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).


     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.


     l: An Imperative DSL to Stochastically Simulate Biological Systems.  [LINK]
     Roberto Zunino, Durica Nikolic, Corrado PriamiOzan Kahramanoğulları, Tommaso Schiavinotto
     Proceedings of Programming Languages with Applications to Biology and Security 2015, 
     LNCS 9465, Springer, 2015.

       * A Theory of Model Equivalence, [LINK]
             Ozan Kahramanoğulları, James Lynch

Collection of essays in honor of Luca Cardelli

         Microsoft Research Technical Report, September 


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

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

BMC Systems Biology, 7: 133,




Invited Talk at the 5th Workshop on Logic and Systems Biology (13.7.2014)
        A theory of model equivalence based on stochastic simulation fluxes [PDF]
             5th Workshop on Logic and Systems Biology, July 13, 2014, 
         associated with CSL/LICS 2014 at the Vienna Summer of Logic

       * Interaction and depth against nondeterminism in proof search. [LINK]  
         Ozan Kahramanoğulları,


 Logical Methods in Computer Science,


10 (2:5),



         interana: interactive Multiplicative Linear Logic prover

       *Algorithmic modeling quantifies the complementary contribution of metabolic inhibitions 
        to gemcitabine efficacy.
        Ozan Kahramanoğulları, Gianluca Fantaccini, Paola Lecca, Daniele Morpurgo, Corrado Priami






        * 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