Bioinformatics

Quantitative and qualitative modelling for simulation-based analysis of biological and biomedical networks with emphasis to 

  1.  understanding behavior of underlying networks.
  2. prediction of molecular targets.
  3. 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.

 Contact PersonProf. Dr. Rza Bashirov

-https-math-emu-edu-tr-en-bioinformatics