Profile

Prof Ozgur Akman

Publications

_{Copyright Notice: Any articles made available for download are for personal use only. Any other use requires prior permission of the author and the copyright holder.}

_{Copyright Notice: Any articles made available for download are for personal use only. Any other use requires prior permission of the author and the copyright holder.}

| 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2006 | 2005 | 2003 | 2002 |

2022

• Foo M, Akman OE, Bates DG. (2022) Restoring circadian gene profiles in clock networks using synthetic feedback control, npj Systems Biology and Applications, volume 8, no. 1, DOI:10.1038/s41540-022-00216-x.

2021

• Alyahya K, Doherty K, Akman OE, Fieldsend JE. (2021) Reduced Models of Gene Regulatory Networks: Visualising Multi-modal Landscapes, Natural Computing Series, 229-258, DOI:10.1007/978-3-030-79553-5_10.
• Karatas MD, Akman OE, Fieldsend JE. (2021) Towards population-based fitness landscape analysis using local optima networks, GECCO Companion, pages 1674-1682. [PDF]
• Abadi RV, Akman OE, Arblaster GE, Clement RA. (2021) Analysing nystagmus waveforms: a computational framework, Scientific Reports, volume 11, no. 1, article no. 9761, DOI:10.1038/s41598-021-89094-7. [PDF]

2020

• Avramidis E, Lalik M, Akman OE. (2020) SODECL, ACM Transactions on Mathematical Software, volume 46, no. 3, pages 1-21, DOI:10.1145/3385076. [PDF]
• Clement RA, Akman OE. (2020) Slow-fast control of eye movements: an instance of Zeeman's model for an action, Biol Cybern, volume 114, no. 4-5, pages 519-532, DOI:10.1007/s00422-020-00845-7. [PDF]
• Akman OE, Fieldsend JE. (2020) Multi-objective optimisation of gene regulatory networks: Insights from a Boolean circadian clock model, EPiC Series in Computing, volume 70, pages 149-162, DOI:10.29007/bvbj. [PDF]
• Foo M, Bates DG, Akman OE. (2020) A simplified modelling framework facilitates more complex representations of plant circadian clocks, PLoS Comput Biol, volume 16, no. 3, DOI:10.1371/journal.pcbi.1007671. [PDF]

2019

• Laiou P, Avramidis E, Lopes MA, Abela E, Müller M, Akman OE, Richardson MP, Rummel C, Schindler K, Goodfellow M. (2019) Quantification and selection of ictogenic zones in epilepsy surgery, DOI:10.1101/602490.
• Avramidis E, Lalik M, Akman OE. (2019) SODECL: An Open Source Library for Calculating Multiple Orbits of a System of Stochastic Differential Equations in Parallel.
• Laiou P, Avramidis E, Lopes MA, Abela E, Müller M, Akman OE, Richardson MP, Rummel C, Schindler K, Goodfellow M. (2019) Quantification and Selection of Ictogenic Zones in Epilepsy Surgery, Frontiers in Neurology, volume 10, DOI:10.3389/fneur.2019.01045. [PDF]
• Alyahya K, Akman O, Fieldsend JE. (2019) Landscape Analysis Under Measurement Error, Genetic and Evolutionary Computation Conference Companion (GECCO), Prague, Czech Republic, 13th - 17th Jul 2019, Genetic and Evolutionary Computation Conference Companion (GECCO ’19 Companion), pages 1415-1418, DOI:10.1145/3319619.3326858. [PDF]
• Fieldsend JE, Doherty K, Alyahya K, Akman O. (2019) Robust Optimisation using Voronoi-Based Archive Sampling, UQOP: Uncertainty Quantification & Optimization, Sorbonne University, Paris, France, 18th - 20th Mar 2019. [PDF]
• Tokuda IT, Akman OE, Locke JCW. (2019) Reducing the complexity of mathematical models for the plant circadian clock by distributed delays, Journal of Theoretical Biology, volume 463, pages 155-166, DOI:10.1016/j.jtbi.2018.12.014. [PDF]

2018

• Doherty K, Alyahya K, Fieldsend JE, Akman O. (2018) Voronoi-Based Archive Sampling for Robust Optimisation, Genetic and Evolutionary Computation Conference, Kyoto, 15th - 19th Jul 2018, GECCO '18 Companion: Genetic and Evolutionary Computation Conference Companion, DOI:10.1145/3205651.3205768. [PDF]
• Alyahya K, Doherty K, Akman O, Fieldsend JE. (2018) Robust Multi-Modal Optimisation, Genetic and Evolutionary Computation Conference, Kyoto, 15th - 19th Jul 2018, GECCO '18 Companion: Genetic and Evolutionary Computation Conference Companion, DOI:10.1145/3205651.3208258. [PDF]

2017

• Doherty K, Alyahya K, Akman OE, Fieldsend JE. (2017) Optimisation and Landscape Analysis of Computational Biology Models: A Case Study, Genetic and Evolutionary Computation Conference, Companion Proceedings, Berlin, Germany, 15th - 19th Jul 2017, DOI:10.1145/3067695.3084609. [PDF]
• Alyahya K, Doherty K, Fieldsend JE, Akman OE. (2017) On the Exploitation of Search History and Accumulative Sampling in Robust Optimisation, Genetic and Evolutionary Computation Conference (GECCO), Companion Publication, Berlin, 15th - 19th Jul 2017, DOI:10.1145/3067695.3076060. [PDF]
• Avramidis E, Akman OE. (2017) Optimisation of an exemplar oculomotor model using multi-objective genetic algorithms executed on a GPU-CPU combination, BMC Systems Biology, volume 11, article no. 40, DOI:10.1186/s12918-017-0416-2. [PDF]

2016

• Steinacher A, Bates DG, Akman OE, Soyer OS. (2016) Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels, PLOS ONE, volume 11, no. 4, pages e0153295-e0153295, DOI:10.1371/journal.pone.0153295. [PDF]
• Montefusco F, Akman OE, Soyer OS, Bates DG. (2016) Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers, PLOS ONE, volume 11, no. 8, pages e0161605-e0161605, DOI:10.1371/journal.pone.0161605. [PDF]
• Cizmeci D, Dempster EL, Champion OL, Wagley S, Akman OE, Prior JL, Soyer OS, Mill J, Titball RW. (2016) Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection, Scientific Reports, volume 6, DOI:10.1038/srep30861. [PDF]

2015

• Abadi RV, Akman OE, Clement RA. (2015) Dynamical Systems Modelling of Eye Movements, Math. Today, volume 51, pages 127-131, article no. 3. [PDF]
• Aitken S, Kilpatrick AM, Akman OE. (2015) Dizzy-Beats: a Bayesian evidence analysis tool for systems biology, Bioinformatics, volume 31, no. 11, pages 1863-1865, DOI:10.1093/bioinformatics/btv062. [PDF]

2014

• Mohammed S, Akman OE, Yang ZR. (2014) A consensus approach to predict regulatory interactions, Proceedings - 2014 7th International Conference on BioMedical Engineering and Informatics, BMEI 2014, pages 769-775, DOI:10.1109/BMEI.2014.7002876.
• Montefusco F, Akman OE, Soyer OS, Bates DG. (2014) Modelling and Analysis of Feedback Control Mechanisms Underlying Osmoregulation in Yeast, A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems, Springer, 83-116.
• Guerriero ML, Akman OE, van Ooijen G. (2014) Stochastic models of cellular circadian rhythms in plants help to understand the impact of noise on robustness and clock structure, Front Plant Sci, volume 5, DOI:10.3389/fpls.2014.00564. [PDF]
• Dixon LE, Hodge SK, van Ooijen G, Troein C, Akman OE, Millar AJ. (2014) Light and circadian regulation of clock components aids flexible responses to environmental signals, New Phytol, volume 203, no. 2, pages 568-577, DOI:10.1111/nph.12853. [PDF]

2013

• Aitken S, Akman OE. (2013) Nested sampling for parameter inference in systems biology: application to an exemplar circadian model, BMC Syst Biol, volume 7, DOI:10.1186/1752-0509-7-72. [PDF]
• Adams R, Clark A, Yamaguchi A, Hanlon N, Tsorman N, Ali S, Lebedeva G, Goltsov A, Sorokin A, Akman OE. (2013) SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology, Bioinformatics, volume 29, no. 5, pages 664-665, DOI:10.1093/bioinformatics/btt023. [PDF]

2012

• Akman O, Watterson S, Parton A, Binns N, Millar A, Ghazal P. (2012) Digital clocks: simple Boolean models can quantitatively describe circadian systems.
• Montefusco F, Steinacher A, Akman OE, Bates DG, Soyer OS. (2012) On the role of ultrasensitivity in biomolecular control systems, Proceedings of the IEEE Conference on Decision and Control, pages 3602-3607, DOI:10.1109/CDC.2012.6426064.
• Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ. (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models, J Biol Rhythms, volume 27, no. 4, pages 328-332, DOI:10.1177/0748730412451077. [PDF]
• Akman OE, Broomhead DS, Abadi RV, Clement RA. (2012) Components of the neural signal underlying congenital nystagmus, Exp Brain Res, volume 220, no. 3-4, pages 213-221, DOI:10.1007/s00221-012-3130-8. [PDF]
• Akman OE, Watterson S, Parton A, Binns N, Millar AJ, Ghazal P. (2012) Digital clocks: simple Boolean models can quantitatively describe circadian systems, J R Soc Interface, volume 9, no. 74, pages 2365-2382, DOI:10.1098/rsif.2012.0080. [PDF]

2011

• Akman OE, Biringen S, Waggy SB. (2011) Analysis of signal propagation in an elastic-tube flow model, Med Eng Phys, volume 33, no. 5, pages 660-663, DOI:10.1016/j.medengphy.2010.12.011. [PDF]

2010

• Akman OE, Guerriero ML, Loewe L, Troein C. (2010) Complementary approaches to understanding the plant circadian clock.
• Akman OE, Guerriero ML, Loewe L, Troein C. (2010) Complementary approaches to understanding the plant circadian clock, Proc of FBTC'10, volume 19, pages 55-69, DOI:10.4204/EPTCS.19.1. [PDF]
• Edwards KD, Akman OE, Knox K, Lumsden PJ, Thomson AW, Brown PE, Pokhilko A, Kozma-Bognar L, Nagy F, Rand DA. (2010) Quantitative analysis of regulatory flexibility under changing environmental conditions, Mol Syst Biol, volume 6, DOI:10.1038/msb.2010.81. [PDF]
• Akman OE, Rand DA, Brown PE, Millar AJ. (2010) Robustness from flexibility in the fungal circadian clock, BMC Syst Biol, volume 4, DOI:10.1186/1752-0509-4-88. [PDF]

2009

• Akman OE, Clement RA, Broomhead DS, Mannan S, Moorhead I, Wilson HR. (2009) Probing Bottom-up Processing with Multistable Images, J Eye Mov Res, volume 1(3):4, pages 1-7. [PDF]
• Akman OE, Ciocchetta F, Degasperi A, Guerriero ML. (2009) Modelling biological clocks with bio-pepa: Stochasticity and robustness for the neurospora crassa circadian network, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), volume 5688 LNBI, pages 52-67, DOI:10.1007/978-3-642-03845-7_4.

2008

• Faulkner C, Akman O, Bell K, Jeffree C, Oparka K. (2008) Peeking into pit fields — A new model of secondary plasmodesmata formation, Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology, volume 150, no. 3, pages s140-s141, DOI:10.1016/j.cbpa.2008.04.347.
• Faulkner C, Akman OE, Bell K, Jeffree C, Oparka K. (2008) Peeking into pit fields: a multiple twinning model of secondary plasmodesmata formation in tobacco, Plant Cell, volume 20, no. 6, pages 1504-1518, DOI:10.1105/tpc.107.056903. [PDF]
• Clement RA, Broomhead DS, Akman OE. (2008) Dynamics of saccadic oscillations, Prog Brain Res, volume 171, pages 131-136, DOI:10.1016/S0079-6123(08)00617-1. [PDF]
• Akman OE, Locke JCW, Tang S, Carré I, Millar AJ, Rand DA. (2008) Isoform switching facilitates period control in the Neurospora crassa circadian clock, Mol Syst Biol, volume 4, DOI:10.1038/msb.2008.5. [PDF]

2006

• Akman OE, Broomhead DS, Clement RA, Abadi RV. (2006) Nonlinear time series analysis of jerk congenital nystagmus, J Comput Neurosci, volume 21, no. 2, pages 153-170, DOI:10.1007/s10827-006-7816-4. [PDF]
• Laptev D, Akman OE, Clement RA. (2006) Stability of the saccadic oculomotor system, Biol Cybern, volume 95, no. 3, pages 281-287, DOI:10.1007/s00422-006-0087-3. [PDF]

2005

• Akman OE, Broomhead DS, Abadi RV, Clement RA. (2005) Eye movement instabilities and nystagmus can be predicted by a nonlinear dynamics model of the saccadic system, J Math Biol, volume 51, no. 6, pages 661-694, DOI:10.1007/s00285-005-0336-4. [PDF]

2003

• Akman OZGUR, Broomhead DS, Clement RA. (2003) Mathematical models of eye movements, MATHEMATICS TODAY-SOUTHEND ON SEA-, volume 39, pages 54-59, article no. 2. [PDF]

2002

• Clement RA, Whittle JP, Muldoon MR, Abadi RV, Broomhead DS, Akman O. (2002) Characterisation of congenital nystagmus waveforms in terms of periodic orbits, Vision research, volume 42, pages 2123-2130, article no. 17.

Showing 51 publications from Symplectic.