phd-thesis

Use when the user runs /acronyms, or asks to find, define, or mark up acronyms in a LaTeX thesis .tex file — e.g. converting literal acronyms like CMB, WIMP, dSph, NFW into glossaries macros and adding any missing definitions to acronyms.tex.

Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.

Critical review of thesis sections or chapters. Evaluates scientific rigor, writing quality, logical flow, and citation completeness. Supports section-level (/referee X.Y) and chapter-level (/referee X) scope.

Research assistant that generates detailed, structural chapter outlines by synthesizing thesis context, local references, and NotebookLM insights.

Use when you need to resolve placeholder citations (e.g., surname_year) or missing bibliography entries in the LaTeX thesis by querying NotebookLM context and InspireHEP.

Use when saving insights from the current conversation to persistent storage, or when retrieving past insights before starting research or writing tasks.

Run latexindent one-sentence-per-line on thesis chapter files. Use when the user asks to format, indent, or break lines in a chapter's LaTeX files.

General-purpose research skill for establishing state of the art, defining concepts, and collecting references for thesis chapters. Produces structured references.md files with data tables and bib-key lookups.

Research assistant for extracting specific methodology and results from the author's papers. Prioritizes Author Papers (001).

Use when you need metadata, figures, full text, citations, or BibTeX for a specific paper. Centralizes InspireHEP and arXiv MCP server usage with decision guidelines.

Research assistant for extracting detailed information from review articles (002). Produces citation-ready content with bib-key lookups for thesis incorporation.

Use when writing actual thesis prose for a specific section or subsection. Orchestrates research, drafting with scientific-writing principles, humanization, and personal style adaptation. Callable via /draft X.Y or /draft X.Y.Z.

Fetches all source IDs from the thesis NotebookLM notebook and categorizes them into author papers (001), review articles (002), and general references. Call once per conversation before using other thesis skills.