Representing and querying disease networks using graph databases. - Artem Lysenko; Irina A. Roznovat; Mansoor A. S. Saqi; Alexander Mazein; Christopher J. Rawlings; Charles Auffray (BioData Min., 2016)

STON: exploring biological pathways using the SBGN standard and graph databases. - Vasundra Touré; Alexander Mazein; Dagmar Waltemath; Irina Balaur; Mansoor A. S. Saqi; Ron Henkel; Johann Pellet; Charles Auffray (BMC Bioinform., 2016)

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. - Irina Balaur; Alexander Mazein; Mansoor A. S. Saqi; Artem Lysenko; Christopher J. Rawlings (Bioinform., 2017)

EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. - Irina Balaur; Mansoor A. S. Saqi; Ana Barat; Artem Lysenko; Alexander Mazein; Christopher J. Rawlings; Heather J. Ruskin; Charles Auffray (J. Comput. Biol., 2017)

A computational framework for complex disease stratification from multiple large-scale datasets. - Bertrand De Meulder; Diane Lefaudeux; Aruna T. Bansal; Alexander Mazein; Amphun Chaiboonchoe; Hassan Ahmed; Irina Balaur; Mansoor A. S. Saqi; Johann Pellet; Stéphane Ballereau; Nathanaël Lemonnier; Kai Sun 005; et al. (BMC Syst. Biol., 2018)

Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. - Adrien Rougny; Vasundra Touré; Stuart L. Moodie; Irina Balaur; Tobias Czauderna; Hanna Borlinghaus; Ugur Dogrusoz; Alexander Mazein; Andreas Dräger; Michael L. Blinov; Alice Villéger; Robin Haw; et al. (J. Integr. Bioinform., 2019)

Human-like layout algorithms for signalling hypergraphs: outlining requirements. - Martin Siebenhaller; Sune S. Nielsen; Fintan McGee; Irina Balaur; Charles Auffray; Alexander Mazein (Briefings Bioinform., 2020)

RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. - Vidisha Singh; George D. Kalliolias; Marek Ostaszewski; Maëva Veyssiere; Eleftherios Pilalis; Piotr Gawron; Alexander Mazein; Eric Bonnet; Elisabeth Petit-Teixeira; Anna Niarakis (Database J. Biol. Databases Curation, 2020)

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats. - Irina Balaur; Ludovic Roy; Alexander Mazein; S. Gökberk Karaca; Ugur Dogrusoz; Emmanuel Barillot; Andrei Yu. Zinovyev (Bioinform., 2020)

Systems biology graphical notation markup language (SBGNML) version 0.3. - Frank T. Bergmann; Tobias Czauderna; Ugur Dogrusoz; Adrien Rougny; Andreas Dräger; Vasundra Touré; Alexander Mazein; Michael L. Blinov; Augustin Luna (J. Integr. Bioinform., 2020)

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. - Alexander Mazein; Adrien Rougny; Jonathan R. Karr; Julio Saez-Rodriguez; Marek Ostaszewski; Reinhard Schneider 002 (Briefings Bioinform., 2021)

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. - Adrien Rougny; Vasundra Touré; John Albanese; Dagmar Waltemath; Denis Shirshov; Anatoly A. Sorokin; Gary D. Bader; Michael L. Blinov; Alexander Mazein (Briefings Bioinform., 2021)

Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. - Hasan Balci; Metin Can Siper; Nasim Saleh; Ilkin Safarli; Ludovic Roy; Merve Kilicarslan; Rumeysa Ozaydin; Alexander Mazein; Charles Auffray; Özgün Babur; Emek Demir; Ugur Dogrusoz (Bioinform., 2021)

GraphML-SBGN bidirectional converter for metabolic networks. - Irina Balaur; Ludovic Roy; Vasundra Touré; Alexander Mazein; Charles Auffray (J. Integr. Bioinform., 2022)

StonPy: a tool to parse and query collections of SBGN maps in a graph database. - Adrien Rougny; Irina Balaur; Augustin Luna; Alexander Mazein (Bioinform., 2023)

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. - Alexander Mazein; Marcio Luis Acencio; Irina Balaur; Adrien Rougny; Danielle Welter; Anna Niarakis; Diana Ramirez Ardila; Ugur Dogrusoz; Piotr Gawron; Venkata P. Satagopam; Wei Gu; Andreas Kremer; et al. (Frontiers Bioinform., 2023)

Graph databases in systems biology: a systematic review. - Ilya Mazein; Adrien Rougny; Alexander Mazein; Ron Henkel; Lea Gütebier; Lea Michaelis; Marek Ostaszewski; Reinhard Schneider 002; Venkata P. Satagopam; Lars Juhl Jensen; Dagmar Waltemath; Judith A. H. Wodke; et al. (Briefings Bioinform., 2024)