From LaTeX to acceptance: typography, math, and reference traps editors notice

Reading time ~9 minutes · Updated September 10, 2025

A clean preamble (copy-paste)

Drop this at the top of your document. Swap the font set if your target journal mandates one.

% -------- principia minimal preamble --------
\documentclass[11pt]{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{lmodern}             % clean T1 Latin Modern fonts
\usepackage{microtype}           % better kerning & protrusion
\usepackage{amsmath,amssymb,mathtools}
\usepackage{siunitx}             % consistent units and numbers
\sisetup{detect-all,per-mode=symbol,output-decimal-marker=.}
\usepackage{csquotes}            % locale aware quotes
\usepackage[hidelinks]{hyperref}
\usepackage[nameinlink,noabbrev]{cleveref} % 'see Eq. (3)'
% Vector/matrix shorthand
\DeclarePairedDelimiter{\abs}{\lvert}{\rvert}
\DeclarePairedDelimiter{\norm}{\lVert}{\rVert}
\newcommand{\vect}[1]{\mathbf{#1}}
\newcommand{\mat}[1]{\mathbf{#1}}
% --------------------------------------------

Typography that passes a 10-second scan

• Minus vs hyphen: in math, use the real minus (entered via - inside $…$). In text, use hyphen -, en-dash -- for ranges (10–12), em-dash --- for breaks.
• Quotes: use csquotes (e.g., \enquote{text}) to avoid straight quotes.
• Non-breaking spaces: tie numbers/units and references: Fig.~2, \SI{10}{\micro\meter}.
• Kerning: microtype cleans cramped letter pairs and improves line breaks automatically.
• Lists: keep parallel grammar; use sentence case in bullets unless the journal says otherwise.

Math spacing and notation traps

• Inline vs display: long equations should be display math; keep inline math short to preserve line spacing.
• Functions vs variables: typeset functions upright: \sin, \exp, \log (not sin).
• Vectors/matrices: choose a convention (bold or arrow) and keep it consistent; the macros above help.
• Units & numbers: use siunitx so 1.0e-3 prints as \SI{1e-3}{{}} consistently; keep a thin space between number and unit.
• Punctuation: equations are part of sentences—punctuate them.
• References: use \label and \cref (from cleveref) to avoid “Eq. ??”.

% examples
Let \(x \in \mathbb{R}\). We define the loss as
\begin{equation}
  \mathcal{L}(\vect{w}) = \norm{\vect{y}-X\vect{w}}_2^2.\label{eq:loss}
\end{equation}
As shown in \cref{eq:loss}, the optimum satisfies \(X^\top X\vect{w}=X^\top \vect{y}\).

Figures, fonts, and PDF quality

• Vector first: export plots as PDF/SVG; avoid blurry PNG text. For raster (microscopy), use 300–600 dpi.
• Embed fonts: make sure EPS/PDF figures embed the fonts; most plot tools have “embed fonts” or “outline text.”
• Color: use color for meaning; check color-blind safety; keep one accent color for your contribution.
• Hyperlinks: use hyperref with hidelinks to avoid colored boxes in the PDF.

BibTeX/BibLaTeX reference pitfalls

• Capitalization: protect proper nouns and acronyms with braces: title = {GPU acceleration for {RNA-seq}}.
• Page ranges: use en-dash (–), not hyphen: pages = {101--109}.
• Duplicates: unique citation keys; run a duplicate check.
• DOIs/URLs: include if required; ensure consistent fields across entries.
• Choose one stack: either natbib or biblatex+biber; do not mix.

% biblatex example
\usepackage[backend=biber,style=numeric,sorting=none]{biblatex}
\addbibresource{refs.bib}
% In refs.bib
@article{smith2024gpu,
  author  = {Smith, A. and Lee, K.},
  title   = {GPU acceleration for {RNA-seq} alignment},
  journal = {Bioinformatics},
  year    = {2024},
  volume  = {40},
  number  = {3},
  pages   = {101--109},
  doi     = {10.1093/bioinformatics/xxxxxx}
}

Submission-ready checklist

• Preamble includes microtype, siunitx, and cleveref; fonts match journal requirements.
• No “Eq. ??” or “Fig. ??”; all cross-refs via \cref.
• Minus signs are real minus in math; ranges use en-dash.
• All figures are vector where possible; raster ≥300 dpi; fonts embedded.
• References: protected capitalization, correct page ranges, duplicate-free.
• PDF metadata set (title, author, keywords); hyperlinks not boxed.

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