a real PMID/DOI, so the "is this citation fabricated?" risk drops sharply versus free-text web search. Still verify per references/citation-verification.md.

Workflow:

Ask the user for their 3–5 key papers (they usually know them) — use these as snowball seeds for find_related_articles
Run the PubMed MCP query; supplement with OpenAlex / Europe PMC / Semantic Scholar for non-PubMed and preprint coverage
De-duplicate by DOI; have the user validate the final list for completeness
Verify every citation resolves to a real record (references/citation-verification.md)

Step 1.2: Build Literature Matrix

Read ~/.claude/skills/paper-writer/templates/literature-matrix.md with the Read tool.

For each relevant paper found, extract and organize:

Author (Year)	Design	N	Population	Key Finding	Limitation	Relevance

Aim for 15-30 papers for an original article, 8-15 for a case report, 30-50 for a systematic review.

Step 1.3: Identify Key Papers

For the 3-5 most important papers, create individual notes in 00_literature/key-papers/ with:

Full citation
Study design and quality assessment
Key results with exact numbers
How it relates to the current paper
What gap it leaves (that our paper addresses)

Phase 1.5: Screening Execution (Systematic Review only)

Applies only to Systematic Reviews. Skip for all other paper types.

Phase 1 builds a search; Phase 3-D writes the PRISMA Methods/Results. Between them sits the actual study selection — dedup, dual screening, and the record counts that fill the PRISMA flow diagram. This phase runs that pipeline.

Read ~/.claude/skills/paper-writer/templates/sr-screening-pipeline.md with the Read tool for the full procedure. In brief:

Prerequisite — registered protocol. Eligibility criteria must exist in 00_literature/protocol.md (from templates/sr-prospero.md) and the protocol must be registered (PROSPERO) BEFORE screening. Do not start otherwise.

Stage 1 — De-duplicate (deterministic). Place raw DB exports in 00_literature/screening/00_imported/ (one file per database), then run:

python ~/.claude/skills/paper-writer/scripts/sr-dedup.py \
  --input 00_literature/screening/00_imported \
  --output 00_literature/screening/01_deduplicated.csv \
  --counts 00_literature/screening/counts/identification.json

Stage 2 — Title/Abstract screening (DUAL). Spawn two independent screener passes (Agent tool, or team mode) that cannot see each other's decisions; each judges include/exclude/unclear against protocol.md only. Reconcile into 02_title_abstract_screen.csv; surface every conflict to the user. An LLM is one arm of a dual review, never the sole arbiter.
Stage 3 — Full-text screening (DUAL). Link PDFs to records, then run two independent full-text passes:
```
python ~/.claude/skills/paper-writer/scripts/sr-pdf-link.py \
  --pdfs 00_literature/screening/full-texts \
  --records 00_literature/screening/02_title_abstract_screen.csv \
  --include-only --rename
```
Every full-text exclude carries a PRISMA reason category. Write 03_fulltext_screen.csv; the human resolves all conflicts.
Stage 4 — Extraction hand-off. For each included study, create one extraction/{record_id}.md from templates/sr-data-extraction.md (dual, no guessing — NR/N/A only).

Produce PRISMA numbers (deterministic).

python ~/.claude/skills/paper-writer/scripts/sr-prisma-count.py \
  --identification 00_literature/screening/counts/identification.json \
  --ta 00_literature/screening/02_title_abstract_screen.csv \
  --ft 00_literature/screening/03_fulltext_screen.csv \
  --output 00_literature/screening/counts/prisma-summary.md

Copy the counts into templates/sr-prisma-flow.md and the Cohen's κ values into the Methods selection-process paragraph (Phase 3-D, item 5).

Team mode: the two screening passes per stage are naturally parallel — run them as two concurrent agents, each given only protocol.md + the records, then reconcile. κ < 0.6 means the criteria are ambiguous: revise protocol.md and re-screen rather than proceeding.

Phase 2: Outline

Create 01_outline.md with the paper skeleton.

Read ~/.claude/skills/paper-writer/references/imrad-guide.md with the Read tool for the detailed IMRAD structure. For Case Reports, this guide does not apply directly — use the CARE structure instead.

The outline should specify:

Each section's key points (bullet list)
Which papers support which points
Which Tables/Figures go where
The story arc: Background Problem → Gap → Our Approach → Findings → Implications
For Case Reports: Background → Why Reportable → Case Details → Clinical Lesson

Get user approval on outline before proceeding to drafting.

Phase 2.5: Tables & Figures

Read ~/.claude/skills/paper-writer/references/tables-figures-guide.md with the Read tool.

Tables and figures are the backbone of a paper — many reviewers look at the abstract, then the tables/figures, before reading the text. Design them before writing prose so the text can reference them naturally.

Step 2.5.1: Plan Tables & Figures

Based on the outline, determine:

Which data belongs in a table vs. a figure vs. the text
Table 1 is almost always "Baseline Characteristics" (use the template in references/tables-figures-guide.md)
How many tables/figures are allowed by the journal (check Phase 0 requirements)

Step 2.5.2: Create Tables

Create table files in tables/ directory:

table1_baseline.md — Baseline characteristics (standard format)
table2_*.md — Additional tables as needed (regression results, outcomes, etc.)

Rules:

Title above the table
No vertical lines (horizontal lines only)
Consistent decimal places within each column
Footnotes for abbreviations and statistical tests
Total sample size in the header row

Step 2.5.3: Plan Figures

Create caption files in figures/ directory:

fig1_caption.md — Often a flow diagram (CONSORT/PRISMA) or study design
fig2_caption.md — Key result visualization

Rules:

Captions must be self-explanatory without reading the main text
Include key statistics in captions
Specify resolution requirements (300+ DPI for print, 600+ for line art)
Use colorblind-friendly palettes

Step 2.5.4: Graphical Abstract (if required)

If the journal requires or encourages a graphical abstract, read ~/.claude/skills/paper-writer/templates/graphical-abstract.md and plan the visual summary.

Get user review on table/figure plan before proceeding to drafting.

Phase 3: Drafting

The writing order is intentional and produces better papers. Follow it strictly.

3-A: Original Article Workflow

Step 3.1: Methods & Results (Write as a pair)

Read ~/.claude/skills/paper-writer/templates/methods.md and ~/.claude/skills/paper-writer/templates/results.md with the Read tool.

Methods rules:

Reproducibility is everything
Include: study design, patients/subjects, data collection, statistical analysis, ethics
Every method must have a corresponding result

Results rules:

Facts only, no interpretation
No references to other studies
Every Table/Figure must be mentioned in text
Methods ↔ Results must correspond 1:1

Write sections/02_methods.md and sections/03_results.md together, ensuring perfect correspondence. Cross-check: every subsection in Methods must map to a corresponding subsection in Results, and vice versa.

Workflow: Write Methods subsection 1 → Results subsection 1 → Methods subsection 2 → Results subsection 2 → ... This interleaving ensures 1:1 correspondence.

Step 3.2: Introduction (Paragraph 3) & Conclusion (Write as a pair)

Read ~/.claude/skills/paper-writer/templates/introduction.md and ~/.claude/skills/paper-writer/templates/conclusion.md with the Read tool.

Why write Paragraph 3 first? The study objective (Introduction P3) and the conclusion must mirror each other. Writing them together guarantees alignment. Paragraphs 1-2 provide background that funnels toward the objective — they are easier to write once the objective is locked.

Introduction structure (3 paragraphs):

General background (everyone agrees with this)
Clinical question / knowledge gap (but we don't know X)
Study objective (therefore, we investigated...)

Conclusion rules:

Must directly answer the objective stated in Introduction paragraph 3
One core message
Brief and direct

Write the final paragraph of sections/04_introduction.md and sections/06_conclusion.md together to ensure they mirror each other.

Step 3.3: Discussion

Read ~/.claude/skills/paper-writer/templates/discussion.md with the Read tool.

Discussion structure:

Summary of main findings 2-N. Comparison with prior literature (use 00_literature/literature-matrix.md) N+1. Limitations — read ~/.claude/skills/paper-writer/templates/limitations-guide.md for categories, templates, and bilingual examples N+2. Clinical implications / future directions

Discussion rules:

No new results
No excessive speculation
Support every claim with a reference
Keep it focused
Limitations subsection is mandatory — be specific about direction of bias and mitigation

Step 3.4: Introduction (Paragraphs 1-2)

Now write paragraphs 1-2 of sections/04_introduction.md. The background should funnel toward the research question already written in paragraph 3.

Step 3.5: Abstract

Read ~/.claude/skills/paper-writer/templates/abstract.md with the Read tool.

Write sections/07_abstract.md as a structured abstract:

Background/Objective (1-2 sentences)
Methods (2-3 sentences)
Results (3-4 sentences)
Conclusions (1-2 sentences)

Check the journal-specific word limit captured in Phase 0. The Abstract must be consistent with the full text. Cross-check all numbers.

Step 3.6: Title

Write sections/08_title.md with 3-5 title candidates. Evaluate each against:

Specific (what was studied?)
Concise (< 15 words ideal)
Contains keywords (searchable)
No conclusion spoilers

Get user approval on final title.

3-B: Case Report Workflow

Step 3.1-CR: Case Presentation

Read ~/.claude/skills/paper-writer/templates/case-report.md with the Read tool.

Write 02_case.md following the CARE structure:

Patient information (demographics, history)
Clinical findings
Timeline (consider a timeline figure)
Diagnostic assessment
Therapeutic intervention
Follow-up and outcomes
Patient perspective (CARE item 10) — when possible, include the patient's own experience in their words

Rules:

Chronological order
Only clinically relevant details
Document informed consent for publication
Report both positive AND negative findings
Patient perspective strengthens the report and is recommended by CARE guidelines

Step 3.2-CR: Discussion

Read ~/.claude/skills/paper-writer/templates/discussion.md with the Read tool.

Write 04_discussion.md:

Why this case is significant (clinical lesson)
Comparison with published literature
Limitations of the case
Clinical implications

Keep it focused and shorter than in an Original Article.

Step 3.3-CR: Introduction

Read ~/.claude/skills/paper-writer/templates/case-introduction.md with the Read tool.

Write 03_introduction.md:

Brief background on the condition
Why this case is reportable (rarity, novelty, instructive value)
Optional: "We report a case of... to highlight..."

Write the Introduction AFTER the Case section — you need to know the full case to justify its reporting.

Step 3.4-CR: Abstract

Read ~/.claude/skills/paper-writer/templates/case-abstract.md with the Read tool.

Write 05_abstract.md using the CARE abstract structure:

Background (1-2 sentences: why this case is worth reporting)
Case Presentation (3-5 sentences: demographics, findings, diagnosis, treatment, outcome)
Conclusions (1-2 sentences: clinical lesson)

Do NOT use Methods/Results structure for Case Report abstracts.

Step 3.5-CR: Title

Write 06_title.md with 3-5 title candidates. For case reports:

Title MUST contain "case report" (CARE requirement)
Include the diagnosis or key finding
Example: "Successful treatment of severe pediatric asthma with dupilumab: a case report"

Get user approval on final title.

3-C: Review Article Workflow

Review articles synthesize existing literature on a topic. The structure is thematic rather than IMRAD.

Step 3.1-RA: Thematic Sections

Read ~/.claude/skills/paper-writer/templates/discussion.md for general writing guidance.

Organize the body into thematic sections based on the outline. Common structures:

Chronological: Evolution of understanding over time
Thematic: Grouped by subtopic (most common)
Methodological: Grouped by study approach

Each section should:

Synthesize findings across studies (not just summarize one at a time)
Identify areas of consensus and controversy
Highlight gaps in the literature
Use the literature matrix to ensure comprehensive coverage

Step 3.2-RA: Introduction

Write the introduction:

Scope and importance of the topic
Why a review is needed now (new evidence, controversy, emerging field)
Objectives and scope of this review

Step 3.3-RA: Conclusion & Future Directions

Write the conclusion:

Synthesize the key themes identified
Current state of knowledge
Gaps and future research directions
Clinical implications (if applicable)

Step 3.4-RA: Abstract

Write an unstructured abstract (unless journal requires structured format):

Purpose of the review
Methods (databases searched, date range, selection criteria)
Key findings synthesized across themes
Conclusions

Step 3.5-RA: Title

Write title candidates. For review articles:

Include "review", "narrative review", or "scoping review" in the title
Clearly state the topic
Example: "Artificial intelligence in diagnostic radiology: a narrative review"

Get user approval on final title.

3-D: Systematic Review Workflow

Read ~/.claude/skills/paper-writer/templates/sr-outline.md with the Read tool for the complete PRISMA 2020-compliant template.

Systematic reviews follow a strict, pre-registered protocol. The template provides the full structure with PRISMA 2020 checklist item numbers.

Step 3.1-SR: Methods

The Methods section is the most critical part. Write it following PRISMA items P-5 through P-18:

Protocol and registration (PROSPERO ID)
Eligibility criteria (PICO/PECO)
Information sources (databases, dates)
Search strategy (full strategy in supplementary)
Selection process (screening, inter-rater reliability)
Data collection process
Data items
Risk of bias assessment (tool selection)
Effect measures
Synthesis methods (narrative and/or meta-analysis)
Subgroup and sensitivity analyses
Reporting bias assessment
Certainty of evidence (GRADE)

Step 3.2-SR: Results

Write Results following PRISMA items P-19 through P-23:

PRISMA flow diagram (Figure 1 — mandatory)
Study characteristics table
Risk of bias summary
Results of individual studies
Results of syntheses (forest plots if meta-analysis)
Reporting biases (funnel plots if ≥10 studies)
Certainty of evidence (GRADE Summary of Findings table)

Step 3.3-SR: Discussion

Write Discussion following PRISMA items P-25 through P-27:

Summary of evidence with certainty levels
Comparison with previous reviews
Strengths and limitations (both evidence and review process)
Implications for practice and research

Step 3.4-SR: Introduction, Abstract, Title

Follow the same principles as Original Article but with SR-specific framing:

Introduction: justify why this SR is needed (no existing SR, outdated SR, new evidence)
Abstract: must include number of studies, total participants, key pooled estimates
Title: must include "systematic review" (and "meta-analysis" if applicable)

Get user approval on final title.

3-E: Letter / Short Communication Workflow

Letters and short communications follow a condensed IMRAD format. The key constraint is the word limit (typically 600-1500 words).

Step 3.1-LT: Condensed Draft

Write a single file covering all sections:

Introduction (1-2 sentences): State the purpose directly. No lengthy background.
Methods (1 paragraph): Essential details only. Reference a fuller description elsewhere if needed.
Results (1-2 paragraphs): Key findings only. Usually 1 table OR 1 figure (not both).
Discussion (1-2 paragraphs): Main interpretation, 1-2 comparisons with literature, key limitation.

Rules:

Every word counts — eliminate all filler
Typically limited to 1 table + 1 figure, or 2 of one type
References usually limited to 10-15
No separate Conclusion section (fold into last Discussion paragraph)

Step 3.2-LT: Abstract

Write a brief abstract (often 100-150 words, unstructured).

Step 3.3-LT: Title

Short, direct titles work best. No need for elaborate structure.

Get user approval on final title.

Phase 4: Humanize

Read ~/.claude/skills/paper-writer/references/humanizer-academic.md with the Read tool.

After drafting, run a humanization pass on every section to remove AI-generated writing patterns.

Step 4.1: Scan for AI Patterns

Read each section file and identify:

English papers — check for these 18 patterns:

Significance inflation ("pivotal", "evolving landscape", "underscores")
Notability claims ("landmark", "renowned", "groundbreaking")
Superficial -ing analyses ("highlighting", "underscoring", "showcasing")
Promotional language ("profound impact", "remarkable", "dramatic")
Vague attributions ("Studies have shown", "Experts argue")
Formulaic challenges ("Despite challenges... future outlook")
AI vocabulary ("Additionally", "crucial", "delve", "landscape", "pivotal")
Copula avoidance ("serves as" instead of "is")
Negative parallelisms ("Not only... but also")
Rule of three overuse (forcing ideas into groups of three)
Synonym cycling ("Patients... Participants... Subjects")
False ranges ("from X to Y" on unrelated scales)
Em dash overuse
Title Case in headings
Curly quotation marks
Filler phrases ("In order to", "It is important to note", "comprehensive investigation")
Excessive hedging ("may suggest... have the potential to")
Generic positive conclusions ("The future looks bright")

Japanese papers (日本語) — Check 13 patterns (A–C) + AI vocabulary list (D):

A. Symbols and notation (3 patterns):

Em dashes, heavy use of quotation marks, too many parenthetical asides

B. Sentence rhythm (3 patterns):

Consecutive identical endings (である。である。である。)
Too many conjunctions (さらに、また、加えて)
Every paragraph ends with a clean closure

C. Problems specific to academic writing (7 patterns):

C-1 Too many hedges (permanent escape routes)
C-2 Unsupported evaluative terms (非常に有効、大きなメリット)
C-3 Pushing through with abstract words alone
C-4 AI vocabulary (包括的、革新的、シームレス、示唆に富む)
C-5 Repeated rephrasing with synonyms
C-6 Excessive use of passive voice (検討が行われた → 検討した)
C-7 Mixing in non-academic style (「参考になれば幸いである」「ポイントは以下の通り」→ delete)

D. AI vocabulary list: references/humanizer-academic.md See section D of the Japanese version. Vocabulary list used for pattern judgment in C-4.

Step 4.2: Rewrite

Consult references/humanizer-academic.md for specific before/after examples. For each identified pattern:

Replace with precise, specific academic language
Preserve all data, statistics, and citations exactly
Use simple constructions ("is" over "serves as")
Remove filler and reduce hedging to match evidence strength
Ensure consistent terminology throughout
If 3+ AI patterns appear in one sentence, rewrite the entire sentence rather than fixing patterns individually

Step 4.3: Section-Specific Focus

English:

Section	Priority Patterns
Introduction	#1 Significance inflation, #5 Vague attributions, #7 AI vocabulary, #3 -ing analyses
Methods	#16 Filler phrases, #8 Copula avoidance
Results	#3 -ing analyses, #4 Promotional language
Discussion	#17 Excessive hedging, #6 Formulaic challenges
Conclusion	#18 Generic conclusions, #1 Significance inflation
Abstract	ALL patterns (most visible section)

Japanese:

Section	Key patterns
Introduction	C-2 Unsupported evaluative terms, B-2 Too many conjunctions
Methods	C-6 Excessive use of passive voice, C-3 Abstract words
Results	B-1 Identical endings, A-3 Heavy use of parentheses
Discussion	C-1 Too many hedges, C-4 AI vocabulary
Conclusion	C-2 Unsupported evaluative terms, C-7 Non-academic style
Abstract	All patterns

Step 4.4: Verify

After humanization:

English:

Scientific content unchanged (no data or citations lost)
No "Additionally" / "Furthermore" at sentence start (max 1 per section)
No "pivotal" / "crucial" / "landscape" / "delve"
No "-ing" phrases tacked on for fake depth
No "serves as" / "stands as" (use "is")
Em dashes used sparingly (< 2 per page)
Consistent terminology (no synonym cycling)
Sentence rhythm varies (short and long sentences mixed)
No generic conclusions remaining
Hedging proportionate to evidence strength

Japanese:

No repeated use of 「さらに」「また」「加えて」 (at most once per section)
The same ending does not continue three or more times
No unsupported 「非常に」「大きな」
No excessive use of passive voice (rewrite in active voice)
No formulaic closing phrases (e.g., 「参考になれば幸いである」)
Not pushing through with abstract words alone
Not overusing quotation marks

Phase 5: References

Read ~/.claude/skills/paper-writer/references/citation-guide.md with the Read tool.

Build references/09_references.md (or references/07_references.md for Case Reports):

Collect all cited papers from all sections
Format according to target journal style captured in Phase 0 (Vancouver, APA, etc.)
Number sequentially as cited
Verify completeness: every reference is cited in text, every citation has a reference entry
Verify authenticity: For EVERY AI-suggested reference, confirm the paper exists against a structured record — mcp__claude_ai_PubMed__lookup_article_by_citation or mcp__claude_ai_PubMed__get_article_metadata (by PMID/DOI), falling back to CrossRef (https://api.crossref.org/works/{DOI}) and WebSearch on the exact title for non-PubMed sources. AI frequently fabricates plausible-sounding citations; a citation that does not resolve to a real PMID/DOI is removed or replaced. See references/citation-verification.md.

Phase 6: Quality Review

Read ~/.claude/skills/paper-writer/references/section-checklist.md with the Read tool. For Case Reports, also check the CARE-specific items in templates/case-report.md.

Run the quality checklist against each section. Update checklists/section-quality.md with results.

Verification checklist:

Methods ↔ Results correspondence (Original Article only)
Introduction objective ↔ Conclusion answer
All Tables/Figures mentioned in text
No interpretation in Results (Original Article only)
No new results in Discussion
Abstract numbers match full text
All references cited and formatted
Word count within target journal limits (check Phase 0 requirements)
Reporting guideline followed (check Phase 0 selected guideline)
AI writing patterns removed (Phase 4 verification passed)
Consistent terminology throughout all sections
Ethics approval and informed consent documented

Phase 6.5: Adversarial Review (red-team the claim)

Before any journal's red team sees the paper, run your own. Quality Review (Phase 6) checks that the manuscript is internally consistent and well-formatted. This phase checks something different and harder: is the central claim actually true and supported? It is the corrective to the Sakana v2 failure mode (nothing in that loop tried to make the paper fail, so hallucinations and novelty inflation shipped).

Read ~/.claude/skills/paper-writer/references/adversarial-review.md. Run a hostile internal panel that attacks the central claim from four angles, plus a "steelman the null" pass:

Statistical reviewer — p-hacking, multiplicity, power, post-hoc subgroups; does every confirmatory claim trace to the pre-registered plan (templates/preregistration.md)?
Methodological reviewer — confounding, selection/information bias, the DAG; is each causal-sounding claim supported by the design?
Novelty reviewer — re-attack the novelty claim against references/novelty-check.md; has a larger/better study already shown this?
Integrity / clinical reviewer — every number traces to raw data (📊 gate), citations are real, no overclaiming, no clinical harm if a reader acts on the conclusion.
Steelman the null — argue as hard as possible that the finding is chance, confounding, or bias; does the paper already answer that argument?

Verdict: KILL (claim not supported → return to Phase −1 Discovery; this is the system working, not a failure) / MAJOR / MINOR / PASS. The human owns the final KILL/PASS adjudication (💡 gate) — the AI panel advises. Record the verdict in log/human-loop-ledger.md. Only a PASS proceeds to Pre-Submission.

In team mode, run the four reviewers as four parallel paper-red-team agents (opus, distinct lenses) and synthesize the verdict. A KILL or MAJOR loops back: fix the affected sections, then re-run Phase 4 (Humanize) and Phase 6 (Quality) before re-entering Phase 6.5.

Phase 7: Pre-Submission

Read ~/.claude/skills/paper-writer/templates/cover-letter.md and ~/.claude/skills/paper-writer/templates/submission-ready.md with the Read tool.

Create:

Title page — read ~/.claude/skills/paper-writer/templates/title-page.md for the template (running head, all authors with ORCID, affiliations, word counts, corresponding author, clinical trial registration)
Highlights / Key Points — read ~/.claude/skills/paper-writer/templates/highlights.md and create the appropriate summary box for the target journal (JAMA Key Points, BMJ "What is known", Elsevier Highlights, Lay Summary, etc.)
Acknowledgments — read ~/.claude/skills/paper-writer/templates/acknowledgments.md and draft (non-author contributions, AI tool disclosure, patient acknowledgment)
Declarations — read ~/.claude/skills/paper-writer/templates/declarations.md and complete (Ethics, COI using references/coi-detailed.md, Funding, Data Availability, AI Disclosure, CRediT)
Cover letter using the template
checklists/submission-ready.md using the template — fill in journal-specific limits from Phase 0
Compile all sections into a single reading-order Markdown file → submissions/v1_{journal}/compiled-manuscript.md
Create submissions/v1_{journal}/submission-log.md with submission date, portal, manuscript ID
Log the submission in log/timeline.md

Final compilation order (reading order):

For Original Article:

Title → Abstract → Introduction → Methods → Results → Discussion → Conclusion → References

For Case Report:

Title → Abstract → Introduction → Case Presentation → Discussion → References

The compiled file should include all section content in sequence. Tables and Figures should be referenced but kept in their separate folders. All submission documents go into submissions/v1_{journal}/.

Phase 8: Revision (Post-Review)

When the user receives reviewer comments (peer review, editorial decision letter):

Step 8.1: Organize Reviewer Comments

Create revisions/r1/reviewer-comments.md:

Parse the decision letter and reviewer comments
Number each comment sequentially (R1-1, R1-2, R2-1, R2-2, etc.)
Categorize each comment:
- Must fix: Factual errors, missing data, methodological concerns
- Should fix: Reasonable suggestions that improve the paper
- Consider: Optional suggestions, stylistic preferences
- Rebut: Comments based on misunderstanding (requires polite explanation)

Step 8.2: Create Response Letter

Create revisions/r1/response-letter.md:

For each comment, use this format:

**Comment R1-1:** [Quote the reviewer's comment]

**Response:** [Your response]

**Changes made:** [Specific changes with page/line numbers, or explanation if no change]

Rules for response letters:

Thank the reviewer for constructive feedback (once at the beginning, not per comment)
Be specific about what was changed and where
For rebuttals, acknowledge the reviewer's perspective, then explain with evidence
Never be defensive or dismissive
If a change was not made, explain why with references or data

Step 8.3: Implement Revisions

Track which sections need modification based on reviewer comments
Make changes in the relevant section files
Mark changed text (many journals require highlighted changes or a diff)
Roll back affected phases: re-run Humanize (Phase 4) and Quality Review (Phase 6) on modified sections
Update word counts and verify journal limits are still met

Step 8.4: Verify Revision Completeness

Every reviewer comment has a response
Every "Must fix" and "Should fix" item has been addressed
Rebuttals are supported by evidence
Changed text is marked/highlighted
References updated if new citations added
Abstract updated if results or conclusions changed
Cover letter for resubmission drafted

Phase 9: Post-Acceptance

Read ~/.claude/skills/paper-writer/templates/proof-correction.md with the Read tool.

After acceptance, the corresponding author receives galley proofs. This is the LAST opportunity to correct errors.

Step 9.1: Proof Review

When proofs arrive (typically 2-8 weeks after acceptance, turnaround: 24-72 hours):

Critical checks:

Author names, affiliations, and ORCID — correct?
Abstract numbers match main text?
All tables — data values correct, no transposition errors?
All figures — correct images, acceptable quality?
Reference list — complete, correct numbering?
Corresponding author email — correct?
Funding and COI statements — accurate?
Clinical trial registration number — present?

NOT allowed at proof stage:

Rewriting sentences or paragraphs
Adding new data, references, or authors
Changing conclusions

Step 9.2: Submit Corrections

Use the journal's proofing system (Proof Central, CATS, eProofing, or direct PDF return). For each correction: state page, column, line, and exact change.

Step 9.3: Post-Publication

After publication:

Verify the final published version matches the accepted manuscript
Share via institutional repository (Green OA) if applicable — see references/open-access-guide.md
Update clinical trial registry with results (if applicable) — see references/clinical-trial-registration.md
Share with co-authors and collaborators

Phase 10: Rejection & Resubmission

Read ~/.claude/skills/paper-writer/references/desk-rejection-prevention.md and references/journal-reformatting.md with the Read tool.

Step 10.1: Assess the Rejection

Decision	Action
Desk rejection (scope)	Reformat and submit to next journal immediately
Desk rejection (quality)	Revise manuscript, then reformat and submit
Peer review rejection	Read reviews carefully; major revision before next journal
Reject with encouragement to resubmit	Treat as major revision; address all comments

Step 10.2: Quick Reformat

Use references/journal-reformatting.md checklist:

Change reference format (use reference manager)
Restructure abstract with new headings — see references/abstract-formats.md
Adjust word count — see references/word-count-limits.md
Add/remove special sections (Key Points, Highlights)
Reformat title page
Write new cover letter (address new editor by name)
Verify no mention of previous journal name in manuscript

Step 10.3: Cascading Submission Strategy

Track submissions:

Journal	Submitted	Decision	Turnaround	Next Action
[Journal 1]	YYYY-MM-DD	—	—	—

Plan cascade: Reach journal → Target journal → Safety journal → Backup journal.

Section-Specific AI Guidelines

What AI Should Do

Section	AI Role
Literature search	Search, organize, summarize — user validates relevance
Methods	Draft based on user's data description — user verifies accuracy
Results	Structure and format — user provides the actual data
Case (Case Report)	Structure chronologically — user provides clinical details
Introduction	Draft background from literature — user refines narrative
Discussion	Suggest comparisons with literature — user controls interpretation
Abstract	Generate from full text — user ensures accuracy
References	Format and organize — user verifies completeness and authenticity

What AI Should NOT Do

Fabricate data or statistics
Invent citations (always verify with WebSearch)
Write Results without user-provided data
Write Case Presentation without user-provided clinical details
Make clinical recommendations beyond the data
Skip the user approval step at outline and title phases

Status Tracking

Update README.md status after each phase. Use these status values:

Not Started: Phase not begun
In Progress: Phase actively being worked on (add details in Notes)
Draft Complete: First draft finished, pending review
Done: Phase completed and reviewed

Use the appropriate status tracker based on paper type:

Original Article:

Phase	Status	Last Updated
Literature Search	Not Started	-
Outline	Not Started	-
Tables & Figures	Not Started	-
Methods & Results	Not Started	-
Introduction & Conclusion	Not Started	-
Discussion	Not Started	-
Abstract	Not Started	-
Title & Keywords	Not Started	-
Humanize	Not Started	-
References	Not Started	-
Declarations	Not Started	-
Quality Review	Not Started	-
Pre-Submission	Not Started	-

Case Report:

Phase	Status	Last Updated
Literature Search	Not Started	-
Outline	Not Started	-
Tables & Figures	Not Started	-
Case Presentation	Not Started	-
Discussion	Not Started	-
Introduction	Not Started	-
Abstract	Not Started	-
Title & Keywords	Not Started	-
Humanize	Not Started	-
References	Not Started	-
Declarations	Not Started	-
Quality Review	Not Started	-
Pre-Submission	Not Started	-

Review Article:

Phase	Status	Last Updated
Literature Search	Not Started	-
Outline	Not Started	-
Tables & Figures	Not Started	-
Thematic Sections	Not Started	-
Introduction	Not Started	-
Conclusion & Future Directions	Not Started	-
Abstract	Not Started	-
Title & Keywords	Not Started	-
Humanize	Not Started	-
References	Not Started	-
Declarations	Not Started	-
Quality Review	Not Started	-
Pre-Submission	Not Started	-

Systematic Review:

Phase	Status	Last Updated
Literature Search	Not Started	-
Outline	Not Started	-
Tables & Figures	Not Started	-
Methods (PRISMA)	Not Started	-
Results (PRISMA)	Not Started	-
Discussion	Not Started	-
Introduction	Not Started	-
Abstract	Not Started	-
Title & Keywords	Not Started	-
Humanize	Not Started	-
References	Not Started	-
Declarations	Not Started	-
Quality Review	Not Started	-
Pre-Submission	Not Started	-

Letter / Short Communication:

Phase	Status	Last Updated
Literature Search	Not Started	-
Outline	Not Started	-
Tables & Figures	Not Started	-
Condensed Draft	Not Started	-
Abstract	Not Started	-
Title & Keywords	Not Started	-
Humanize	Not Started	-
References	Not Started	-
Quality Review	Not Started	-
Pre-Submission	Not Started	-

Resuming a Project

When the user invokes this skill on an existing project directory:

Read README.md to understand current status, paper type, target journal, and research question
Scan section files to assess actual content state:
- Read each section file that shows "In Progress" or "Draft Complete"
- Check word count and completeness (empty sections, TODO markers, partial drafts)
- Compare actual file state with the status tracker — the files are the source of truth
Present a summary to the user: "Here is where we left off: [status]. The next step is [phase]. Shall I continue?"
Check for workflow updates: Compare the README status table against the canonical phase list above. If phases are missing (e.g., old project created before "Humanize" was added), add them with "Not Started" status and inform the user
Resume from the next incomplete phase
Update status tracker

Handling Mid-Project Changes

Changing target journal: If the user wants to change the target journal:

Update README.md Paper Info and Journal Requirements
Re-check: citation style, word limits, abstract format, reporting guideline
Reformat references if citation style changed
Check word counts against new limits
Update cover letter

Adding data or revisions: If the user has new data or reviewer feedback:

Identify which sections are affected
Roll back affected phases to "In Progress"
Re-run from that phase forward (including Humanize and Quality Review)

Language Support

English Papers

Use standard academic English
Follow target journal's style guide
Flag awkward phrasing for user review

Japanese Papers

IMRAD format is the same as for English papers (exception for Case Reports: CARE format)
Use the 「である」 style, not 「です・ます」
Technical terms in Japanese in principle (with English given at first mention)
For case reports, use standard headings such as 「症例提示」「臨床経過」
If a separate guide on how to write papers exists, refer to it

Team Mode

If the user instructs 「チームで」「team mode」「並列で」, execute each phase with parallel agents to greatly speed things up.

Team composition

Agent	Role	Agent definition	Model
Literature search	Parallel paper search by database	`~/.claude/agents/paper-lit-searcher.md`	sonnet
Table/figure design	Parallel design of tables and figures	`~/.claude/agents/paper-table-figure-planner.md`	sonnet
Section writing	General section writing	`~/.claude/agents/paper-section-drafter.md`	sonnet
Humanizer	AI writing style pattern removal	`~/.claude/agents/paper-humanizer.md`	haiku
References	Citation collection and verification	`~/.claude/agents/paper-ref-builder.md`	sonnet
Section Review	Section quality check	`~/.claude/agents/paper-section-reviewer.md`	sonnet
Quality gate	Final verification of cross-sectional consistency	`~/.claude/agents/paper-quality-gate.md`	opus
Red Team	Adversarial scientific review of the central claim (Phase 6.5)	`~/.claude/agents/paper-red-team.md`	opus

Phase-specific team workflow

Phase 0, 2: Sequential execution (no changes)

Since interaction with the user is required, execute with the existing flow.

Phase 1: Literature search (parallel x3)

paper-lit-searcher を3つIn parallellaunch from the Agent tool:

Agent A: PubMed search (using MeSH terms)
Agent B: Google Scholar search (free text)
Agent C: Review of key papers provided by the user + domain-specific databases (CiNii, EMBASE, etc.)

After the 3 agents complete, the lead merges the results and 00_literature/literature-matrix.md is created (deduplication).

Phase 2.5: Tables and figures (parallel x2)

paper-table-figure-planner を2つIn parallellaunch:

Agent A: Table design (tables/ output to)
Agent B: Figure design (figures/ output to)

Phase 3: Drafting (group parallel)

paper-section-drafter are executed in rounds based on dependencies.

For Original Article:

Round 1: Methods + Results (paired writing, 1 agent)
Round 2: Introduction P3 + Conclusion (parallel x2, mirror relationship)
Round 3: Discussion + Introduction P1-P2 + Abstract (parallel x3)
Round 4: Title (1 Agent)

For Case Report:

Round 1: Case Presentation (sequential, requires user's clinical information)
Round 2: Discussion + Introduction (parallel x2)
Round 3: Abstract + Title (parallel x2)

For Systematic Review:

Round 1: Methods (sequential, most important section)
Round 2: Results (sequential, depends on Methods structure)
Round 3: Discussion + Introduction + Abstract (parallel x3)
Round 4: Title (1 Agent)

Phase 4: Humanize (parallel x up to 6)

paper-humanizer for the number of sectionsIn parallellaunch:

Each agent handles 1 section
All agents references/humanizer-academic.md refer to
After completion, the lead executes the Phase 4.4 verification checklist

Phase 5: References (2 stages)

paper-ref-builder execute in 2 stages:

Builder Mode: Collect citations from all sections → format in journal style
Verifier Mode: Verify the existence of each reference via WebSearch → flag fabrications

Phase 6: Quality review (parallel + gate)

Round 1: paper-section-reviewer for the number of sectionsIn parallellaunch with

Each agent references/section-checklist.md evaluate based on

Round 2: paper-quality-gate launch one (opus model)

Verify cross-sectional consistency of all sections
PASS is mandatory. If FAIL, fix the relevant section and re-review

Phase 6.5: Adversarial review (parallel x4 + integration)

paper-red-team（opus）を4つin paralleland attack the central claims from different perspectives:

Agent A: Statistics reviewer (p-hacking, multiple comparisons, power, traceability to preregistration)
Agent B: Methodology reviewer (confounding, bias, DAG, validity of causal claims)
Agent C: Novelty reviewer (references/novelty-check.md re-attack novelty in light of)
Agent D: Consistency/clinical reviewer (raw data traceability, citation existence, overclaiming, clinical harm)

After the 4 agents complete, the lead integrates and performs steelman-the-null, then issues a verdict (KILL/MAJOR/MINOR/PASS).Final adjudication of KILL/MAJOR is by a human (💡 gate). KILL is sent back to Phase −1 (evidence that the system worked). Only PASS proceeds to Phase 7.

Phase 7: Submission preparation (parallel x4)

paper-section-drafter を4つin parallellaunch:

Agent A: Title Page (templates/title-page.md reference)
Agent B: Highlights / Key Points (templates/highlights.md reference)
Agent C: Acknowledgments/declarations (templates/acknowledgments.md + templates/declarations.md reference)
Agent D: Cover Letter (templates/cover-letter.md reference)

After completion,scripts/compile-manuscript.sh final integration.

Phase 8: Revision (parallel x3)

Parsing and categorizing reviewer comments is sequential (user dialogue). After that:

Agent A (paper-section-drafter): Handle Must Fix comments
Agent B (paper-section-drafter): Handle Should Fix comments
Agent C (paper-section-drafter): Draft rebuttals (Rebut)

After completion, re-run Phase 4 (humanize) and Phase 6 (quality review) on the revised sections.

Phase 9-10: Sequential execution (no changes)

Because it is event-driven (proof arrival, rejection notification), the existing flow remains as is.

How to use team modes

Scenario	Recommended mode
Original Article (multiple sections)	Team Mode
Systematic Review (large volume of literature)	Team Mode
Case Report (few sections)	Sequential mode
Letter / Short Communication	Sequential mode
When the deadline is approaching	Team Mode

Autonomous Stage-Gate System (autonomous quality gate)

In team mode, a quality gate is set for each Phase. If the gate FAILs, the fix agent is automatically restarted and loops until PASS. After a maximum of 3 iterations, escalate to the user.

Gate Flow

Phase N 完了 → [ゲートエージェント] → PASS? → 次のPhaseへ
                                    → FAIL + iter<3 → FEEDBACK.md生成 → [修正エージェント(revision_mode)] → ゲートに戻る
                                    → FAIL + iter≥3 → ユーザーにエスカレーション（checklists/escalation-log.md）

Gate definitions by Phase

Phase	Gate name	PASS condition	Gate owner	Fix owner
1	Literature quality	≥10 papers, all with DOI/URL, no fabrication	paper-section-reviewer	paper-lit-searcher
2	Outline	All IMRAD present, ≥2 citation mappings	paper-section-reviewer	Escalate to user immediately
2.5	Tables/figures	All design files complete, within journal limits	paper-section-reviewer	paper-table-figure-planner
3	Section	score≥80%、Must Fix=0	paper-section-reviewer	paper-section-drafter
4	Humanize	High-priority AI patterns remaining: 0	paper-section-reviewer	paper-humanizer
5	References	Fabrications: 0, orphan citations: 0	paper-ref-builder(verifier)	paper-ref-builder(builder)
6	Cross-sectional consistency	PASS or CONDITIONAL_PASS	paper-quality-gate(opus)	paper-section-drafter
7	Submission preparation	All required documents present, within word count limit	paper-section-reviewer	paper-section-drafter

Feedback file format

When a gate FAILs, the orchestrator generates checklists/feedback-{phase}-{section}.md :

---
revision_mode: true
iteration: {N} of 3
section: {section_name}
source_file: {path/to/section_file.md}
gate_verdict: FAIL
---

## Must Fix
### Issue 1
- item: {チェックリスト項目名}
- location: {段落番号 or 行範囲}
- problem: {問題の1文記述}
- fix: {具体的な修正指示}

## Should Fix
### Issue 2
- item: {項目名}
- fix: {修正指示}

## Context (変更不可)
- reporting_guideline: {PRISMA等}
- journal: {ジャーナル名}
- language: {English/Japanese}

How to launch the revision agent

When a gate FAILs, pass the following to the revision agent:

revision_mode: true
feedback_file: {project_dir}/checklists/feedback-{phase}-{section}.md
source_file: {project_dir}/{section_file.md}

All revision agents (paper-section-drafter, paper-humanizer, paper-lit-searcher, paper-table-figure-planner), upon receiving revision_mode: true , process only the Must Fix items in the feedback and skip the normal initial workflow.

Persisting gate state

checklists/gate-state.md Manage the iteration count with:

| Phase | Section | Iteration | Status | Last Run |
|-------|---------|-----------|--------|----------|
| phase3 | methods | 2 | IN_PROGRESS | 2026-03-05 |
| phase4 | intro | 0 | PASS | 2026-03-05 |

Escalation Protocol

When 3 iterations are reached:

checklists/escalation-log.md Record the list of unresolved Must Fix items and explanations in
Display a message to the user (clearly indicating the relevant file paths and issues)
Pause the workflow
After the user manually fixes the issues, resume with "continue" → reset the iteration counter to 0

Loop determination via YAML verdict

section-reviewer and quality-gate add a YAML header at the beginning of the output file:

# section-reviewer
---
gate_verdict: PASS | FAIL
must_fix_count: {N}
score_percent: {N}
section: {name}
---

# quality-gate
---
gate_verdict: PASS | CONDITIONAL_PASS | FAIL
must_fix_count: {N}
affected_sections: [methods, results]
---

The orchestrator reads only the YAML header to determine whether to continue or end the loop. CONDITIONAL_PASS (only Should Fix items remaining) is treated as PASS.

Parallel gate execution

Some gates can be executed in parallel:

Phase 3: Methods+Results pair ‖ Introduction+Conclusion pair (Discussion is independent)
Phase 4: Execute the humanize gates for all sections simultaneously
Phase 6: quality-gate after all section reviews (order-dependent)

The Abstract gate is executed after all sections PASS (because it depends on numerical values from other sections).

Reference Files

AI-for-Science layer (Phase −1 Discovery + Phase 6.5 Adversarial Review)

references/ai-for-science-model.md - Read first. Operating model: the two human-sovereign inputs (💡 IDEA, 📊 DATA), the discovery loop, the three integrity guardrails, the autonomy dial
templates/research-question.md - Phase −1 hypothesis forge (clinical observation → FINER-scored candidates → human selects)
references/novelty-check.md - Live-literature novelty sweep via real APIs (PubMed MCP, OpenAlex, Europe PMC, Semantic Scholar); four-verdict gap classification
templates/study-design.md - Design selection, PICO→variables, DAG/confounding, sample-size/power, pre-specified analysis plan
templates/preregistration.md - Pre-registration lock (anti-HARKing): registry selection, fillable record, confirmatory/exploratory firewall, deviations log
references/adversarial-review.md - Phase 6.5 red-team: four hostile reviewers + steelman-the-null; KILL/MAJOR/MINOR/PASS verdict
templates/human-loop-ledger.md - Accountability ledger (💡/📊/🤖 decision tagging) → rolls up into AI-disclosure + CRediT
agent paper-red-team (~/.claude/agents/paper-red-team.md, opus) - Adversarial reviewer for team mode

Core writing layer

references/imrad-guide.md - IMRAD structure and writing principles
references/section-checklist.md - per-section quality checklist (Original Article + Case Report)
references/citation-guide.md - citation formatting and management
references/reporting-guidelines.md - CONSORT, STROBE, PRISMA, CARE summaries
references/humanizer-academic.md - AI writing pattern detection (EN 18 + JP 13 patterns)
templates/project-init.md - project README template (Original Article)
templates/project-init-case.md - project README template (Case Report)
templates/literature-matrix.md - literature comparison matrix
templates/methods.md - Methods section writing guide (Original Article)
templates/results.md - Results section writing guide (Original Article)
templates/case-report.md - Case presentation writing guide (Case Report, CARE-compliant)
templates/case-introduction.md - Case Report introduction guide
templates/case-abstract.md - Case Report abstract guide (CARE format)
templates/introduction.md - Introduction section writing guide (Original Article)
templates/discussion.md - Discussion section writing guide
templates/conclusion.md - Conclusion writing guide
templates/abstract.md - Abstract writing guide (Original Article)
templates/cover-letter.md - Cover letter template
templates/submission-ready.md - Pre-submission checklist template
templates/sr-outline.md - Systematic review outline (PRISMA 2020)
templates/sr-screening-pipeline.md - SR screening execution (dedup → dual TA → dual FT → extraction → PRISMA counts); Phase 1.5
scripts/sr-dedup.py - Deterministic de-duplication of RIS/NBIB/BibTeX/CSV exports + identification counts
scripts/sr-pdf-link.py - Link full-text PDFs to records by DOI, rename to canonical names (originals untouched)
scripts/sr-prisma-count.py - Compute PRISMA flow numbers + Cohen's κ + internal-consistency checks from stage CSVs
templates/declarations.md - Declarations templates (Ethics, COI, Funding, AI, CRediT)
templates/graphical-abstract.md - Graphical abstract design guide
references/ai-disclosure.md - AI tool disclosure guide (ICMJE 2023)
references/tables-figures-guide.md - Tables and figures creation guide
references/keywords-guide.md - Keywords and MeSH term selection guide
references/supplementary-materials.md - Supplementary materials strategy guide
references/citation-verification.md - Citation authenticity verification guide
references/pubmed-query-builder.md - PubMed search query construction guide
templates/title-page.md - Title page template (running head, ORCID, affiliations)
templates/highlights.md - Key Points / Highlights / Summary boxes (JAMA, BMJ, Elsevier, etc.)
templates/limitations-guide.md - Limitations section writing guide with templates
templates/acknowledgments.md - Acknowledgments template (AI tools, medical writing)
templates/proof-correction.md - Post-acceptance proof correction guide
references/submission-portals.md - Submission portal guide (ScholarOne, Editorial Manager, etc.)
references/open-access-guide.md - Open Access models, APCs, preprints, funder mandates
references/clinical-trial-registration.md - Clinical trial registration guide (ClinicalTrials.gov, UMIN-CTR, jRCT)
references/abstract-formats.md - Journal-specific abstract formats (JAMA, NEJM, Lancet, BMJ, etc.)
references/word-count-limits.md - Word count limits by journal and paper type
references/coi-detailed.md - Detailed COI categories, CRediT taxonomy, ORCID guide
references/desk-rejection-prevention.md - Desk rejection prevention and journal selection
references/journal-reformatting.md - Quick reformatting guide after rejection
references/statistical-reporting-full.md - Extended SAMPL statistical reporting guide
references/reporting-guidelines-full.md - Comprehensive reporting guidelines (20+ guidelines with checklists)
references/master-reference-list.md - Master reference list with URLs (all resources)
templates/data-management.md - Data management template (raw/processed/analysis, data dictionary, de-identification)
templates/analysis-workflow.md - Data analysis workflow guide (Table 1, regression, survival, figures)
scripts/table1.py - Table 1 generator (auto-detect variable types, normality test, group comparison)
scripts/analysis-template.py - Statistical analysis template (descriptive, t-test, logistic, survival)

About this skill

Overview

AI-for-Science Operating Model

Supported Paper Types

Workflow

Phase −1: Discovery (the research engine)

Step −1.1: Forge the research question (💡 IDEA gate)

Step −1.2: Novelty check (guardrail: anti-reinvention)

Step −1.3: Design the study & power it

Step −1.4: Pre-register & lock (guardrail: anti-HARKing)

Phase 0: Project Initialization

Step 0.1: Capture Journal Requirements

Step 0.2: Select Reporting Guideline

Step 0.3: Create Project Directory

Step 0.4: Organize Research Data

Step 0.5: Data Analysis

Phase 1: Literature Search & Organization

Step 1.1: Define Search Strategy

Step 1.2: Build Literature Matrix

Step 1.3: Identify Key Papers

Phase 1.5: Screening Execution (Systematic Review only)

Phase 2: Outline

Phase 2.5: Tables & Figures

Step 2.5.1: Plan Tables & Figures

Step 2.5.2: Create Tables

Step 2.5.3: Plan Figures

Step 2.5.4: Graphical Abstract (if required)

Phase 3: Drafting

3-A: Original Article Workflow

Step 3.1: Methods & Results (Write as a pair)

Step 3.2: Introduction (Paragraph 3) & Conclusion (Write as a pair)

Step 3.3: Discussion

Step 3.4: Introduction (Paragraphs 1-2)

Step 3.5: Abstract

Step 3.6: Title

3-B: Case Report Workflow

Step 3.1-CR: Case Presentation

Step 3.2-CR: Discussion

Step 3.3-CR: Introduction

Step 3.4-CR: Abstract

Step 3.5-CR: Title

3-C: Review Article Workflow

Step 3.1-RA: Thematic Sections

Step 3.2-RA: Introduction

Step 3.3-RA: Conclusion & Future Directions

Step 3.4-RA: Abstract

Step 3.5-RA: Title

3-D: Systematic Review Workflow

Step 3.1-SR: Methods

Step 3.2-SR: Results

Step 3.3-SR: Discussion

Step 3.4-SR: Introduction, Abstract, Title

3-E: Letter / Short Communication Workflow

Step 3.1-LT: Condensed Draft

Step 3.2-LT: Abstract

Step 3.3-LT: Title

Phase 4: Humanize

Step 4.1: Scan for AI Patterns

Step 4.2: Rewrite

Step 4.3: Section-Specific Focus

Step 4.4: Verify

Phase 5: References

Phase 6: Quality Review

Phase 6.5: Adversarial Review (red-team the claim)

Phase 7: Pre-Submission

Phase 8: Revision (Post-Review)

Step 8.1: Organize Reviewer Comments

Step 8.2: Create Response Letter

Step 8.3: Implement Revisions

Step 8.4: Verify Revision Completeness

Phase 9: Post-Acceptance

Step 9.1: Proof Review

Step 9.2: Submit Corrections

Step 9.3: Post-Publication

Phase 10: Rejection & Resubmission

Step 10.1: Assess the Rejection

Step 10.2: Quick Reformat

Step 10.3: Cascading Submission Strategy

Section-Specific AI Guidelines