April 2024
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I answer some open questions that go back to my PhD thesis on proof search with deep inference.
[LINK]
Proof Search in Deep Inference: The Need for Shallow Inference
Ozan Kahramanoğulları
Logic for Programming, Artificial Intelligence, and Reasoning, 25th International Conference,
LPAR-25, Mauritius, 26-31st May 2024,
Proceedings of LPAR'24, to appear.
[ Keywords: proof search, deep inference, BV, MLL, Maude ]
January 2023
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Our paper, accompanying our previous modeling paper, reports
observations about early development in Mediterranean corals Corallium rubrum.
[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]
August 2022
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Our paper describes the processes that drive early colony formation in Mediterranean corals Corallium rubrum.
[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 ]
July 2022
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Check out our paper to see how epidemics spread on scale-free networks!
[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 ]
November 2021
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Our recent paper demonstrates a mechanism with which bacteria manage their resource economy. Check it out!
[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, Positive autoregulation, Robustness, PhoBR ]
July 2021
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Our paper on analysing noise in synthetic biology applications via stochastic simulaitons is now published.
[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 ]
June 2020
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My proposal “Understanding Coral Colony Morphology via Stochastic Modelling” (UNICOMS)
has been accepted for the 7th call of the
ASSEMBLE Plus Transnational Access program.
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James Lynch and I are
editing a special issue on
Computational Methods in Synthetic Biology at the MDPI Biology journal. Submissions are welcome!
Please email us for any inquiries.
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I talked about
modelling life at TiramiScience.
January 2020
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I presented an abstract
on our model of growth and branching in mediterranean red coral colonies
at the DSABNS conference.
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Elena presented her preliminary results on
Signal fidelity in Escherichia coli phosphate response with synthetic promoters
at the DSABNS conference.
December 2019
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I presented a model of growth and branching in mediterranean red coral colonies
at the TPNC conference.
Stochastic Mechanisms of Growth and Branching in Mediterranean Coral Colonies
O. Kahramanoğulları, L. Bramanti, M. C. Benedetti
Proceedings of 8th International Conference on the Theory and Practice of Natural Computing
TPNC 2019, Kingston, Canada, December 9-11, LNCS, Springer, 2019.
Here is a video of the colony growth generated by a stochastic simulation with the model.
October 2019
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The paper of my invited talk at NUMTA
is now in press. The slides of the talk are
here.
Stochastic Mechanisms of Information Flow in Phosphate Economy of Escherichia Coli
O. Kahramanoğulları, C. Uluseker, M. M. Hancyzc
Proceedings of 3rd International Conference on Numerical Computations: Theory and Applications,
NUMTA 2019, Le Castella, Italy, June 15-21, LNCS, Springer, 2019.
Here is a video that displays the dynamic evolution of the
fluxes after a sudden change in external phosphate concentration at 7000
secs into the simulation.
September 2019
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Our paper on growth and branching in mediterranean red coral colonies
is accepted at the TPNC conference.
Stochastic Mechanisms of Growth and Branching in Mediterranean Coral Colonies
O. Kahramanoğulları, L. Bramanti, M. C. Benedetti
Proceedings of 8th International Conference on the Theory and Practice of Natural Computing
TPNC 2019, Kingston, Canada, December 9-11, LNCS, Springer, 2019.
July 2019
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We are finalizing the
Living Architecture
project with the final review. Check out the below video.
Here is the PDF brochure as well.
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I gave a talk about E. coli phosphate economy
at the Italian Regional Conference on Complex Systems
CCS/italy.
June 2019
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I gave a talk about "deep inference for proof search" at the
Structures and Deduction Workshop.
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I gave an invited talk at NUMTA
on the stochastic analysis of our model that quantifies the phosphate economy of E. coli.
Here are the slides.
May 2019
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Here
are some ideas that put together static considerations of biological networks with stochastic dynamic ones.
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.
April 2019
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I gave a talk about this paper, "On Quantitative Comparison of Chemical Reaction Network Models" at the
PERR Workshop.
March 2019
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I gave a talk about artificial intelligence at a high school: "Possiamo fare ragionare i computer?"
Here are the slides.
February 2019
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The paper
with our results on phosphate economy is now published at the Scientific Reports Journal.
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 ]
