2019
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Jiang, Shouyong; Kaiser, Marcus ; Yang, Shengxiang ; Kollias, Stefanos ; Krasnogor, Natalio A scalable test suite for continuous dynamic multiobjective optimisation Journal Article IEEE Transactions on Cybernetics, vol.1 (no.1), pp. 1–12, 2019. BibTeX | Tags: @article{Jiang2019,
title = {A scalable test suite for continuous dynamic multiobjective optimisation},
author = { Shouyong Jiang and Marcus Kaiser and Shengxiang Yang and Stefanos Kollias and Natalio Krasnogor},
year = {2019},
date = {2019-01-01},
journal = {IEEE Transactions on Cybernetics},
volume = {vol.1},
number = {no.1},
pages = {1--12},
note = {accepted and will go online soon},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Fellermann, Harold; Shirt-Ediss, Ben ; Kozyra, Jerzy ; Linsley, Matt ; Lendrem, Dennis ; Isaacs, John ; Howard, Thomas Design of experiments and the virtual PCR simulator: An online game for pharmaceutical scientists and biotechnologists Journal Article Pharmaceutical Statistics, 2019. Links | BibTeX | Tags: @article{Fellermann2019,
title = {Design of experiments and the virtual PCR simulator: An online game for pharmaceutical scientists and biotechnologists},
author = { Harold Fellermann and Ben Shirt-Ediss and Jerzy Kozyra and Matt Linsley and Dennis Lendrem and John Isaacs and Thomas Howard},
doi = {10.1002/pst.1932},
year = {2019},
date = {2019-01-01},
journal = {Pharmaceutical Statistics},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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2018
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Torelli, Emanuela; Kozyra, Jerzy Wieslaw ; Gu, Jing-Ying ; Stimming, Ulrich ; Piantanida, Luca ; Voïtchovsky, Kislon ; Krasnogor, Natalio Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon Journal Article Scientific Reports, 8 (1), 2018. Links | BibTeX | Tags: @article{Torelli2018a,
title = {Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon},
author = { Emanuela Torelli and Jerzy Wieslaw Kozyra and Jing-Ying Gu and Ulrich Stimming and Luca Piantanida and Kislon Voïtchovsky and Natalio Krasnogor},
doi = {10.1038/s41598-018-25270-6},
year = {2018},
date = {2018-12-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Jiang, Shouyong; Kaiser, Marcus ; Wan, Shuzhen ; Guo, Jinglei ; Yang, Shengxiang ; Krasnogor, Natalio An Empirical Study of Dynamic Triobjective Optimisation Problems Inproceedings CEC 2018, pp. 1–8, Rio, Brazil, 2018. BibTeX | Tags: @inproceedings{Jiang2018a,
title = {An Empirical Study of Dynamic Triobjective Optimisation Problems},
author = { Shouyong Jiang and Marcus Kaiser and Shuzhen Wan and Jinglei Guo and Shengxiang Yang and Natalio Krasnogor},
year = {2018},
date = {2018-07-01},
booktitle = {CEC 2018},
pages = {1--8},
address = {Rio, Brazil},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
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Jiang, Shouyong; Torres, Marina ; Pelta, David ; Krabben, Preben ; Daniel, Richard ; Luzardo, Jonathan Tellechea ; Kaiser, Marcus ; Krasnogor, Natalio Improving microbial strain design via multiobjective optimisation and decision making Inproceedings AI for sythetic biology 2, IJCIA, pp. 1–6, stockholm, sweden, 2018. BibTeX | Tags: @inproceedings{Jiang2018b,
title = {Improving microbial strain design via multiobjective optimisation and decision making},
author = { Shouyong Jiang and Marina Torres and David Pelta and Preben Krabben and Richard Daniel and Jonathan Tellechea Luzardo and Marcus Kaiser and Natalio Krasnogor},
year = {2018},
date = {2018-07-01},
booktitle = {AI for sythetic biology 2, IJCIA},
pages = {1--6},
address = {stockholm, sweden},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
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Jiang, Shouyong; Yang, Shengxiang ; Yao, Xin ; Tan, Kay Chen ; Kaiser, Marcus ; Krasnogor, Natalio Benchmark Problems for CEC2018 Competition on Dynamic Multiobjective Optimisation Technical Report Newcastle University (1), 2018. BibTeX | Tags: @techreport{Jiang2018c,
title = {Benchmark Problems for CEC2018 Competition on Dynamic Multiobjective Optimisation},
author = { Shouyong Jiang and Shengxiang Yang and Xin Yao and Kay Chen Tan and Marcus Kaiser and Natalio Krasnogor},
year = {2018},
date = {2018-07-01},
number = {1},
institution = {Newcastle University},
keywords = {},
pubstate = {},
tppubtype = {techreport}
}
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Markovitch, Omer; Krasnogor, Natalio Predicting species emergence in simulated complex pre-biotic networks Journal Article PLOS ONE, 13 (2), pp. e0192871, 2018. Links | BibTeX | Tags: @article{Markovitch2018,
title = {Predicting species emergence in simulated complex pre-biotic networks},
author = { Omer Markovitch and Natalio Krasnogor},
doi = {10.1371/journal.pone.0192871},
year = {2018},
date = {2018-02-01},
journal = {PLOS ONE},
volume = {13},
number = {2},
pages = {e0192871},
note = {10.5281/zenodo.56534},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Torelli, Emanuela; Manzano, Marisa ; Srivastava, Sachin K; Marks, Robert S DNA origami nanorobot fiber optic genosensor to TMV Journal Article Biosensors and Bioelectronics, 99 (C), pp. 209–215, 2018. Links | BibTeX | Tags: @article{Torelli2018,
title = {DNA origami nanorobot fiber optic genosensor to TMV},
author = { Emanuela Torelli and Marisa Manzano and Sachin K. Srivastava and Robert S. Marks},
doi = {10.1016/j.bios.2017.07.051},
year = {2018},
date = {2018-01-01},
journal = {Biosensors and Bioelectronics},
volume = {99},
number = {C},
pages = {209--215},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Jiang, Shouyong; Kaiser, Marcus ; Guo, Jinglei ; Yang, Shengxiang ; Krasnogor, Natalio Less Detectable Environmental Changes in Dynamic Multiobjective Optimisation Inproceedings GECCO, pp. 1–8, Kyoto, Japan, 2018. BibTeX | Tags: @inproceedings{Jiang2018,
title = {Less Detectable Environmental Changes in Dynamic Multiobjective Optimisation},
author = { Shouyong Jiang and Marcus Kaiser and Jinglei Guo and Shengxiang Yang and Natalio Krasnogor},
year = {2018},
date = {2018-01-01},
booktitle = {GECCO},
pages = {1--8},
address = {Kyoto, Japan},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
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McLaughlin, James Alastair; Myers, Chris J; Zundel, Zach ; Mısırlı, Göksel ; Zhang, Michael ; Ofiteru, Irina Dana ; Goñi-Moreno, Angel ; Wipat, Anil SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology Journal Article ACS Synthetic Biology, 2018. Links | BibTeX | Tags: @article{McLaughlin2018,
title = {SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology},
author = { James Alastair McLaughlin and Chris J. Myers and Zach Zundel and Göksel Mısırlı and Michael Zhang and Irina Dana Ofiteru and Angel Goñi-Moreno and Anil Wipat},
doi = {10.1021/acssynbio.7b00403},
year = {2018},
date = {2018-01-01},
journal = {ACS Synthetic Biology},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Hordijk, Wim; Naylor, Jonathan ; Krasnogor, Natalio ; Fellermann, Harold Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World Journal Article Life, 8 (3), pp. 33, 2018. Links | BibTeX | Tags: @article{Hordijk2018,
title = {Population Dynamics of Autocatalytic Sets in a Compartmentalized Spatial World},
author = { Wim Hordijk and Jonathan Naylor and Natalio Krasnogor and Harold Fellermann},
doi = {10.3390/life8030033},
year = {2018},
date = {2018-01-01},
journal = {Life},
volume = {8},
number = {3},
pages = {33},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Shirt-Ediss, Ben; Krasnogor, Natalio ; Fellermann, Harold The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators Inproceedings The 2018 Conference on Artificial Life, pp. 370–371, Tokyo, Japan, 2018. Links | BibTeX | Tags: @inproceedings{Shirt-Ediss2018,
title = {The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators},
author = { Ben Shirt-Ediss and Natalio Krasnogor and Harold Fellermann},
doi = {10.1162/isal_a_00070},
year = {2018},
date = {2018-01-01},
booktitle = {The 2018 Conference on Artificial Life},
pages = {370--371},
address = {Tokyo, Japan},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
|
Torres, Marina; Jiang, Shouyong ; Pelta, David ; Kaiser, Marcus ; Krasnogor, Natalio Strain design as multiobjective network interdiction problem: A preliminary approach Inproceedings CAEPIA 2018, pp. 1–10, Granada, Spain, 2018. BibTeX | Tags: @inproceedings{Torres2018,
title = {Strain design as multiobjective network interdiction problem: A preliminary approach},
author = { Marina Torres and Shouyong Jiang and David Pelta and Marcus Kaiser and Natalio Krasnogor},
year = {2018},
date = {2018-01-01},
booktitle = {CAEPIA 2018},
pages = {1--10},
address = {Granada, Spain},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
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Revell, Jeremy; Zuliani, Paolo Stochastic Rate Parameter Inference Using the Cross-Entropy Method Incollection Computational Methods in Systems Biology, pp. 146–164, Springer International Publishing, 2018. Links | BibTeX | Tags: @incollection{Revell2018,
title = {Stochastic Rate Parameter Inference Using the Cross-Entropy Method},
author = { Jeremy Revell and Paolo Zuliani},
doi = {10.1007/978-3-319-99429-1_9},
year = {2018},
date = {2018-01-01},
booktitle = {Computational Methods in Systems Biology},
pages = {146--164},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
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Fellermann, Harold; Shirt-Ediss, Ben ; Kozyra, Jerzy W; Linsley, Matthew ; Lendrem, Dennis ; Howard, Thomas The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction Journal Article bioRxiv, 415042v2 , 2018. Links | BibTeX | Tags: @article{Fellermann2018,
title = {The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction},
author = { Harold Fellermann and Ben Shirt-Ediss and Jerzy W Kozyra and Matthew Linsley and Dennis Lendrem and Thomas Howard},
doi = {10.1101/415042},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
volume = {415042v2},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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2017
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Lazzarini, Nicola; Bacardit, Jaume RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers Journal Article BMC Bioinformatics, 18 (1), 2017. Links | BibTeX | Tags: @article{Lazzarini2017,
title = {RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers},
author = { Nicola Lazzarini and Jaume Bacardit},
doi = {10.1186/s12859-017-1729-2},
year = {2017},
date = {2017-12-01},
journal = {BMC Bioinformatics},
volume = {18},
number = {1},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Lazzarini, N; Runhaar, J; Bay-Jensen, A C; Thudium, C S; Bierma-Zeinstra, S M a; Henrotin, Y; Bacardit, J A machine learning approach for the identification of new biomarkers for knee osteoarthritis development in overweight and obese women Journal Article Osteoarthritis and Cartilage, 2017. Links | BibTeX | Tags: @article{Lazzarini2017a,
title = {A machine learning approach for the identification of new biomarkers for knee osteoarthritis development in overweight and obese women},
author = { N. Lazzarini and J. Runhaar and A. C. Bay-Jensen and C. S. Thudium and S. M.a. Bierma-Zeinstra and Y. Henrotin and J. Bacardit},
doi = {10.1016/j.joca.2017.09.001},
year = {2017},
date = {2017-09-01},
journal = {Osteoarthritis and Cartilage},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Kaiser, Marcus Mechanisms of Connectome Development Journal Article Trends in Cognitive Sciences, 21 (9), pp. 703–717, 2017. Links | BibTeX | Tags: @article{Kaiser2017,
title = {Mechanisms of Connectome Development},
author = { Marcus Kaiser},
doi = {10.1016/j.tics.2017.05.010},
year = {2017},
date = {2017-09-01},
journal = {Trends in Cognitive Sciences},
volume = {21},
number = {9},
pages = {703--717},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Wang, Yujiang; Trevelyan, Andrew J; Valentin, Antonio ; Alarcon, Gonzalo ; Taylor, Peter N; Kaiser, Marcus Mechanisms underlying different onset patterns of focal seizures Journal Article PLOS Computational Biology, 13 (5), pp. e1005475, 2017. Links | BibTeX | Tags: @article{Wang2017,
title = {Mechanisms underlying different onset patterns of focal seizures},
author = { Yujiang Wang and Andrew J Trevelyan and Antonio Valentin and Gonzalo Alarcon and Peter N Taylor and Marcus Kaiser},
doi = {10.1371/journal.pcbi.1005475},
year = {2017},
date = {2017-05-01},
journal = {PLOS Computational Biology},
volume = {13},
number = {5},
pages = {e1005475},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Sinha, Nishant; Dauwels, Justin ; Kaiser, Marcus ; Cash, Sydney S; Westover, Brandon M; Wang, Yujiang ; Taylor, Peter N Predicting neurosurgical outcomes in focal epilepsy patients using computational modelling Journal Article Brain, 140 (2), pp. 319–332, 2017. Links | BibTeX | Tags: @article{Sinha2017,
title = {Predicting neurosurgical outcomes in focal epilepsy patients using computational modelling},
author = { Nishant Sinha and Justin Dauwels and Marcus Kaiser and Sydney S. Cash and M. Brandon Westover and Yujiang Wang and Peter N. Taylor},
doi = {10.1093/brain/aww299},
year = {2017},
date = {2017-02-01},
journal = {Brain},
volume = {140},
number = {2},
pages = {319--332},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Baron, Simon; Lazzarini, Nicola ; Bacardit, Jaume Characterising the Influence of Rule-Based Knowledge Representations in Biological Knowledge Extraction from Transcriptomics Data Incollection Applications of Evolutionary Computation, pp. 125–141, Springer International Publishing, 2017. Links | BibTeX | Tags: @incollection{Baron2017,
title = {Characterising the Influence of Rule-Based Knowledge Representations in Biological Knowledge Extraction from Transcriptomics Data},
author = { Simon Baron and Nicola Lazzarini and Jaume Bacardit},
doi = {10.1007/978-3-319-55849-3_9},
year = {2017},
date = {2017-01-01},
booktitle = {Applications of Evolutionary Computation},
pages = {125--141},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
|
Kozyra, Jerzy; Ceccarelli, Alessandro ; Torelli, Emanuela ; Lopiccolo, Annunziata ; Gu, Jing-Ying ; Fellermann, Harold ; Stimming, Ulrich ; Krasnogor, Natalio Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami Journal Article ACS Synthetic Biology, 2017. Links | BibTeX | Tags: @article{Kozyra2017,
title = {Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami},
author = { Jerzy Kozyra and Alessandro Ceccarelli and Emanuela Torelli and Annunziata Lopiccolo and Jing-Ying Gu and Harold Fellermann and Ulrich Stimming and Natalio Krasnogor},
doi = {10.1021/acssynbio.6b00271},
year = {2017},
date = {2017-01-01},
journal = {ACS Synthetic Biology},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Sinha, Nishant; Dauwels, Justin ; Kaiser, Marcus ; Cash, Sydney S; Westover, Brandon M; Wang, Yujiang ; Taylor, Peter N Reply: Computer models to inform epilepsy surgery strategies: prediction of postoperative outcome Journal Article Brain, 2017. Links | BibTeX | Tags: @article{Sinha2017a,
title = {Reply: Computer models to inform epilepsy surgery strategies: prediction of postoperative outcome},
author = { Nishant Sinha and Justin Dauwels and Marcus Kaiser and Sydney S. Cash and M. Brandon Westover and Yujiang Wang and Peter N. Taylor},
doi = {10.1093/brain/awx068},
year = {2017},
date = {2017-01-01},
journal = {Brain},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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Naylor, Jonathan; Fellermann, Harold ; Ding, Yuchun ; Mohammed, Waleed K; Jakubovics, Nicholas S; Mukherjee, Joy ; Biggs, Catherine A; Wright, Phillip C; Krasnogor, Natalio Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations Journal Article ACS Synthetic Biology, 2017. Links | BibTeX | Tags: @article{Naylor2017,
title = {Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations},
author = { Jonathan Naylor and Harold Fellermann and Yuchun Ding and Waleed K. Mohammed and Nicholas S. Jakubovics and Joy Mukherjee and Catherine A. Biggs and Phillip C. Wright and Natalio Krasnogor},
doi = {10.1021/acssynbio.6b00315},
year = {2017},
date = {2017-01-01},
journal = {ACS Synthetic Biology},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Shmarov, Fedor; Paoletti, Nicola ; Bartocci, Ezio ; Lin, Shan ; Smolka, Scott A; Zuliani, Paolo SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems Incollection Hardware and Software: Verification and Testing, pp. 131–146, Springer International Publishing, 2017. Links | BibTeX | Tags: @incollection{Shmarov2017,
title = {SMT-based Synthesis of Safe and Robust PID Controllers for Stochastic Hybrid Systems},
author = { Fedor Shmarov and Nicola Paoletti and Ezio Bartocci and Shan Lin and Scott A. Smolka and Paolo Zuliani},
doi = {10.1007/978-3-319-70389-3_9},
year = {2017},
date = {2017-01-01},
booktitle = {Hardware and Software: Verification and Testing},
pages = {131--146},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
|
Kozyra, Jerzy; Fellermann, Harold ; Shirt-Ediss, Ben ; Lopiccolo, Annunziata ; Krasnogor, Natalio Optimizing nucleic acid sequences for a molecular data recorder Inproceedings Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17, pp. 1145–1152, Berlin, Germany, 2017. Links | BibTeX | Tags: @inproceedings{Kozyra2017a,
title = {Optimizing nucleic acid sequences for a molecular data recorder},
author = { Jerzy Kozyra and Harold Fellermann and Ben Shirt-Ediss and Annunziata Lopiccolo and Natalio Krasnogor},
doi = {10.1145/3071178.3071345},
year = {2017},
date = {2017-01-01},
booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '17},
pages = {1145--1152},
address = {Berlin, Germany},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
|
Goñi-Moreno, Angel; Wipat, Anil ; Krasnogor, Natalio CSBB: synthetic biology research at Newcastle University Journal Article Biochemical Society Transactions, 45 (3), pp. 781–783, 2017. Links | BibTeX | Tags: @article{Goni-Moreno2017a,
title = {CSBB: synthetic biology research at Newcastle University},
author = { Angel Goñi-Moreno and Anil Wipat and Natalio Krasnogor},
doi = {10.1042/BST20160437},
year = {2017},
date = {2017-01-01},
journal = {Biochemical Society Transactions},
volume = {45},
number = {3},
pages = {781--783},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
2016
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Lazzarini, Nicola; Widera, Paweł ; Williamson, Stuart ; Heer, Rakesh ; Krasnogor, Natalio ; Bacardit, Jaume Functional networks inference from rule-based machine learning models Journal Article BioData Mining, 9 (1), 2016. Links | BibTeX | Tags: @article{Lazzarini2016,
title = {Functional networks inference from rule-based machine learning models},
author = { Nicola Lazzarini and Paweł Widera and Stuart Williamson and Rakesh Heer and Natalio Krasnogor and Jaume Bacardit},
doi = {10.1186/s13040-016-0106-4},
year = {2016},
date = {2016-01-01},
journal = {BioData Mining},
volume = {9},
number = {1},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Shmarov, Fedor; Zuliani, Paolo Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques Incollection Hardware and Software: Verification and Testing, pp. 152–168, Springer International Publishing, 2016. Links | BibTeX | Tags: @incollection{Shmarov2016,
title = {Probabilistic Hybrid Systems Verification via SMT and Monte Carlo Techniques},
author = { Fedor Shmarov and Paolo Zuliani},
doi = {10.1007/978-3-319-49052-6_10},
year = {2016},
date = {2016-01-01},
booktitle = {Hardware and Software: Verification and Testing},
pages = {152--168},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
|
Fellermann, Harold; Lopiccolo, Annunziata ; Kozyra, Jerzy ; Krasnogor, Natalio In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement Incollection Unconventional Computation and Natural Computation, pp. 87–98, Springer International Publishing, 2016. Links | BibTeX | Tags: @incollection{Fellermann2016,
title = {In Vitro Implementation of a Stack Data Structure Based on DNA Strand Displacement},
author = { Harold Fellermann and Annunziata Lopiccolo and Jerzy Kozyra and Natalio Krasnogor},
doi = {10.1007/978-3-319-41312-9_8},
year = {2016},
date = {2016-01-01},
booktitle = {Unconventional Computation and Natural Computation},
pages = {87--98},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
|
