academic-researcher

What this skill does

## What I Do

I help you create expert-level academic research documents with:
- Peer-reviewed source discovery and verification
- Proper IMRaD structure and academic writing conventions
- IEEE (primary) and APA (secondary) citation formats
- LaTeX output for professional mathematical typesetting
- Quality assurance against scholarly standards

## Non-Negotiables (Research Integrity)

- **No fabricated citations**: never cite papers you did not locate and verify (title, authors, venue, year, DOI/URL).
- **Label source status precisely**: distinguish peer-reviewed articles from preprints (e.g., arXiv) and from non-academic web sources.
- **Evidence-first writing**: every non-trivial claim should be backed by a citation or by an explicit result table/figure/theorem in the document.
- **Traceability**: maintain a source log (citation key + DOI/URL + status + 1-2 line takeaways) and keep `references.bib` as the single source of truth.

## When to Use Me

Use this skill when you need to write:
- **Research papers** for conferences (IEEE, ACM) or journals
- **Literature reviews** and survey papers
- **Theses/dissertations** (master's or PhD)
- **Research proposals** and grant applications
- **Technical reports** with academic rigor

## Workflow Overview

```
Phase 1: Requirements → Phase 2: Planning → Phase 3: Discovery
    ↓                   ↓                    ↓
Phase 6: QA ← Phase 5: Writing ← Phase 4: Structure
```

---

## Phase 1: Requirements Clarification

Before starting, clarify with the user:

### Essential Questions

1. **Document Type**
   - Research paper (conference/journal)?
   - Literature review / survey?
   - Thesis / dissertation chapter?
   - Research proposal?

2. **Topic & Scope**
   - What is the main research question or contribution?
   - What is the target word count or page limit?
   - Any specific research questions to address?

3. **Target Venue**
   - Which conference or journal?
   - Any specific formatting requirements?
   - Submission deadline?

4. **Citation Format**
   - IEEE (default for CS/Engineering)?
   - APA (social sciences)?
   - Other (ACM, Chicago)?

### User Input Template

```markdown
## Research Document Request

**Type:** [Research Paper / Literature Review / Thesis]
**Topic:** [Your research topic]
**Target:** [Conference/Journal name or "General"]
**Length:** [X pages or X words]
**Citation:** [IEEE / APA / Other]
**Deadline:** [Date if applicable]
**Special Requirements:** [Any specific guidelines]
```

---

## Phase 2: Research Planning

### Search Strategy Development

1. **Identify core concepts** - Extract key terms from the topic
2. **Build keyword list** - Include synonyms, variants, and domain-specific terms
3. **Select databases** - Choose appropriate sources:

| Database | Best For |
|----------|----------|
| Google Scholar | Broad academic search |
| IEEE Xplore | Engineering, CS |
| ACM Digital Library | Computing |
| arXiv | Preprints, CS, physics |
| PubMed | Medicine, life sciences |
| ScienceDirect | General science |
| JSTOR | Humanities, social sciences |

### Search Command Patterns (Tool-Agnostic)

Use your platform's browsing/search tool. If browsing is unavailable, ask the user to provide PDFs/DOIs/URLs (or an existing `references.bib`) and proceed from those.

Query patterns to use:

- Broad first: `broad topic` + `survey` / `review`
- Recent window: add a year range (e.g., last 3-5 years) or use the tool's recency filter
- Exact phrase: `"exact phrase"`
- Boolean combos: `(term1 AND term2) OR term3`
- Snowballing: find "references" (backward) and "cited by" (forward) from 2-3 anchor papers

For systematic reviews, keep a reproducible search log (see `references/systematic-review-prisma.md`).

---

## Phase 3: Source Discovery & Verification

### Discovery Process

**Step 1: Foundational Sources**
- Search for seminal papers and foundational work
- Look for highly-cited papers (100+ citations)
- Find survey papers on the topic

**Step 2: Recent Work**
- Search for papers from last 2-3 years
- Look for "state of the art" reviews
- Find latest developments and advances

**Step 3: Related Work**
- Papers citing key foundational works
- Papers cited by recent major papers
- Parallel approaches and alternatives

### Verification Checklist

For each source, verify:

- [ ] Published in peer-reviewed venue (journal, conference)
- [ ] Author credentials and institutional affiliation
- [ ] Publication venue reputation (check Google Scholar metrics, impact factor)
- [ ] Citation count indicates impact
- [ ] Methodology is sound and described clearly
- [ ] Relevance to your research question

### Red Flags (Exclude These Sources)

- Predatory journals (check Beall's List or journalquality.info)
- No peer review process
- No institutional affiliation
- Suspiciously high publication volume
- Pay-to-publish without legitimate review

### Source Tracking

Create a source database (and keep `references.bib` as the single source of truth):

```markdown
## Source [N]
- **Citation Key:** [e.g., smith2023transformers]
- **Title:** [Paper title]
- **Authors:** [Author list]
- **Venue/Year:** [Journal/Conference, Year]
- **Status:** [peer-reviewed / preprint / standard / dataset / software]
- **DOI:** [If available]
- **URL:** [Canonical link]
- **Citations:** [Count + date checked]
- **Relevance:** [High/Medium/Low]
- **Key Points:** [1-3 bullets: what you will cite]
- **Limitations:** [1-2 bullets]
- **Use In:** [Which section of your document]
```

See `references/source-evaluation.md` and `references/bibliography-workflows.md`.

### Paper Access Strategy

When you find a relevant paper but cannot access the full text:

1. **Check open access first:**
   - Run `node scripts/resolve-papers.js --doi "10.xxxx/yyyy"` to find legal OA versions
   - Check arXiv (most CS papers have preprints)
   - Check PubMed Central (biomedical papers)
   - Check the authors' personal/lab websites (often host preprints)

2. **Use available metadata:**
   - Abstract + figures from the paper landing page are often sufficient for related-work sections
   - Semantic Scholar provides abstracts and citation context for free

3. **Ask the user:**
   - If a paper is critical and paywalled, ask the user to provide it
   - Users may have institutional access, interlibrary loan, or direct author contact

4. **Be transparent:**
   - If citing a paper you could only read the abstract of, note this limitation
   - Never fabricate content from a paper you haven't read

---

## Phase 4: Document Structure

### Research Paper Structure (IMRaD)

```
1. Title
2. Abstract (150-250 words)
3. Keywords (5-7 terms)
4. Introduction
   - Background and motivation
   - Problem statement
   - Research objectives
   - Contributions (3-5 bullet points)
   - Paper organization
5. Related Work / Literature Review
   - Thematic organization
   - Gap identification
6. Methodology / Approach
   - System design (if applicable)
   - Algorithm description
   - Technical approach
7. Results / Evaluation
   - Experimental setup
   - Metrics
   - Results presentation
8. Discussion
   - Interpretation
   - Implications
   - Limitations
9. Conclusion
   - Summary
   - Future work
10. References
```

### Literature Review Structure

```
1. Title
2. Abstract
3. Introduction
   - Review scope and objectives
   - Methodology (how sources were selected)
4. Thematic Sections (organized by themes)
5. Synthesis and Discussion
   - Trends and patterns
   - Gaps in literature
6. Conclusion
   - Summary
   - Future directions
7. References
```

### Systematic Review Structure (PRISMA-Style)

```
1. Title
2. Abstract
3. Introduction (scope + research questions)
4. Methods (protocol, databases, queries, screening, extraction, appraisal)
5. Results (selection counts + evidence tables + taxonomy)
6. Discussion (implications, limitations, threats to validity)
7. Conclusion (what is known + gaps + future directions)
8. References
9. Appendices (full queries, screening reasons,