[LINK]
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]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK] 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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
[LINK]
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 ]
Journals - Proof Theory
[LINK]
Interaction and Depth against Nondeterminism in Proof Search.
Ozan Kahramanoğulları
Logical Methods in Computer Science, 10 (2:5), 2014.
[LINK]
On Linear Logic Planning and Concurrency.
Ozan Kahramanoğulları
Information and Computation, 207(11):1229-1258, 2009.
[LINK]
System BV is NP-complete.
Ozan Kahramanoğulları
Annals of Pure and Applied Logic, 152(1-3):107-121, 2008.
Books and chapters
[LINK]
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.
[LINK]
Process algebra models in biology: the case of phagocytosis.
Ozan Kahramanoğulları
Bioinformatics & Computational Systems Biology: Recent Advances and Applications,
IGI Global, 2012.
[LINK]
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.
International conferences and workshops
[LINK]
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, to appear.
[LINK]
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.
[LINK]
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.
[LINK] 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.
[LINK] 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.
[LINK]
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.
[LINK]
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.
[LINK][TALK-PDF]
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.
[LINK][TALK-PDF]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[PDF]
Composability: Perspectives in Ecological Modeling.
Ozan Kahramanoğulları, Ferenc Jordan, Corrado Priami
Proceedings of ANB 2011, LNCS 6479, Springer, 2011.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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.
[LINK]
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
[LINK]
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.