A computational model for genetic and epigenetic signals in colon cancer. - Irina A. Roznovat; Heather J. Ruskin (BIBM Workshops, 2012)

Methylation Inhibitors and Carcinogens in an Agent-Based Model for Colon Crypt Dynamics during Cancer Development. - Irina A. Roznovat; Heather J. Ruskin (EMS, 2013)

Interdependencies of Genetic and Epigenetic Events in a Computational Model for Colon Cancer Dynamics. - Irina-Afrodita Roznovat; Heather J. Ruskin (ERCIM News, 2013)

LogisticCrypt - A logistic model of intestinal crypt structure. - Irina A. Roznovat; Heather J. Ruskin (BIBM, 2014)

A computational analysis on methylation inhibition during intestinal cancer initiation. - Irina A. Roznovat; Heather J. Ruskin (BIBM, 2014)

Building cross-scale models of epigenetic mechanisms. - Heather J. Ruskin; Dimitri Perrin; Irina A. Roznovat (BIBM, 2014)

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)

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)

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)

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

Experiences From FAIRifying Community Data and FAIR Infrastructure in Biomedical Research Domains. - Dagmar Waltemath; Esther Thea Inau; Lea Michaelis; Venkata P. Satagopam; Irina Balaur (CoRDI, 2023)

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)

Generation of Synthetic Clinical Text: A Systematic Review. - Basel Alshaikhdeeb; Ahmed Abdelmonem Hemedan; Soumyabrata Ghosh; Irina Balaur; Venkata P. Satagopam (CoRR, 2025)