Research Output

Developed & Contributed Tools

  • Jan. 2017 - present - ySBGN: A GraphML-SBGN bidirectional converter aiming to enable the use of the general-purpose yEd Graph Editor for development of biological maps in SBGN Process Description and Activity Flow.

  • Jan. 2017 - present - cd2sbgnml: A bidirectional converter for translation between CellDesigner-flavoured SBML and SBGN-ML.

  • Jan. 2015 - Sept. 2016 - Recon2Neo4j: A resource in Neo4j graph database format for managing and querying the genome-scale human metabolic network reconstruction Recon2. Publication: Balaur et al., 2016, Bioinformatics, PMID 27993779.

  • Febr. 2015 - Dec. 2016 - STON (SBGN to Neo4j): A Java-based application for translation between SBGN standard and Neo4j database. Publication: TourĂ© et al., 2016, BMC Bioinformatics, PMID 27919219.

Publications

Five selected peer-reviewed Journal Publications - complete list is available on my GoogleScholar.

  • Mazein A., Ivanova O., Balaur I., Berzhitskaya V., Serebriyskaya T. , Ligon T., Hasenauer J., De Meulder B., Knowles R.G., Wheelock C.E., Dahlen S.E., Chung K.F., Adcock I., Roberts G., Djukanovic R., Pellet J., Gawron P., Ostaszewski M., Schneider R., Balling R., Maitland-van der Zee A.H., Sterk P.J., Auffray C. (2021), The AsthmaMap: advanced machine- and human-readable representations of disease mechanisms underlying asthma using domain expert knowledge. Journal of Allergy and Clinical Immunology. DOI: 10.1016/j.jaci.2020.11.032 . (IF: 10.22)

  • Balaur I.*, Roy L.*, Mazein A., Karaca S.G., Dogrusoz U., Barillot E. and Zinovyev A. (2020), cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats (*equal contribution), Bioinformatics. DOI: https://doi.org/10.1093/bioinformatics/btz969 . (IF: 4.53)

  • Balaur I., Mazein A., Saqi M., Lysenko A., Rawlings C. and Auffray C. (2017), Recon2Neo4j: Applying graph database technologies for managing comprehensive genome-scale networks, Bioinformatics, 33(7):1096-1098. DOI: 10.1093/bioinformatics/btw731. (IF: 7.30)

  • Lysenko* A., Roznovat* I., Saqi* M., Mazein A., Rawlings C. and Auffray C. (2016), Representing and querying disease networks using graph databases. BioData Mining, 9(1), pp. 9-23. DOI: 10.1186/s13040-016-0102-8. (* = joint first author). (IF: 1.64)

  • Roznovat I. and Ruskin H.J. (2015), A Theoretical Cross-Comparative Analysis on Dynamics of Small Intestine and Colon Crypts during Cancer Initiation, IET Systems Biology 9(6), pp. 259 - 267; DOI: 10.1049/iet-syb.2015.0048: Special Issue on 'Computational Models & Methods in Systems Biology & Medicine'. (IF: 1.05)

Conference Proceedings

  • Roznovat I. and Ruskin H.J., LogisticCrypt - a Logistic Model of Intestinal Crypt Structure, Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Belfast, UK, November 2-5, 2014, pp. 14 - 21. DOI: 10.1109/BIBM.2014.6999254.

  • Roznovat I. and Ruskin H.J., A Computational Analysis on Methylation Inhibition during Intestinal Cancer Initiation, Proceedings of the 2014 IEEE BIBM, Belfast, UK, November 2-5, 2014, pp. 22-29. DOI: 10.1109/BIBM.2014.6999255.

  • Ruskin H.J., Perrin D. and Roznovat I., Building Cross-Scale Models of Epigenetic Mechanisms, Proceedings of the 2014 IEEE BIBM, Belfast, UK, November 2-5, 2014, pp. 30-37. DOI: 10.1109/BIBM.2014.6999256.

  • Roznovat I. and Ruskin H.J., Methylation Inhibitors and Carcinogens in an Agent-Based Model for Colon Crypt Dynamics during Cancer Development, Proceedings of the UKSim/AMSS 7th European Modelling Symposium (EMS2013), Manchester, UK, November 20-22, 2013, pp. 144 - 149. DOI:10.1109/EMS.2013.27. Published by IEEE Computer Society.

  • Roznovat I. and Ruskin H.J., A Computational Model for Genetic and Epigenetic Signals in Colon Cancer, Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), Philadelphia, USA, October 4-7, 2012, pp. 188 -195. DOI: 10.1109/BIBMW.2012.6470302.

  • Roznovat I. and Ruskin H.J., Modelling the Genetic and Epigenetic Signals in Colon Cancer using a Bayesian Network, Proceedings of the 12th European Conference on Complex Systems (ECCS'12), Springer Proceedings in Complexity, Brussels, Belgium, September 3-7, 2012, pp. 1059-1062. DOI: 10.1007/978-3-319-00395-5_126.

PhD Thesis

  • Roznovat I. (2014), A Computational Model for Colon Cancer Dynamics, School of Computing, Dublin City University, Dublin, Ireland.

Book Chapter

  • Saqi M., Pellet J., Roznovat I., Mazein A., Ballereau S., DeMeulder B. and Auffray C. (2016), Systems Medicine: the Future of Medical Genomics, Healthcare and Wellness, Systems Medicine, Schmitz, U. et Wolkenhauer, O. (Eds.), Springer New York, pp. 43-60. DOI 10.1007/978-1-4939-3283-2_3, ISBN 978-1-4939-3282-5.

Book of abstracts

  • Szczesna, K., Sandoval, J., Modhukur, V., Kull, M., Rajashekar, B., Perrin, D., Barat, A., Raghavan, K., Roznovat, I., Huertas, D., Vilo, J. and Ruskin, H.J., Complexity of Interdependent Epigenetic Signals in Cancer Initiation, Book of abstracts of the "Complexity-NET projects: Interdisciplinary Challenges for Complexity Science" Workshop, ECCS'13, Barcelona, Spain, Sept. 16-20, 2013, pp. 16 - 23.

Magazines

Invited talks

  • Data management and engineering in Biomap Data Platform: a FAIRytale, the 3rd FAIRplus Innovation and SME Forum, Berlin, May 17, 2022. (Invited talk to present experience from the FAIRplus Fellowship; co-presenter with S. Ghosh, LCSB)

  • An Integrative Framework for Data Management in Systems Biology and Medicine, GraphConnect Europe, London, UK, April 26, 2016. (Presentation url: https://www.youtube.com/watch?v=ukvVVMhJACE)

  • Introduction of the DiseaseNetwork project, Amsterdam Medical Center, Amsterdam, October 23, 2015

  • Application of graph databases for the integration of biological data, SCI-SYM, School of Computing, Dublin City University, Dublin, Ireland, July 13, 2015

Contributed talks

  • Initial FAIR assessment of the biological diagrams available in the MINERVA platform within the COVID-19 Disease Map, The 6th Disease Maps Community Meeting (DMCM2021), Nov. 29-30, 2021, Online

  • Integrating disease maps using a graph database approach, The 3rd Disease Maps Community Meeting (DMCM2018), Paris, France, Jun. 21-22, 2018

  • Towards a knowledge network for asthma: a graph based data integration approach for contextualisation of asthma related genes, The 1st Conference of the European Association of Systems Medicine (EASyM), Berlin, Germany, Oct. 26-28, 2016 (Poster)

  • An integrative Graph-database Approach for Respiratory Disease, The 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology, (ISMB/ECCB 2015), Dublin, Ireland, Jul. 10-14, 2015 (Poster)

  • LogisticCrypt - a Logistic Model of Intestinal Crypt Structure, The 2014 IEEE International Conference on Bioinformatics and BiomedicineWorkshops (BIBMW), Belfast, UK, Nov. 2-5, 2014

  • A Computational Analysis on Methylation Inhibition during Intestinal Cancer Initiation, The 2014 IEEE BIBMW, Belfast, UK, Nov. 2-5, 2014

  • Building Cross-Scale Models of Epigenetic Mechanisms, The 2014 IEEE BIBMW, Belfast, UK, Nov. 2-5, 2014

  • Toward A Multi-scale Model for Colon Cancer Dynamics, Modelling Approaches in Epigenetics 2014 - An EpiGeneSys and BLUEPRINT joint workshop, Cambridge, UK, Mar. 20-21, 2014

  • Methylation Inhibitors and Carcinogens in an Agent-Based model for Colon Crypt Dynamics during Cancer Development, UKSim/AMSS 7th European Modelling Symposium (EMS2013), Manchester, UK, Nov. 20-22, 2013

  • Dynamics of Genetic and Epigenetic Events in a Network-based framework for Colon Cancer Initiation, European Conference on Complex Systems 2013 (ECCS'13), Barcelona, Spain, Sept. 16-20, 2013

  • Interdependencies of Genetic and Epigenetic Mechanisms in a framework for Colon Cancer Dynamics, Workshop "Young Researchers Network on Complex Systems (YRNCS)", ECCS'13, Barcelona, Spain, Sept. 16-20, 2013

  • A Computational Model for Genetic and Epigenetic Signals in Colon Cancer, The Fifth InternationalWorkshop on Biomolecular Network Analysis (IWBNA), The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, USA, Oct. 4-7, 2012

  • Complexity of Interdependent Epigenetic Signals in Cancer Initiation, Workshop "Complexity-NET projects: Interdisciplinary Challenges for Complexity Science", ECCS'13, Barcelona, Spain, Sept. 16-20, 2013

  • Bayesian Network for Interdependent Genetic and Epigenetic Signals in Colon Cancer, The 23rd Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2012), Dublin, Ireland, Sept. 17-19, 2012

  • Ageing and micromolecular events in a Bayesian Network for Colon Cancer, The Virtual Institute of Bioinformatics (VIBE 2012), Dublin, Ireland, Nov. 2, 2012

  • Complexity of Interdependent Epigenetic Signals in Cancer Initiation, Computational Biology and Innovation - PhD Symposium, UCD, Dublin, Ireland, Dec. 6-7, 2011 (Poster)

Press interview on use of graph databases