Publications of Ozan Kahramanoğulları

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 Journals

     Interaction and Depth against Nondeterminism in Proof Search[PDF]  
     Ozan Kahramanoğulları
     

Logical Methods in Computer Science,

in press.


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

BMC Systems Biology, 7:133,

 

2013.


     An Intuitive Modelling Interface for Systems Biology[PDF]   [LINK]
     Ozan Kahramanoğulları, Luca Cardelli

     International Journal of Software and Informatics, 7:4, 

2013. 

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

     PLoS ONE,

 

2012.

 
[PLOS-ONE-LINK]  [PRESS-TRENTINO]  [PRESS-L'ADIGE]

     CoSBiLab LIME: a language interface for stochastic dynamical modelling in ecology.  [LINK]
     Ozan Kahramanoğulları, James Lynch, Ferenc Jordan

     Environmental Modelling and Software,

 26:685-687, 2011.

 
 

     A Process Model of Rho GTP-binding Proteins. [PDF]
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Andrew Phillips

     Theoretical Computer Science,

 410:3166-3185, 2009.

 


     Biophysical Mechanism for Ras-Nanocluster Formation and Signaling in Plasma Membrane[LINK] 
     Thomas Gurry, Ozan Kahramanoğulları, Robert Endres

     PLoS ONE,

 

 4, 2009.

 
 

     On Linear Logic Planning and Concurrency. [LINK] 
     Ozan Kahramanoğulları
     

Information and Computation,

 207(11):1229-1258, 2009.

 
     System BV is NP-complete. [LINK]
     Ozan Kahramanoğulları

     Annals of Pure and Applied Logic,

 152(1-3):107-121, 2008.



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

    

Biomechanics of cells and tissues: experiments, models and simulations
     Springer, Lecture Notes in Computational Vision and Biomechanics, Volume 9, 2013.
     
     Nondeterminism and Language Design in Deep Inference
     A Proof Theoretic Approach to Logic Programming
     Ozan Kahramanoğulları

     

Lambert Academic Publishing, ISBN 978-3-659-13475-3, 

2012.

 
 
     Process algebra models in biology: the case of phagocytosis.  
     Ozan Kahramanoğulları

     

Bioinformatics & Computational Systems Biology: Recent Advances and Applications

     IGI Global, 2012.

 



 International conferences and workshops

     Algorithmic Systems Ecology: Experiments on Multiple Interaction Types and Patches.  [PDF]
     Ozan Kahramanoğulları, James Lynch, Corrado Priami
     Keynote Paper, Proceedings of InSuEdu 2012, LNCS 7991, Springer, 2014.
     
     Composability: Perspectives in Ecological Modeling[PDF]
     Ozan Kahramanoğulları, Ferenc Jordan, Corrado Priami
     Proceedings of ANB 2011, LNCS 6479, Springer, 2011.
     
     Modelling and estimating dynamics of tumor shrinkage with BlenX and KInfer[PDF]
     Paola Lecca, Ozan Kahramanoğulları, Daniele Morpurgo, Corrado Priami, Ross A. Soo

     13th International Conference on Modelling and Simulation, March 30 - April 1, 2011


     Proceedings of UKSim 2011, IEEE, 75 - 80, 2011.

     Flux Analysis in Process Models via Causality. [PDF]
     Ozan Kahramanoğulları
     

3rd Workshop "From Biology To Concurrency and back", March 27,  2010.

     

Proceedings of FBTC'10, EPTCS 19, 20-39, 2010.

 
     An Intuitive Automated Modelling Interface for Systems Biology[PDF]
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron
     

Fifth Workshop on Developments in Computational Models - 

     

Computational Models From Nature, Rhodes, Greece, July 11, 2009.

     Proceedings of DCM'09, EPTCS 9, 73-86, 2009.

     A Process Model of Actin Polymerisation. [PDF]
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Andrew Phillips
     2nd Workshop "From Biology To Concurrency and back", Reykjavik, Iceland, July 12, 2008.
     Proceedings of FBTC'08, ENTCS 229(1), Elsevier, 127-144, 2009.   

     On Linear Logic Planning and Concurrency. [PDF] 
     Ozan Kahramanoğulları
     Language and Automata Theory and Applications, Second International Conference, 
     Tarragona, Spain, March 13-19, 2008. 
     

Proceedings of LATA'08, LNCS 5196, Springer

 

, 250-262, 2008.

 


     Maude as a Platform for Designing and Implementing Deep Inference Systems. [PDF]
     Ozan Kahramanoğulları
     Eighth International Workshop on Rule Based Programming, Paris, France, July 12, 2007. 
     Proceedings of RULE'07, ENTCS 219, Elsevier, 35-50, 2008. 

     A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis. [PDF]
     Ozan Kahramanoğulları, Luca Cardelli, Philippa Gardner
     1st Workshop "From Biology To Concurrency and back", Lisbon, Portugal, September 8, 2008.
     Proceedings of FBTC'07, ENTCS 194(3), Elsevier, 87-102, 2008 



     Reducing Nondeterminism in the Calculus of Structures. [LINK]
     Ozan Kahramanoğulları
     Logic for Programming, Artificial Intelligence, and Reasoning, 13th International Conference,
     Phnom Penh, Cambodia, November 13-17, 2006. 
     Proceedings of LPAR'06, LNCS 4246, Springer, 272-286, 2006.

     System BV is NP-complete. [PDF]


     Ozan Kahramanoğulları
     12th Workshop on Logic, Language, Information and Computation, 
     Florianopolis, Santa Catarina, Brazil, July 19-22, 2005. 
     Proceedings of WoLLIC'05, ENTCS 143, Elsevier, 87-99, 2006.  

     Towards Planning as Concurrency.  [PDF]


     Ozan Kahramanoğulları
     IASTED International Conference on Artificial Intelligence and Applications, 
     Innsbruck, Austria, February 14-16, 2005. 
     Proceedings of AIA'05, Acta Press, 387-393, 2005.  


     

System BV without the Equalities for Unit, 

 [PDF]
     Ozan Kahramanoğulları
     

19th International Symposium on Computer and Information Sciences,

     

Kemer, Antalya, Turkey, October 27- 29, 2004.

     

Proceedings of ISCIS'04, LNCS 3280, Springer, 986-995,

 

 2004.


     

A Formal Assessment Result for Fluent Calculus Using the Action Description Language  A

 . 

     Ozan Kahramanoğulları, Michael Thielscher
     

26th Annual German Conference on AI, Hamburg, Germany, September 15-18, 2003.

     

Proceedings of KI'03, LNCS 2821, Springer, 209-223,

 

 2003.



 Other papers

     Ingredients of a Deep Inference Theorem Prover. [PDF] 
     Ozan Kahramanoğulları
     Second International Workshop on Classical Logic and Computation, 
     CL&C'08, Rejkjavik, Iceland, 13th July 2008.

     On Linear Logic Planning and Concurrency. 
     Ozan Kahramanoğulları
     Logic for Programming, Artificial Intelligence and Reasoning, 14th International Conference,
     Yeravan, Armenia, October 15-19, 2007 

     Interaction and Depth Against Nondeterminism in Proof Search. [PDF] 
     Ozan Kahramanoğulları
     Workshop on Automated Reasoning, ARW 2007, 
     Imperial College London, April19-20, 2007. 

     Implementing Deep Inference in TOM. [PDF]
     Ozan Kahramanoğulları, Pierre-Ettiene Moreau, Antoine Reilles
     Workshop on Structures and Deduction 2005, ICALP 2005, 
     Lisbon, Portugal, July 16- 17, 2005.
     
     Labelled Event Structure Semantics of Linear Logic Planning. [PDF]
     Ozan Kahramanoğulları
     1st World Congress and School on Universal Logic, 
     Montreux, Switzerland, March 26- April 3, 2005. 

     Using Partial Order Plans for Project Management[PDF]
     Ozan Kahramanoğulları
     Leipziger Informatik Tage, Das Internet als sicherer Marktplatz, 
     HTWK Leipzig, September 29 - October 1, 2004. 

     Implementing System BV of the Calculus of Structures in Maude. [PDF]
     Ozan Kahramanoğulları
     ESSLLI-04 Student Session, European Summer School in Logic, Language and Information, 
     Universite Henri Poincare, Nancy, France, August 9-20, 2004. 

     

A Formal Assessment Result for Fluent Calculus Using the Action Description Language  A

[PDF]
     Ozan Kahramanoğulları, Michael Thielscher
     

AAAI Spring Symposium, Logical Formalizations of Commonsense Reasoning 2003, 

     

Stanford University, Palo Alto, California, March 24-26, 2003.



 Posters

     Using the compositionality feature of LIME in building a multinetwork model.
     Ozan Kahramanoğulları, Ferenc Jordan
     7th European Conference on Ecological Modelling, ECEM 2004,
     Riva del Garda, Italy, May 30 - June 2, 2011.

     Predicting the gemcitabine efficacy by a BlenX model.
     Paola Lecca, Ozan Kahramanoğulları, Gianluca Fantaccini, Daniele Morpurgo,Corrado Priami 
     Population Age Group Europe Meeting,
     Athens, Greece, June 7 - 10, 2011.

     A BlenX pharmacodynamics model of tumour shrinkage by gemcitabine+carboplatin 
     in lung cancer patients.
     Paola Lecca, Ozan Kahramanoğulları, Daniele Morpurgo, Corrado Priami 
     MedChem Europe Conference 2011,
     Munich, Germany, March 28 - 29, 2011.

     A Modelling the tumor shrinkage pharmacodynamics with BlenX.
     Paola Lecca, Ozan Kahramanoğulları, Daniele Morpurgo, Corrado Priami, Ross A. Soo 
     1st IEEE International Conference on Computational Advances in Bio and medical Sciences,
     Orlando, Florida, USA, February 3 - 5, 2011.

     An Intuitive Automated Modelling Interface for Systems Biology.
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron
     Imperial College, Institute of Systems and Synthetic Biology - Autumn Symposium,
     London, UK, November 13 - 14, 2008.

     A Process Model of Actin Polymerisation.
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron, Philippa Gardner,Andrew Phillips
     Synthetic Biology, Systems Biology and Bioinformatics Conference, BioSysBio'08,
     Imperial College London, April 20 -22, 2008.

     A Process Model of Rho GTP-binding Proteins.
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron, Philippa Gardner,Andrew Phillips
     Computational and Systems Biology Course at The Microsoft Research-Uni. of Trento COSBI
     Trento, Italy, March 10 -14, 2008.

     A Process Model of Rho GTP-binding Proteins.
     Ozan Kahramanoğulları, Luca Cardelli, Emmanuelle Caron, Philippa Gardner,Andrew Phillips
     The Eight International Conference on Systems and Biology,
     Long Beach, California, October 1 - 6, 2007.

     A Deductive Compositional Approach to Petri Nets. [PDF] [POSTER]
     Ozan Kahramanoğulları
     Computational Methods in Systems Biology, CMSB'07,
     Edinburgh, UK, September 19 - 21, 2007.


Thesis

     Nondeterminism and Language Design in Deep Inference. [PDF] 
     Ozan Kahramanoğulları
     PhD thesis, TU Dresden, 2006.

     A Translation From the Action Description Language Ato the Fluent Calculus. [PDF] 
     Ozan Kahramanoğulları
     MSc thesis, TU Dresden, 2002.