Manuscript Formatting

Manuscript Formatting and Submission Preparation

Format manuscripts to meet journal-specific requirements and prepare submission packages.

When to Use

• Formatting a manuscript for a specific journal
• Preparing a submission package (cover letter, figures, supplementary)
• Converting between formats (Word to LaTeX, markdown to LaTeX)
• Checking compliance with author guidelines
• Managing references and BibTeX

Common Journal Formats

IEEE

• Template: IEEEtran class
• Columns: Two-column
• References: Numbered, [1] style
• Figures: Fit within column or span both columns
• Page limit: Varies (typically 6-8 for conference, 12-14 for journal)

\documentclass[journal]{IEEEtran}
\usepackage{cite}
\usepackage{amsmath}
\usepackage{graphicx}

Nature/Science

• Format: Single column, specific heading hierarchy
• References: Superscript numbered
• Word limit: ~3000-5000 words (main text)
• Figures: Max 6-8, submitted as separate files
• Methods: Often separate section with no word limit

PNAS

• Template: pnas-new class
• Columns: Two-column in print, single for review
• Word limit: ~4500 words
• References: Numbered
• Significance statement: Required, 120 words max

PLoS ONE

• Format: No specific template required
• References: Numbered, Vancouver style
• No length restriction
• Data availability: Statement required

Elsevier

• Template: elsarticle class
• Multiple formats: preprint, review, final

\documentclass[preprint,12pt]{elsarticle}

LaTeX Essentials

Document Structure

\documentclass[options]{class}
\usepackage{packages}

\title{Title}
\author{Authors}

\begin{document}
\maketitle
\begin{abstract}
\end{abstract}

\section{Introduction}
\section{Methods}
\section{Results}
\section{Discussion}

\bibliography{references}
\end{document}

BibTeX Management

@article{smith2024,
  author  = {Smith, John and Doe, Jane},
  title   = {Title of the Paper},
  journal = {Journal Name},
  year    = {2024},
  volume  = {10},
  pages   = {1--15},
  doi     = {10.1000/example}
}

Common BibTeX styles:

• plain - numbered, sorted alphabetically
• unsrt - numbered, order of citation
• ieeetr - IEEE transactions style
• apalike - APA-like author-year

Cross-references

\label{fig:results}   % Label a figure
\ref{fig:results}     % Reference by number
Figure~\ref{fig:results}  % Standard format

Submission Checklist

Before Submission

• [ ] Manuscript formatted per journal template
• [ ] Title page: title, authors, affiliations, corresponding author, ORCID
• [ ] Abstract within word limit
• [ ] Keywords provided (if required)
• [ ] Main text within page/word limit
• [ ] Figures as separate high-resolution files (typically 300+ DPI)
• [ ] Figure captions in a separate list
• [ ] Tables formatted per journal style
• [ ] References complete and consistently formatted
• [ ] Supplementary materials prepared separately
• [ ] Cover letter drafted (run manuscript:humanizer on it; cover letters are particularly prone to AI-tell phrasing)
• [ ] manuscript:humanizer natural-writing pass applied to all narrative sections, then journal house style (title case, citation format, etc.) re-applied where it overrides humanizer defaults
• [ ] Conflict of interest statement
• [ ] Data availability statement
• [ ] Ethics approval statement (if applicable)
• [ ] Author contributions (CRediT format if required)
• [ ] Suggested reviewers (if required)

Cover Letter Template

Dear Editor,

We submit our manuscript titled "{TITLE}" for consideration
in {JOURNAL}.

{1-2 sentences: what the study did and found}

{1-2 sentences: why this matters to the journal's readership}

{1 sentence: confirmation of originality and no concurrent submission}

We suggest the following reviewers:
1. {Name, Affiliation, Email}
2. {Name, Affiliation, Email}

Sincerely,
{Corresponding Author}

Format Conversion

Markdown to LaTeX

pandoc manuscript.md -o manuscript.tex --template=journal-template.tex --bibliography=refs.bib --citeproc

Word to LaTeX

pandoc manuscript.docx -o manuscript.tex --extract-media=figures/

LaTeX to Word (for journals requiring .docx)

pandoc manuscript.tex -o manuscript.docx --bibliography=refs.bib --citeproc

Additional Resources

• Reference: [references/journal-requirements.md](references/journal-requirements.md) - Detailed requirements for major journals
• Reference: [references/latex-troubleshooting.md](references/latex-troubleshooting.md) - Common LaTeX issues and fixes

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: neuromechanist
• Source: neuromechanist/research-skills
• License: BSD-3-Clause

Install and usage instructions live in the source repository linked above.