Quantitative and qualitative modelling for simulation-based analysis of biological and biomedical networks with emphasis to
- understanding behavior of underlying networks.
- prediction of molecular targets.
- identification of efficient drug and drug combinations in line with target-based drug discovery.
PhD Thesis
- Duranay, R., Exploiting fuzzy stochastic Petri nets to predict targeted efficient drug combinations for Spinal Muscular Atrophy, EMU, September 2019.
- Mehraei, M., Exploiting hybrid functional Petri nets to investigate transcriptional activity of hemoglobin switching, EMU, July 2016.
- Akçay, İ.N., Petri net-based quantitative modeling and validation of p16-mediated signaling pathway, EMU, February 2016.
MS Thesis
- Ngandjoug, G. Y., Qualitative analysis of cancer pathways with transition and place invariants, EMU, January 2019.
- Adam, M. L., Biomodeling with discrete, continuous and hybrid Petri nets, EMU, January 2019.
- Krivdić, A., Comprehensive analysis of mathematical and computational models of cell cycle, EMU, September 2015.
- Akgün, G., Performance Analysis of Hill cipher and its modifications, EMU, February 2014.
- Dolma, F., Implementing Petri nets for modeling and simulation in biosciences, EMU, January 2012
Project
- BAP-C research project (PDGC-04-18-0006) of Eastern Mediterranean University: Predicting efficient drug combinations for Spinal Muscular Atrophy using Petri net technologies (Director: Rza Bashirov; Researchers: Recep Duranay, Adil Şeytanoğlu; Start Date: 01.10.2018; Duration: 12 months; Budget: 8,000 TL; Project completed on 29.09.2019)
Publications
- Bashirov, R., Duranay, R., Şeytanoğlu, A., Mehraei, M., Akçay, İ.N., Exploiting fuzzy stochastic Petri nets to predict effective drug combinations for Spinal Muscular Atrophy, Turkish Journal of Electrical Engineering and Computer Sciences (SCIE), 27, 2019, 4009-4022, DOI: 10.3906/elk-1902-133.
- Bashirov, R., Akçay, İ., Stochastic simulation-based prediction of the behavior of p16-mediated signaling pathway, Fundamenta Informaticae (SCIE) 160, 2018, 167–179, DOI: 10.3233/FI-2018-1679.
- Bashirov, R., Mehraei, M., Identifying targets for gene therapy of β-globin disorders using quantitative modeling approach, Information Sciences (SCI) 397-398, 2017, 37-47.
- Mehraei, M., Bashirov, R., Tüzmen, Ş., Target based drug discovery for β-globin disorders: drug target prediction implementing quantitative modeling with hybrid functional Petri nets, Journal of Bioinformatics and Computational Biology (SCIE) 14(4), 2016, 1650026, DOI: 10.1142/S0219720016500268.
- Akçay, İ., Bashirov, B., Tüzmen, Ş., Validation of signaling pathways: case study of the p16-mediated pathway, Journal of Bioinformatics and Computational Biology (SCIE) 13(2), 2015, 1550007, DOI: 10.1142/S0219720015500079.
- Bashirov, R., Ngandjoug, G.R.Y.,Understanding behavior of biological network via invariant computation, Advances in Intelligent Systems and Computing (Web of Science, Scopus) 1095, 2020, 390-396.
- Duranay R., Bashirov, R., Şeytanoğlu, A., Simulation-based identification of optimal combination of drug candidates for Spinal Muscular Atrophy, Procedia Computer Science (Web of Science, Scopus) 120, 2018, 253-259
Conference presentations
- Bashirov, R., Ngandjoug, G.R.Y.,Understanding behavior of biological network via invariant computation, In: Proc. 10th International Conference on Theory and Application of Soft Computing, Computing with Words and Perception, Prague, Czech Republic, 27-28 August, 2019.
- Duranay, R., Bashirov, R., Şeytanoğlu, A., Simulation-based identification of optimal combination of drug candidates for Spinal Muscular Atrophy, In: Proc. 9th International Conference on Theory and Application of Soft Computing, Computing with Words and Perception, Budapest, Hungary, 24-25 August, 2017.
- Bashirov, R., The integrated modelling of biological processes with differential equations and Petri nets, In: Proc. 11th International Conference on Applications of Fuzzy Systems and Soft Computing, Rouen, France, 2-3 September, 2014, 47-55.
- Çetin, İ.N., Bashirov, R., Tüzmen, Ş., Petri net based modelling and simulation of p16-Cdk4/6-Rb pathway, In: Proc. 4th International Workshop on Biological Processes and Petri nets, CEUR, Vol. 988, Milan, Italy, 24-25 June, 2013, 30-44.
