Archive 4 checkpoints (1-4)

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paper-releases/pbisc-diffusion/updates/20261012T090327Z-uniform-manuscript-margins/diffusion/dataset/server_1/manuscript/main.pdf

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paper-releases/pbisc-diffusion/updates/20261012T090327Z-uniform-manuscript-margins/diffusion/dataset/server_1/manuscript/main.tex

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+% Overleaf main document. Uses the official Springer Nature authoring class.
+% Select pdfLaTeX on Overleaf; all figures and citations are local files.
+% Rewritten from scratch on 2026-10-10 from the paper-summary deck (76 slides, 2026-10-08).
+% The previous version is kept in archive/pre_rewrite_20261010/.
+\documentclass[pdflatex,sn-nature]{sn-jnl}
+% Keep identical left/right margins on every page for screen reading.
+\geometry{twoside=false,bindingoffset=0pt}
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs}
+\usepackage{array}
+\usepackage{multirow}
+\usepackage{longtable}
+\usepackage{microtype}
+\usepackage{xcolor}
+\input{macros}
+\begin{document}
+\raggedbottom
+\title{Diffusion model with bulk expression conditioning can generate precise single cell dataset from bulk transcriptome with preserved disease specific gene expression signature}
+\input{authors}
+\abstract{\input{sections/abstract}}
+\keywords{bulk RNA sequencing, single-cell generation, diffusion model, low-rank adaptation, paired bulk and single-cell data, immune cells}
+\maketitle
+\raggedbottom
+\input{sections/introduction}
+\section*{Results}
+\input{sections/results_fig1}
+\input{sections/results_fig2}
+\input{sections/results_fig3}
+\input{sections/results_fig4}
+\input{sections/results_fig5}
+\input{sections/results_fig6}
+\input{sections/discussion}
+\input{sections/methods_model}
+\input{sections/methods_paired}
+\input{sections/methods_eval}
+\input{sections/declarations}
+\bibliography{references}
+% Figures with their legends, each on its own page(s). Panels are the deck's vector graphics, placed as-is;
+% the 180 mm journal layout is still to be drawn.
+\input{sections/fig1}
+\input{sections/fig2}
+\input{sections/fig3}
+\input{sections/fig4}
+\input{sections/fig5}
+\input{sections/fig6}
+\end{document}

paper-releases/pbisc-diffusion/updates/20261012T090327Z-uniform-manuscript-margins/diffusion/dataset/server_1/manuscript/supplementary.pdf

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paper-releases/pbisc-diffusion/updates/20261012T090327Z-uniform-manuscript-margins/diffusion/dataset/server_1/manuscript/supplementary.tex

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+% Supplementary Information. Compile independently with pdfLaTeX; all dependencies are local.
+% Rewritten from scratch on 2026-10-10 from the paper-summary deck; previous version in archive/pre_rewrite_20261010/.
+\documentclass[pdflatex,sn-nature]{sn-jnl}
+% Keep identical left/right margins on every page for screen reading.
+\geometry{twoside=false,bindingoffset=0pt}
+\usepackage{graphicx}
+\usepackage{amsmath,amssymb}
+\usepackage{booktabs,array,longtable,multirow}
+\usepackage{microtype}
+\usepackage{xcolor}
+\usepackage{adjustbox}
+\input{macros}
+\renewcommand{\theequation}{S\arabic{equation}}
+\begin{document}
+\raggedbottom
+\renewcommand\tablename{Supplementary Table}
+\title{Supplementary Information for: Diffusion model with bulk expression conditioning can generate precise single cell dataset from bulk transcriptome with preserved disease specific gene expression signature}
+\input{authors}
+\maketitle
+\raggedbottom
+
+\section*{Supplementary Notes}
+\renewcommand{\thesection}{Supplementary Note \arabic{section}:}
+\input{sections/supp_notes}
+
+\section*{Supplementary Methods}
+\input{sections/supp_methods_model}
+\input{sections/supp_methods_eval}
+
+\section*{Supplementary Tables}
+\input{sections/supp_table_cohorts}
+\input{sections/supp_tables}
+
+\section*{Supplementary Figures}
+\input{sections/supp_figures}
+
+\clearpage
+\bibliography{references}
+\end{document}