Publications of Ozan Kahramanoğulları

• 47. [LINK] [Chapter 3] [Synthetic Biology] [Systems Biology] [Molecular Mechanisms]
  Chemical Reaction Models in Synthetic Promoter Design in Bacteria
  Ozan Kahramanoğulları
  Synthetic Promoters, Methods and Protocols
  Springer, Methods in Molecular Biology, MIMB, volume 2844, 2024.


• 46. [LINK] [Proceeding 26] [Computer Science] [Logic]
  Proof Search in Deep Inference: The Need for Shallow Inference.
  Ozan Kahramanoğulları
  Logic for Programming, Artificial Intelligence, and Reasoning, 25th International Conference,
  Mauritius, 26-31st May, 2024.
  Proceedings of LPAR'24, EPiC Series in Computing.


• 45. [LINK] [Journal 17] [Marine Biology]
  Early stages of development in Mediterranean red coral (Corallium rubrum): the key role of sclerites.
  Bruna Giordano, Lorenzo Bramanti, Jonathan Perrin, Ozan Kahramanoğulları, Daniel Vielzeuf
  Frontiers in Marine Science, 2023.
  [ Keywords: Coralium rubrum, early life stages, recruitment, biomineralization, skeletogenesis, sclerites, skeleton]


• 44. [LINK] [Journal 16] [Systems Biology] [Marine Biology]
  Stochastic diffusion characterises early colony formation in Mediterranean coral Corallium rubrum.
  Ozan Kahramanoğulları, Bruna Giordano, Jonathan Perrin, Daniel Vielzeuf, Lorenzo Bramanti
  Journal of Theoretical Biology, 2022.
  [ Keywords: Mediterranean coral, Coralium rubrum, early development, morphology, stochastic simulation, diffusion ]


• 43. [LINK] [Journal 15] [Applied Mathematics] [Systems Biology] [Epidemiology]
  How network properties and epidemic parameters influence stochastic SIR dynamics on scale-free random networks.
  S. Sottile, O. Kahramanoğulları, M. Sensi
  Journal of Simulation, 2022.
  [ Keywords: epidemic models, configuration model, scale-free networks, spreaders in network, Gillespie algorithm, stochastic simulation ]


• 42. [LINK] [Journal 14] [Applied Mathematics] [Systems Biology] [Synthetic Biology] [Molecular Mechanisms]
  The inverse correlation between robustness and sensitivity to autoregulation in two-component systems.
  E. Righetti, O. Kahramanoğulları
  Mathematical Biosciences, 2021.
  [ Keywords: two-component systems, robustness, auto-regulation, E. coli, PhoB, PhoR ]


• 41. [LINK] [Journal 13] [Systems Biology] [Synthetic Biology] [Molecular Mechanisms]
  Stochastic Simulations as a Tool for Assessing Signal Fidelity in Gene Expression in Synthetic Promoter Design.
  E. Righetti, C. Uluseker, O. Kahramanoğulları
  MDPI Biology, 2021.
  [ Keywords: synthetic biology, E. coli, modelling, stochasticity, simulation, noise, two-component systems, PhoB, PhoR ]


• 40. [LINK] [Proceeding 25] [Systems Biology] [Marine Biology]
  Stochastic Mechanisms of Growth and Branching in Mediterranean Coral Colonies.
  Ozan Kahramanoğulları, Lorenzo Bramanti, Maria Carla Benedetti
  Proceedings of 8th International Conference on the Theory and Practice of Natural Computing
  TPNC 2019, Kingston, Canada, December 9-11, LNCS, Springer, 2019.


• 39. [LINK] [Proceeding 24] [Systems Biology] [Synthetic Biology] [Molecular Mechanisms]
  Stochastic Mechanisms of Information Flow in Phosphate Economy of Escherichia Coli.
  Ozan Kahramanoğulları, Cansu Uluseker, Martin Hancyzc
  Proceedings of 3rd International Conference on Numerical Computations: Theory and Applications
  NUMTA 2019, Le Castella, Italy, June 15-21, LNCS, Springer, 2019.


• 38. [LINK] [Proceeding 23] [Systems Biology] [Molecular Mechanisms]
  Enumerating Dominant Pathways in Biological Networks by Information Flow Analysis.
  Ozan Kahramanoğulları
  Proceedings of 6th International Conference on Algorithms for Computational Biology
  AlCoB 2019, Berkley, California, May 28-30, LNCS/LNBI, Springer, 2019.


• 37. [LINK] [Proceeding 22] [Computer Science] [Systems Biology]
  On Quantitative Comparison of Chemical Reaction Network Models.
  Ozan Kahramanoğulları
  Proceedings of 3rd Workshop on Program Equivalence and Relational Reasoning
  PERR 2019, Prague, April 6, EPTCS, 2019.


• 36. [LINK] [Journal 12] [Applied Mathematics] [Systems Biology] [Synthetic Biology] [Molecular Mechanisms]
  Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels.
  C. Uluseker, J. Torres-Bacete, J. L. Garcia, M. M. Hancyzc, Juan Nogales, O. Kahramanoğulları
  Scientific Reports, 2019.
  [ Keywords: Systems Biology, Synthetic Biology, Modelling, E. coli, Phosphate intake ]


• 35. [LINK] [Proceeding 21] [Applied Mathematics] [Systems Biology] [Synthetic Biology]
  Mechanisms of Switching Response to External Phosphate Levels in Escherichia coli.
  C. Uluseker, M. M. Hanczyc and O. Kahramanoğulları
  Artificial Life Conference Proceedings, 23-27 July, 2018, Tokyo.


• 34. [LINK] [Proceeding 20] [Applied Mathematics] [Systems Biology] [Synthetic Biology]
  A Dynamic Model of the Phosphate Response System with Synthetic Promoters in E. coli.
  C. Uluseker, J. Torres, J. L. Garcia, M. M. Hanczyc, J. Nogales and O. Kahramanoğulları
  Proc. of the International Conference on Artificial Life, 4-8 September, 2017, Lyon.


• 33. [LINK] [TALK-PDF] [Proceeding 19] [Computer Science] [Systems Biology]
  Quantifying Information Flow in Chemical Reaction Networks.
  Ozan Kahramanoğulları
  Proceedings of 4th International Conference on Algorithms for Computational Biology
  AlCoB 2017, Aveiro, Portugal, June 5-6, LNCS 10252, Springer, 2017.


• 32. [LINK] [TALK-PDF] [Proceeding 18] [Computer Science] [Logic]
  Deep Proof Search in MELL.
  Ozan Kahramanoğulları
  Logic for Programming, Artificial Intelligence, and Reasoning, 21st International Conference,
  Maun, Botswana, May 7-12, 2017.
  Proceedings of LPAR'17, EPiC Series in Computing, Volume 46.


• 31. [LINK] [Journal 11] [Applied Mathematics] [Systems Biology] [Synthetic Biology] [Molecular Mechanisms]
  Mechanistic interplay between ceramide and insulin resistance.
  F. Reali, M. Morine, O. Kahramanoğulları, S. Raichur, H. Schneider, D. Crowther, C. Priami
  Scientific Reports, 2017.
  [ Keywords: Computational Biology, Systems Biology, Modelling, Ceramides, Insulin resistance ]


• 30. [LINK] [Proceeding 17] [Computer Science] [Systems Biology]
  Simulating Stochastic Dynamic Interactions with Spatial Information and Flux.
  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.


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


• 28. [LINK] [Journal 10] [Computer Science] [DNA Computing] [Bioinformatics]
  Gener: a minimal programming module for chemical controllers based on DNA strand displacement.
  Ozan Kahramanoğulları, Luca Cardelli
  Bioinformatics, 2015.
  [ Keywords: DNA Computing, Synthetic Biology, Language Design ]


• 27. [LINK] [Proceeding 15] [Computer Science] [Systems Biology]
  l: An Imperative DSL to Stochastically Simulate Biological Systems.
  Roberto Zunino, Durica Nikolic, Corrado Priami, Ozan Kahramanoğulları, Tommaso Schiavinotto
  Proceedings of Programming Languages with Applications to Biology and Security 2015,
  LNCS 9465, Springer, 2015.


• 26. [LINK] [Journal 8] [Computer Science] [Logic]
  Interaction and Depth against Nondeterminism in Proof Search.
  Ozan Kahramanoğulları
  Logical Methods in Computer Science, 10 (2:5), 2014.
  [ Keywords: Proof theory, Deep Inference, Proof search, Automated reasoning ]


• 25. [LINK] [Journal 9] [Systems Biology] [Molecular Mechanisms]
  Stochastic Flux Analysis of Chemical Reaction Networks.
  Ozan Kahramanoğulları, James Lynch
  BMC Systems Biology, 7:133, 2013.
  [ Keywords: Stochastic Simulation Analysis, Modelling, Chemical Reaction Networks, CTMC ]


• 24. [LINK] [Journal 7] [Computer Science] [Systems Biology] [Molecular Mechanisms]
  An Intuitive Modelling Interface for Systems Biology.
  Ozan Kahramanoğulları, Luca Cardelli
  International Journal of Software and Informatics, 7:4, 2013.
  [ Keywords: Modelling, Language Design, Stochastic Simulation ]


• 23. [LINK] [Chapter 2] [Systems Biology] [Molecular Mechanisms]
  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.


• 22. [LINK] [Proceeding 14] [Computer Science] [Systems Biology] [Ecology]
  Algorithmic Systems Ecology: Experiments on Multiple Interaction Types and Patches.
  Ozan Kahramanoğulları, James Lynch, Corrado Priami
  Keynote Paper, Proceedings of InSuEdu 2012, LNCS 7991, Springer, 2014.


• 21. [LINK] [Journal 6] [Systems Biology] [Systems Pharmacology] [Molecular Mechanisms]
  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.
  [ Keywords: Modelling, Chemical Reaction Networks, Stochastic Simulation, Gemcitabine ]


• 20. [LINK] [Chapter 1] [Systems Biology] [Molecular Mechanisms] Process algebra models in biology: the case of phagocytosis.
  Ozan Kahramanoğulları
  Bioinformatics & Computational Systems Biology: Recent Advances and Applications,
  IGI Global, 2012.


• 19. [LINK] [Book 1] [Computer Science] [Logic]
  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.


• 18. [LINK] [Journal 5] [Systems Biology] [Ecology]
  CoSBiLab LIME: a language interface for stochastic dynamical modelling in ecology.
  Ozan Kahramanoğulları, James Lynch, Ferenc Jordan
  Environmental Modelling and Software, 26:685-687, 2011.
  [ Keywords: Systems Ecology, Modelling, Stochastic Simulation ]


• 17. [LINK] [Proceeding 13] [Computer Science] [Systems Biology]
  Modelling and estimating dynamics of tumor shrinkage with BlenX and KInfer.
  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.


• 16. [PDF] [Proceeding 12] [Computer Science] [Systems Biology] [Ecology]
  Composability: Perspectives in Ecological Modeling.
  Ozan Kahramanoğulları, Ferenc Jordan, Corrado Priami
  Proceedings of ANB 2010, LNCS 6479, Springer, 2010.


• 15. [LINK] [Proceeding 11] [Computer Science] [Systems Biology]
  Flux Analysis in Process Models via Causality.
  Ozan Kahramanoğulları
  3rd Workshop "From Biology To Concurrency and back", March 27, 2010.
  Proceedings of FBTC'10, EPTCS 19, 20-39, 2010.


• 14. [LINK] [Journal 4] [Computer Science] [Logic]
  On Linear Logic Planning and Concurrency.
  Ozan Kahramanoğulları
  Information and Computation, 207(11):1229-1258, 2009.
  [ Keywords: Proof theory, Deep Inference, Planning, Proof search, Automated reasoning ]


• 13. [LINK] [Journal 3] [Systems Biology] [Molecular Mechanisms]
  A Process Model of Rho GTP-binding Proteins.
  Luca Cardelli, Emmanuelle Caron, Philippa Gardner, Ozan Kahramanoğulları, Andrew Phillips
  Theoretical Computer Science, 410:3166-3185, 2009.
  [ Keywords: Modelling, Chemical Reaction Networks, Stochastic Simulation, Rho GTP-binding proteins ]


• 12 .[LINK] [Journal 2] [Systems Biology] [Molecular Mechanisms]
  Biophysical Mechanism for Ras-Nanocluster Formation and Signaling in Plasma Membrane.
  Thomas Gurry, Ozan Kahramanoğulları, Robert Endres
  PLoS ONE, 4, 2009.
  [ Keywords: Modelling, Monte Carlo simulation, Ras GTPases ]


• 11. [LINK] [Proceeding 10] [Computer Science] [Systems Biology]
  An Intuitive Automated Modelling Interface for Systems Biology.
  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.


• 10. [LINK] [Proceeding 9] [Computer Science] [Systems Biology]
  A Process Model of Actin Polymerisation.
  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.


• 9. [LINK] [Journal 1] [Computer Science] [Logic]
  System BV is NP-complete.
  Ozan Kahramanoğulları
  Annals of Pure and Applied Logic, 152(1-3):107-121, 2008. [ Keywords: Proof theory, Deep Inference, System BV, Complexity, Proof search, Automated reasoning ]


• 8. [LINK] [Proceeding 8] [Computer Science] [Logic]
  On Linear Logic Planning and Concurrency.
  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.


• 7. [LINK] [Proceeding 7] [Computer Science] [Systems Biology]
  A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis.
  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


• 6. [LINK] [Proceeding 6] [Computer Science] [Logic]
  Maude as a Platform for Designing and Implementing Deep Inference Systems.
  Ozan Kahramanoğulları
  Eighth International Workshop on Rule Based Programming, Paris, France, July 12, 2007.
  Proceedings of RULE'07, ENTCS 219, Elsevier, 35-50, 2008.


• 5. [LINK] [Proceeding 5] [Computer Science] [Logic]
  Reducing Nondeterminism in the Calculus of Structures.
  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.


• 4. [LINK] [Proceeding 4] [Computer Science] [Logic]
  System BV is NP-complete.
  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.


• 3. [LINK] [Proceeding 3] [Computer Science] [Logic]
  Towards Planning as Concurrency.
  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.


• 2. [LINK] [Proceeding 2] [Computer Science] [Logic]
  System BV without the Equalities for Unit.
  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.


• 1. [LINK] [Proceeding 1] [Computer Science]
  A Formal Assessment Result for Fluent Calculus Using the Action Description Language Ak.
  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

• Causal Analysis in Bio-pathways via Stochastically Simulated Perturbations
  Ozan Kahramanoğulları, Anton Dignös, Johann Gamper
  20th International Symposium on Bioinformatics Research and Application
  ISBRA 2024 in Kunming, China.


• Deep inference for proof search.
  Ozan Kahramanoğulları
  5th International Workshop on Structures and Deduction,
  Affiliated with FSCD '19. Dortmund, Germany, June 29-30, 2019.


• A Theory of Model Equivalence.
  Ozan Kahramanoğulları, James Lynch
  Collection of essays in honor of Luca Cardelli,
  Microsoft Research Technical Report, September 2014.


• Ingredients of a Deep Inference Theorem Prover.
  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.
  Ozan Kahramanoğulları
  Workshop on Automated Reasoning, ARW 2007,
  Imperial College London, April19-20, 2007.


• Implementing Deep Inference in TOM.
  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.
  Ozan Kahramanoğulları
  1st World Congress and School on Universal Logic,
  Montreux, Switzerland, March 26- April 3, 2005.


• Using Partial Order Plans for Project Management.
  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.
  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 Ak . [PDF]
  Ozan Kahramanoğulları, Michael Thielscher
  AAAI Spring Symposium, Logical Formalizations of Commonsense Reasoning 2003,
  Stanford University, Palo Alto, California, March 24-26, 2003.

Posters

• Signal fidelity in Escherichia coli phosphate response with synthetic promoters
  Elena Righetti, Ozan Kahramanoğulları
  DSABNS, 4-7 February, 2020, Trento.


• Scheduling multi-armed liquid handling robot tasks by exploiting resource sensitive concurrency.
  Ozan Kahramanoğulları, M. M. Hanczyc
  Artificial Life Conference, 23-27 July, 2018, Tokyo.


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


• Modelling the tumor shrinkage pharmacodynamics with BlenX.
  Paola Lecca, Ozan Kahramanogullari, Daniele Morpurgo, Corrado Priami, Ross A. Soo
  IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011.
  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.
  Ozan Kahramanoğulları
  Computational Methods in Systems Biology, CMSB'07,
  Edinburgh, UK, September 19 - 21, 2007.

Thesis

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


• A Translation From the Action Description Language Ak to the Fluent Calculus.
  Ozan Kahramanoğulları
  MSc thesis, TU Dresden, 2002.