Academic Researcher

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

## 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:

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):

## 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, extraction schema)

See references/systematic-review-prisma.md.

Thesis Structure

1. Abstract
2. Introduction
   - Background
   - Problem statement
   - Research questions
   - Thesis objectives
   - Contributions
3. Literature Review
   - Theoretical framework
   - Related work
   - Research gap
4. Methodology
   - Research design
   - Data collection
   - Analysis methods
5. Results/Findings
6. Discussion
7. Conclusion
8. References
9. Appendices

Phase 5: Writing & LaTeX

LaTeX Document Setup

For submission, prefer official publisher templates (see references/official-templates.md). The templates below are scaffolds for learning the structure.

Included templates:

• references/templates/ieee-conference.tex (IEEE conference paper)
• references/templates/literature-review.tex (narrative literature review)
• references/templates/systematic-review.tex (systematic review)
• references/templates/thesis.tex (thesis/dissertation)
• references/templates/apa7-manuscript.tex (APA 7 manuscript)
• references/templates/research-proposal.tex (research proposal)

Minimal IEEE skeleton (BibTeX):

\documentclass[conference]{IEEEtran}
\IEEEoverridecommandlockouts

\usepackage{cite}
\usepackage{amsmath,amssymb,amsfonts}
\usepackage{graphicx}
\usepackage{xcolor}

\title{Your Paper Title}

\author{
\IEEEauthorblockN{First Author}
\IEEEauthorblockA{Department, University\\
City, Country\\
[email protected]}
}

\begin{document}
\maketitle

\begin{abstract}
Your abstract goes here (150--250 words).
\end{abstract}

\begin{IEEEkeywords}
keyword1, keyword2, keyword3
\end{IEEEkeywords}

\section{Introduction}
...

\bibliographystyle{IEEEtran}
\bibliography{references}
\end{document}

Academic Writing Style

Tone:

• Formal and objective
• Use "we" for multi-author papers when describing your work (standard in CS/Engineering)
• Use third person for discussing other work ("Smith et al. proposed...")
• Precise technical terminology
• Present tense for established facts, past tense for specific studies

Avoid:

• Colloquial language
• Unsupported claims
• Excessive quotations (paraphrase instead)
• Vague terms ("very", "significant") without data

Citation Integration

IEEE Style (numbered):

Recent work has shown this approach is effective \cite{smith2023}.
Multiple studies support this finding \cite{smith2023, jones2022, doe2021}.

APA Style (author-date):

% Parenthetical (APA author-date)
Recent work has shown this approach is effective \parencite{smith2023}.
Multiple studies support this finding \parencite{smith2023,jones2022}.

% Narrative
\textcite{smith2023} demonstrated this approach is effective.

Paragraph Structure

Each paragraph should follow a clear pattern:

1. Topic sentence — state the main point
2. Evidence/Support — cite sources or present data
3. Analysis — explain what the evidence means
4. Transition — connect to the next paragraph

Transition Patterns

• Contrast: "However," "In contrast," "While X focuses on..."
• Extension: "Building on this," "Furthermore," "Similarly,"
• Consequence: "As a result," "Therefore," "This suggests that"
• Gap: "Despite these advances," "However, X remains unexplored"

Mathematical Typesetting

Inline math: $E = mc^2$

Displayed equations:

\begin{equation}
f(x) = \sum_{i=1}^{n} a_i x^i
\end{equation}

Multi-line equations:

\begin{align}
a &= b + c \\
  &= d + e + f
\end{align}

Matrices:

\begin{bmatrix}
a_{11} & a_{12} \\
a_{21} & a_{22}
\end{bmatrix}

Proofs:

\begin{proof}
Let $x$ be any element...
Therefore, we conclude...
\end{proof}

See references/latex-math-guide.md for more examples.

Phase 6: Quality Assurance

Pre-Submission Checklist

Content:

• Clear research question/objective
• Logical flow and organization
• Minimum 15-20 sources for full paper
• All sources verified and labeled (peer-reviewed vs preprint vs other)
• All claims supported by citations
• Methodology clearly explained
• Results clearly presented with metrics
• Limitations acknowledged
• Contributions clearly stated

Technical (IEEE):

• Reference format correct
• All citations match reference list
• No missing references
• Consistent citation numbering
• Figure/table captions complete
• Margins match venue requirements

Writing Quality:

• Academic tone maintained
• No grammatical errors
• Smooth transitions
• Abstract matches content
• Keywords present

Evidence & Citations:

• No invented citations; every reference is verifiable (title/authors/venue/year/DOI or canonical URL)
• Every citation key used in LaTeX exists in references.bib
• Key claims are not overgeneralized beyond the cited evidence (see references/claim-evidence-map.md)

Reproducibility (If Empirical):

• Dataset versions, splits, and preprocessing are specified
• Baseline selection and tuning budget fairness are stated
• Seeds/variance reporting policy is stated
• Compute and environment details are included (see references/reproducibility-checklist.md)

Statistics (If Applicable):

• Uncertainty is reported where appropriate (CIs/SE/bootstrap)
• Statistical tests (if used) are specified with assumptions and multiple-comparison handling
• Effect sizes are emphasized over p-values alone (see references/statistical-reporting.md)

Threats to Validity:

• Threats are enumerated (internal/construct/statistical/external) with concrete mitigations (see references/threats-to-validity.md)

Citation Formats

Prefer managing references via references.bib (BibTeX/BibLaTeX) and generating the reference list automatically; see references/bibliography-workflows.md. The examples below are reference list patterns for manual verification.

IEEE Format

Journal Article:

[1] A. Author, B. Author, and C. Author, "Title of article," Journal Name, vol. X, no. Y, pp. ZZ-ZZ, Month Year.

Conference Paper:

[2] A. Author and B. Author, "Title of paper," in Proc. Conference Name, City, Country, Year, pp. ZZ-ZZ.

Book:

[3] A. Author, Title of Book, Edition. City, State: Publisher, Year.

See references/ieee-citation-guide.md for complete reference.

APA Format (7th Edition)

Journal Article:

Author, A. A., & Author, B. B. (Year). Title of article. Journal Name, Volume(Issue), pages. https://doi.org/xxxxx

Conference Paper:

Author, A. A., & Author, B. B. (Year, Month). Title of paper. In Conference Name (pp. pages). Publisher.

See references/apa-citation-guide.md for complete reference.

Output

Primary Output: LaTeX Source

I generate .tex files that you can compile with:

• Overleaf (online, recommended)
• Local LaTeX: TinyTeX, MacTeX, TeX Live
• VS Code: LaTeX Workshop extension

Compilation Commands

# IEEE-style (BibTeX)
pdflatex paper.tex
bibtex paper
pdflatex paper.tex
pdflatex paper.tex

# APA-style (BibLaTeX + biber)
pdflatex paper.tex
biber paper
pdflatex paper.tex
pdflatex paper.tex

# Or use latexmk (recommended if available)
latexmk -pdf -bibtex paper.tex
latexmk -pdf -usebiber paper.tex

Alternative Outputs

If LaTeX is not suitable, I can also generate:

• Markdown with MathJax support
• DOCX via Pandoc conversion

Important Notes

• Quality over quantity - Fewer well-chosen sources are better than many weak ones
• Recent sources preferred - Last 5-7 years unless historical context needed
• Research integrity - Always cite properly, never plagiarize
• Be honest about limitations - Acknowledge gaps in your research
• User provides content - I structure and write; you provide the research contributions

References

• references/ieee-citation-guide.md - Complete IEEE reference examples
• references/apa-citation-guide.md - Complete APA reference examples
• references/latex-math-guide.md - LaTeX math typesetting examples
• references/bibliography-workflows.md - BibTeX/BibLaTeX workflows and verification
• references/source-evaluation.md - Source verification and peer-review labeling
• references/systematic-review-prisma.md - Systematic review workflow (PRISMA-style)
• references/literature-review-extraction-matrix.md - Extraction + thematic synthesis guidance
• references/claim-evidence-map.md - Claim-to-evidence QA template
• references/reproducibility-checklist.md - Reproducibility QA checklist
• references/statistical-reporting.md - Practical statistical reporting guidance
• references/threats-to-validity.md - Threats-to-validity prompts
• references/acm-citation-guide.md - ACM citation format reference
• references/revision-response-guide.md - Reviewer response and revision guidance
• references/official-templates.md - Links to official publisher LaTeX templates
• references/templates/ - LaTeX templates (IEEE, APA, thesis, reviews, proposals)
• examples/ - Protocols and working templates (vocabulary, extraction matrix, claim-evidence map)
• scripts/resolve-papers.js - Paper discovery and open-access resolution via Semantic Scholar, Unpaywall, CrossRef
• scripts/validate-bib.js - BibTeX entry validation against CrossRef
• scripts/check-citations.js - Citation key consistency checker