Academic Writing in Markdown with Pandoc

A skill for writing academic papers in plain-text Markdown and converting them to PDF, Word, LaTeX, and HTML using Pandoc. Covers YAML metadata, citation management, cross-references, templates, and workflows for collaborative academic writing.

Why Markdown for Academic Writing?

Advantages

1. Plain text: Version-controllable with Git (diff-friendly)
2. Portable: Works on any OS, any editor
3. Pandoc: Convert to PDF, DOCX, LaTeX, HTML, EPUB
4. Focus: Content-first writing without formatting distractions
5. Citations: Pandoc-citeproc handles bibliography automatically
6. Collaboration: Easy to review diffs in pull requests

When to Use Markdown vs. LaTeX

Use Markdown when:
  - You need multi-format output (PDF + Word + HTML)
  - Collaborators prefer Word but you prefer plain text
  - The paper has standard formatting needs
  - You want a simpler syntax than LaTeX

Use LaTeX directly when:
  - The journal provides a mandatory LaTeX template
  - You need advanced typesetting (complex math layouts, custom floats)
  - You are writing a thesis with institutional LaTeX requirements

Document Structure

YAML Front Matter

---
title: "Your Paper Title: A Markdown-Based Approach"
author:
  - name: Jane Smith
    affiliation: Department of Computer Science, University X
    email: [email protected]
    orcid: 0000-0002-1234-5678
  - name: John Doe
    affiliation: School of Engineering, University Y
date: 2026-03-09
abstract: |
  This paper demonstrates how academic manuscripts can be written
  in plain Markdown and converted to publication-quality documents
  using Pandoc. We show that this approach reduces formatting overhead
  while maintaining full citation and cross-reference capabilities.
keywords: [academic writing, Markdown, Pandoc, reproducible research]
bibliography: references.bib
csl: apa-7th-edition.csl
link-citations: true
numbersections: true
---

Body Text with Citations

# Introduction

Academic writing often involves tedious formatting tasks that
distract from content creation [@smith2024; @jones2023, pp. 45-50].
Recent tools enable plain-text workflows that separate content
from presentation [see @garcia2022, chap. 3].

## Background

As @lee2021 demonstrated, Markdown-based workflows reduce
formatting errors by 40% compared to WYSIWYG editors.

### Subsection Example

Inline math: $E = mc^2$

Display math:
$$
\hat{\beta} = (X^T X)^{-1} X^T y
$$