Journal Club


Data Map



Personal Statement

As side technical interests, I like to develop and simulate some toy models to describe complex events within the computational social sciences and quantitative finance from the complexity paradigm's point of view. Also, I always enjoy having a cup of tea while reading in the philosophy of science, politics or so.

Research Statement

We are currently working on a simulation-based bottom-up approach to identify the community profile of real networks. Unlike the spectral analysis and GN algorithm which are top-down in nature, the method developed in our studies detects the community-like structures within the networks as the emergent property of an agent's local stochastic movements on those networks. As the structural modularity of a networked system may have corresponding functional modularity, by analysing its community profile we aim to describe the system level complex behavior of networked systems as the collective manifestation of its interacting functional modules.


[2] Modeling of complex biological systems.
[1] Modeling robust signaling pathways as an emergent phenomena of the dynamics of competing signaling cascades.


[3] 2010-2015 TUBITAK BIDEB Fellowship for PhD Study
[2] 2013-2014 TUBITAK BIDEB International Research Fellowship
[1] 2008-2010 TUBITAK BIDEB Fellowship for MSc study


[1] Yucel, M. and Hershberg, U. (March 2014) Network modularity as an emergent result of network based dynamics - a potential model for intracellular signalling and control in innate immunity. Poster presented at the workshop of Quantitative Immunology, Les Houches, France.

Invited Talk

[1] Memory As an Organizer of Dynamic Modules In a Network of Potential Interactions. Spatial Computing Workshop at the AAMAS Conference, Paris, France, May 2014.


[5] Chernova, I., Jones, D. D., Wilmore, J. R., Bortnick, A., Yucel, M., Hershberg, U. and Allman, D. (2014) Lasting antibody responses are mediated by a combination of newly formed and established bone marrow plasma cells drawn from clonally distinct precursors. J Immunol. 193(10):4971-9.
[4] Yucel, M. and Hershberg, U. (2014) Memory as an organizer of dynamic modules in a network of potential interactions. AAMAS Proceedings.
[3] Demir, T., Gube, O., Yucel, M. and Hames-Kocabas, E. E. (2013) Increased alkalotolerant and thermostable ribonuclease (RNase) production from alkaliphilic Streptomyces sp. M49-1 by optimizing the growth conditions using response surface methodology<\i>. World J. Microbiol. Biotechnol. 29(9):1625-33.
[2] Pilavtepe, M., Yucel, M., Helvaci, S. S., Demircioglu, M. and Yesil-Celiktas, O. (2012) Optimization and mathematical modelling of mass transfer between Zostera marina residues and supercritical CO2 modified with ethanol. J. of Supercritical Fluids 68(2012)87-93.
[1] Ongen, G., Sargin, S., Ustun, O., Kutlu, C. and Yucel, M. (2012) Dipeptidyl peptidase IV production by solid state fermentation using alternative fungal sources. Turk J Biol 36(2012)665-671.
* Co-Advised by Murat Elibol