Ozan Kahramanoğulları

Ozan Kahramanoğulları is an assistant professor 
at the Department of Mathematics, University of Trento.
and a senior researcher at
The Microsoft Research - University of Trento
Centre for Computational and Systems Biology. 

His research focuses on theoretical aspects of computer science
with practical problems in
 biology in perspective,
in particular
 modeling and simulation languages, 
stochastic simulation and analysis,
automated reasoning and proof theory,
and their applications in computational biology.
Between 2006 and 2009, Ozan worked at the Imperial CollegeDepartment of Computing
in collaboration with Prof. Luca Cardelli (Microsoft Research Cambridge)
in a joint project with the Centre for Integrative Systems Biology at Imperial College (CISBIC)
on a BBSRC grant (BB/C519670/1), “Computational Modelling of Biological Processes”. 

Ozan obtained his PhD in theoretical computer science from the TU Dresden (2006), 
MSc in computer science and artificial intelligence from the TU Dresden (2002), and
BSc in mathematics from the Hacettepe University in Ankara (1999). 
His PhD thesis with the title "Nondeterminism and Language Design in Deep Inference", 
supervised by Alessio Guglielmi, is on the interface between proof theory, 
in particular deep inference, and its applications to computer science. 

During his PhD and Masters, he spent a month at LORIA in Nancy, France (2004), and 7 months
at the Institute for Logic, Language and Computation (ILLC) at the University of Amsterdam (2001).


     Mechanistic interplay between ceramide and insulin resistance[LINK]
     F. Reali, M. Morine, O. Kahramanoğulları, S. Raichur

, H. Schneider, 

D. Crowther, C. Priami



Nature Scientific Reports 


      [ Keywords: Computational Biology, Systems Biology, Modelling, Ceramides, Insulin resistance ]

     Simulating Stochastic Dynamic Interactions with Spatial Information and Flux. [PDF]
     Ozan Kahramanoğulları
     Proceedings of 5th International Conference on the Theory and Practice of Natural Computing
     TPNC 2016, Sendai, Japan December 12-13, LNCS 10071, Springer, 2016.

     True Concurrency of Deep Inference Proofs. [PDF]
     Ozan Kahramanoğulları
     Proceedings of 23rd Workshop on Logic, Language, Information and Computation,
    WoLLIC 2016, August 16-19, 2016, Puebla, Mexico, Springer, 2016.

     Gener: A minimal programming module for chemical controllers based on DNA strand displacement.
     Ozan Kahramanoğulları, Luca Cardelli






       * Gener is a tool for performing reductions on DNA strands wrt. a strand displacement algebra.


       Among 100 most viewed articles of 2014 at BMC Systems Biology (5.7.2014)

       * Stochastic Flux Analysis of Chemical Reaction Networks, [LINK]
             Ozan Kahramanoğulları, James Lynch

BMC Systems Biology, 7: 133,



        * Rendering 3D Process Models: Actin


         Process Modeling and Rendering of Biochemical Structures: Actin.  
         Ozan Kahramanoğulları, Andrew Phillips, Federico Vaggi 

         Biomechanics of cells and tissues: experiments, models and simulations


Lecture Notes in Computational Vision and Biomechanics,  Volume 9, 2013