2018
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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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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 (-), 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 = {2018-01-01},
number = {-},
institution = {Newcastle University},
keywords = {},
pubstate = {},
tppubtype = {techreport}
}
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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}
}
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Torres, Marina; Jiang, Shouyong ; Pelta, David ; Kaiser, Marcus ; Krasnogor, Natalio Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach Incollection Advances in Artificial Intelligence, pp. 273–282, Springer International Publishing, 2018. Links | BibTeX | Tags: @incollection{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},
doi = {10.1007/978-3-030-00374-6_26},
year = {2018},
date = {2018-01-01},
booktitle = {Advances in Artificial Intelligence},
pages = {273--282},
publisher = {Springer International Publishing},
keywords = {},
pubstate = {},
tppubtype = {incollection}
}
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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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Gonzalez-De-Aledo, Pablo; Vladimirov, Andrey ; Manca, Marco ; Baugh, Jerry ; Asai, Ryo ; Kaiser, Marcus ; Bauer, Roman An optimization approach for agent-based computational models of biological development Journal Article Advances in Engineering Software, 121 (C), pp. 262–275, 2018. Links | BibTeX | Tags: @article{Gonzalez-De-Aledo2018,
title = {An optimization approach for agent-based computational models of biological development},
author = { Pablo Gonzalez-De-Aledo and Andrey Vladimirov and Marco Manca and Jerry Baugh and Ryo Asai and Marcus Kaiser and Roman Bauer},
doi = {10.1016/j.advengsoft.2018.03.010},
year = {2018},
date = {2018-01-01},
journal = {Advances in Engineering Software},
volume = {121},
number = {C},
pages = {262--275},
keywords = {},
pubstate = {published},
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}
}
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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 = {2017-04-01},
journal = {ACS Synthetic Biology},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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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 = {2017-03-01},
journal = {Brain},
keywords = {},
pubstate = {},
tppubtype = {article}
}
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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}
}
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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}
}
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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}
}
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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}
}
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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}
}
|
Bauer, Roman; Kaiser, Marcus Nonlinear growth: an origin of hub organization in complex networks Journal Article Royal Society Open Science, 4 (3), pp. 160691, 2017. Links | BibTeX | Tags: @article{Bauer2017,
title = {Nonlinear growth: an origin of hub organization in complex networks},
author = { Roman Bauer and Marcus Kaiser},
doi = {10.1098/rsos.160691},
year = {2017},
date = {2017-01-01},
journal = {Royal Society Open Science},
volume = {4},
number = {3},
pages = {160691},
keywords = {},
pubstate = {published},
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 = {2016-12-01},
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}
}
|
