docs(manuscript): fix template errors and update author list

- Fix undefined \authormark in OUP cls (providecommand shim)
- Fix broken UTF-8 in reference.bib (LaTeX accent commands)
- Fix abstract bold rendering in OUP template (mdseries reset)
- Add Fabio Baumgärtel, update Samuel M Walter
- Add contributed equally (#) and dual corresponding author (*)
- Fix address numbering and LaTeX-safe special characters
- Update biorxiv abstract, keywords, and author formatting

Author: Mnikley

manuscript/biorxiv/main.tex

@@ -27,25 +27,33 @@
 \graphicspath{{../shared/Fig/}}
 
 % ── Title ────────────────────────────────────────────────────────────────────
-\title{Graph Lens Lite: An interactive biological network viewer for displaying, sharing, and exploring disease pathobiology and drug mechanism of action models}
+\title{Graph Lens Lite: An interactive biological network viewer for displaying, exploring, and sharing disease pathobiology and drug mechanism of action models}
 
 % ── Authors & affiliations ───────────────────────────────────────────────────
-\author[1,2,*]{Matthias Ley}
-\author[1]{Kinga Kęska-Izworska}
+\renewcommand\Authfont{\normalsize}
+\renewcommand\Affilfont{\small}
+\renewcommand\Authsep{, }
+\renewcommand\Authand{, }
+\renewcommand\Authands{, }
+
+\author[1,2]{Matthias Ley\textsuperscript{,*}}
+\author[1]{Kinga K\k{e}ska-Izworska}
 \author[1]{Lucas Fillinger}
-\author[1]{Samuel Walter}
+\author[1]{Samuel M Walter}
+\author[1]{Fabio Baumg\"{a}rtel}
 \author[1,2]{Enrico Bono}
 \author[1,2]{Louiza Galou}
 \author[1]{Peter Andorfer}
 \author[3]{Pirmin Hauser}
 \author[3]{Johannes Leierer}
-\author[1,2]{Klaus Kratochwill}
-\author[1,3]{Paul Perco}
+\author[1,2]{Klaus Kratochwill\textsuperscript{,\#,*}}
+\author[1,3]{Paul Perco\textsuperscript{,\#}}
 
-\affil[1]{Delta4 GmbH, Alser Straße 23/30, 1080 Vienna, Austria}
+\affil[1]{Delta4 GmbH, Alser Stra\ss{}e 23/30, 1080 Vienna, Austria}
 \affil[2]{Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria}
 \affil[3]{Department of Internal Medicine IV, Medical University Innsbruck, Anichstrasse 35, 6020 Innsbruck, Austria}
-\affil[*]{Corresponding author: \href{mailto:matthias.ley@delta4.ai}{matthias.ley@delta4.ai}}
+\affil[ ]{\textsuperscript{\#}Contributed equally}
+\affil[ ]{\textsuperscript{*}Corresponding authors: \href{mailto:matthias.ley@delta4.ai}{matthias.ley@delta4.ai}, \href{mailto:klaus.kratochwill@delta4.ai}{klaus.kratochwill@delta4.ai}}
 
 \date{}  % suppress date
 
@@ -54,12 +62,13 @@
 
 % ── Abstract ─────────────────────────────────────────────────────────────────
 \begin{abstract}
-Biological networks are important ..
-We have developed Graph Lens Lite, a lightweight but powerful interactive network viewer for displaying, sharing, and exploring disease pathobiology and drug mechanism of action molecular models. …
-Graph Lens Lite is available at GitHub (\url{https://github.com/Delta4AI/GraphLensLite}).
+\noindent\textbf{Motivation:} Biological network visualization together with graph-based analyses are key techniques in systems biology and network medicine to detect patterns and generate new hypotheses regarding disease pathobiology, drug target identification, or digital drug discovery. Network representations are also a way to communicate research findings and share results with colleagues and coworkers. \\
+\textbf{Results:} We have developed Graph Lens Lite, a browser-based tool that combines rich visualization capabilities with a streamlined interface for exploring and sharing biological networks. It offers an expressive query language, topological network analysis, GUI-based filtering, visual grouping, customizable layouts, a data-editor, and fine-grained property-based styling options, particularly suited for visualizing molecular models of disease pathobiology or drug mechanism of action. \\
+\textbf{Availability:} Graph Lens Lite is available at GitHub (\url{https://github.com/Delta4AI/GraphLensLite}). \\
+\textbf{Supplementary information:} Supplementary data are available at \textit{Bioinformatics} online.
 
 \medskip
-\noindent\textbf{Keywords:} Network Viewer, Graph Exploration, Visualization, Drug Mechanism of Action, Disease Pathobiology
+\noindent\textbf{Keywords:} network visualization, graph exploration, disease pathobiology, drug mechanism of action
 \end{abstract}
 
 % ── Shared body ──────────────────────────────────────────────────────────────

manuscript/oxford/main.tex

@@ -25,6 +25,7 @@
 \theoremstyle{thmstylethree}
 \newtheorem{definition}{Definition}
 
+\providecommand{\authormark}[1]{\gdef\@authormark{#1}}
 \begin{document}
 
 % ── Journal metadata ─────────────────────────────────────────────────────────
@@ -37,44 +38,46 @@
 \firstpage{1}
 
 % ── Title ────────────────────────────────────────────────────────────────────
-\title[Graph Lens Lite]{Graph Lens Lite: An interactive biological network viewer for displaying, sharing, and exploring disease pathobiology and drug mechanism of action models}
+\title{Graph Lens Lite: An interactive biological network viewer for displaying, exploring, and sharing disease pathobiology and drug mechanism of action models}
 
 % ── Authors & affiliations ───────────────────────────────────────────────────
 \author[1,2,$\ast$]{Matthias Ley\ORCID{0000-0001-6853-8542}}
 \author[1]{Kinga Kęska-Izworska\ORCID{0000-0002-4329-1499}}
 \author[1]{Lucas Fillinger\ORCID{0000-0001-5341-8097}}
-\author[1]{Samuel Walter}
+\author[1]{Samuel M Walter}
+\author[1]{Fabio Baumg\"{a}rtel}
 \author[1,2]{Enrico Bono\ORCID{0009-0007-7272-5034}}
 \author[1,2]{Louiza Galou\ORCID{0009-0008-5176-2802}}
 \author[1]{Peter Andorfer\ORCID{0009-0003-3492-4017}}
 \author[3]{Pirmin Hauser}
 \author[3]{Johannes Leierer}
-\author[1,2]{Klaus Kratochwill\ORCID{0000-0003-0803-614X}}
-\author[1,3]{Paul Perco\ORCID{0000-0003-2087-5691}}
+\author[1,2,$\#$,$\ast$]{Klaus Kratochwill\ORCID{0000-0003-0803-614X}}
+\author[1,3,$\#$]{Paul Perco\ORCID{0000-0003-2087-5691}}
 
 \authormark{Ley et al.}
 
-\address[1]{\orgname{Delta4 GmbH}, \orgaddress{\street{Alser Straße 23/30}, \postcode{1080}, \state{Vienna}, \country{Austria}}}
+\address[1]{\orgname{Delta4 GmbH}, \orgaddress{\street{Alser Stra\ss{}e 23/30}, \postcode{1080}, \state{Vienna}, \country{Austria}}}
 \address[2]{\orgdiv{Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics}, \orgname{Medical University Vienna}, \orgaddress{\street{Waehringer Guertel 18-20}, \postcode{1090}, \state{Vienna}, \country{Austria}}}
-\address[4]{\orgdiv{Department of Internal Medicine IV}, \orgname{Medical University Innsbruck}, \orgaddress{\street{Anichstrasse 35}, \postcode{6020}, \state{Innsbruck}, \country{Austria}}}
+\address[3]{\orgdiv{Department of Internal Medicine IV}, \orgname{Medical University Innsbruck}, \orgaddress{\street{Anichstrasse 35}, \postcode{6020}, \state{Innsbruck}, \country{Austria}}}
 
-\corresp[$\ast$]{Corresponding author. \href{email:matthias.ley@delta4.ai}{matthias.ley@delta4.ai}}
+\corresp[$\ast$]{Corresponding authors. \href{mailto:matthias.ley@delta4.ai}{matthias.ley@delta4.ai}, \href{mailto:klaus.kratochwill@delta4.ai}{klaus.kratochwill@delta4.ai}\\}
+
+\corresp[$\#$]{Contributed equally}
 
 \received{Date}{0}{Year}
 \revised{Date}{0}{Year}
 \accepted{Date}{0}{Year}
 
 % ── Abstract ─────────────────────────────────────────────────────────────────
-\abstract{
-\textbf{Motivation:} Biological networks are important .. \\
-\textbf{Results:} We have developed Graph Lens Lite, a lightweight but powerful interactive network viewer for displaying, sharing, and exploring disease pathobiology and drug mechanism of action molecular models. … \\
-\textbf{Availability and implementation:} Graph Lens Lite is available at GitHub (\url{https://github.com/Delta4AI/GraphLensLite}).\\
+\abstract{\mdseries
+\textbf{Motivation:} Biological network visualization together with graph-based analyses are key techniques in systems biology and network medicine to detect patterns and generate new hypotheses regarding disease pathobiology, drug target identification, or digital drug discovery. Network representations are also a way to communicate research findings and share results with colleagues and coworkers. \\
+\textbf{Results:} We have developed Graph Lens Lite, a browser-based tool that combines rich visualization capabilities with a streamlined interface for exploring and sharing biological networks. It offers an expressive query language, topological network analysis, GUI-based filtering, visual grouping, customizable layouts, a data-editor, and fine-grained property-based styling options, particularly suited for visualizing molecular models of disease pathobiology or drug mechanism of action. \\
+\textbf{Availability:} Graph Lens Lite is available at GitHub (\url{https://github.com/Delta4AI/GraphLensLite}).\\
 \textbf{Contact:} \href{mailto:matthias.ley@delta4.ai}{matthias.ley@delta4.ai}\\
-\textbf{Supplementary information:} Supplementary data are available at \textit{Bioinformatics}
-online.
+\textbf{Supplementary information:} Supplementary data are available at \textit{Bioinformatics} online.
 }
 
-\keywords{Network Viewer, Graph Exploration, Visualization, Drug Mechanism of Action, Disease Pathobiology}
+\keywords{network visualization, graph exploration, disease pathobiology, drug mechanism of action}
 
 \maketitle
 

manuscript/shared/reference.bib

@@ -81,7 +81,7 @@ @article{chembl2017
 	number = {D1},
 	urldate = {2023-02-07},
 	journal = {Nucleic Acids Research},
-	author = {Gaulton, Anna and Hersey, Anne and Nowotka, Michał and Bento, A. Patrícia and Chambers, Jon and Mendez, David and Mutowo, Prudence and Atkinson, Francis and Bellis, Louisa J. and Cibrián-Uhalte, Elena and Davies, Mark and Dedman, Nathan and Karlsson, Anneli and Magariños, María Paula and Overington, John P. and Papadatos, George and Smit, Ines and Leach, Andrew R.},
+	author = {Gaulton, Anna and Hersey, Anne and Nowotka, Micha{\l} and Bento, A. Patr{\'i}cia and Chambers, Jon and Mendez, David and Mutowo, Prudence and Atkinson, Francis and Bellis, Louisa J. and Cibri{\'a}n-Uhalte, Elena and Davies, Mark and Dedman, Nathan and Karlsson, Anneli and Magari{\~n}os, Mar{\'i}a Paula and Overington, John P. and Papadatos, George and Smit, Ines and Leach, Andrew R.},
 	month = jan,
 	year = {2017},
 	pages = {D945--D954},
@@ -210,7 +210,7 @@ @article{liu_paintomics_2022
 	issue = {W1},
 	journaltitle = {Nucleic Acids Research},
 	shortjournal = {Nucleic Acids Research},
-	author = {Liu, Tianyuan and Salguero, Pedro and Petek, Marko and Martinez-Mira, Carlos and Balzano-Nogueira, Leandro and Ramšak, Živa and {McIntyre}, Lauren and Gruden, Kristina and Tarazona, Sonia and Conesa, Ana},
+	author = {Liu, Tianyuan and Salguero, Pedro and Petek, Marko and Martinez-Mira, Carlos and Balzano-Nogueira, Leandro and Ram{\v{s}}ak, {\v{Z}}iva and {McIntyre}, Lauren and Gruden, Kristina and Tarazona, Sonia and Conesa, Ana},
 	urldate = {2025-05-14},
 	date = {2022-07-05},
 	file = {Full Text PDF:/home/glory/Zotero/storage/45Q2VGT4/Liu et al. - 2022 - PaintOmics 4 new tools for the integrative analysis of multi-omics datasets supported by multiple p.pdf:application/pdf;Snapshot:/home/glory/Zotero/storage/9MTJAQDX/6591534.html:text/html},
@@ -358,19 +358,19 @@ @article{valenzuela-escarcega_large-scale_2018
 	pages = {bay098},
 	journaltitle = {Database},
 	shortjournal = {Database},
-	author = {Valenzuela-Escárcega, Marco A and Babur, Özgün and Hahn-Powell, Gus and Bell, Dane and Hicks, Thomas and Noriega-Atala, Enrique and Wang, Xia and Surdeanu, Mihai and Demir, Emek and Morrison, Clayton T},
+	author = {Valenzuela-Esc{\'a}rcega, Marco A and Babur, {\"O}zg{\"u}n and Hahn-Powell, Gus and Bell, Dane and Hicks, Thomas and Noriega-Atala, Enrique and Wang, Xia and Surdeanu, Mihai and Demir, Emek and Morrison, Clayton T},
 	urldate = {2025-05-26},
 	date = {2018-01-01},
 	keywords = {{REACH};biolinker},
-	file = {Full Text PDF:/home/glory/Zotero/storage/FNPHT96G/Valenzuela-Escárcega et al. - 2018 - Large-scale automated machine reading discovers new cancer-driving mechanisms.pdf:application/pdf;Snapshot:/home/glory/Zotero/storage/GDVUL6L6/5107029.html:text/html},
+	file = {Full Text PDF:/home/glory/Zotero/storage/FNPHT96G/Valenzuela-Escarcega et al. - 2018 - Large-scale automated machine reading discovers new cancer-driving mechanisms.pdf:application/pdf;Snapshot:/home/glory/Zotero/storage/GDVUL6L6/5107029.html:text/html},
 }
 
 @software{noauthor_gephigephi-lite_2025,
 	title = {gephi/gephi-lite},
 	rights = {{GPL}-3.0},
 	url = {https://github.com/gephi/gephi-lite},
 	abstract = {A web-based, lighter version of Gephi},
-    author = {Jacomy, Mathieu and Jacomy, Alexis and Girard, Paul and Simard, Benoît},
+    author = {Jacomy, Mathieu and Jacomy, Alexis and Girard, Paul and Simard, Beno{\^i}t},
 	publisher = {Gephi},
 	urldate = {2025-05-26},
 	date = {2025-05-19},