2021
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Huang, Yiming; Smith, Wendy ; Harwood, Colin ; Wipat, Anil ; Bacardit, Jaume Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis Journal Article Sensors, 21 (7), pp. 2436, 2021. Links | BibTeX | Tags: @article{Huang2021,
title = {Computational Strategies for the Identification of a Transcriptional Biomarker Panel to Sense Cellular Growth States in Bacillus subtilis},
author = { Yiming Huang and Wendy Smith and Colin Harwood and Anil Wipat and Jaume Bacardit},
doi = {10.3390/s21072436},
year = {2021},
date = {2021-04-01},
journal = {Sensors},
volume = {21},
number = {7},
pages = {2436},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
de Lorenzo, Víctor; Krasnogor, Natalio ; Schmidt, Markus For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is! Journal Article New Biotechnology, 60 (C), pp. 44–51, 2021. Links | BibTeX | Tags: @article{Lorenzo2021,
title = {For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is!},
author = { Víctor de Lorenzo and Natalio Krasnogor and Markus Schmidt},
doi = {10.1016/j.nbt.2020.08.004},
year = {2021},
date = {2021-01-01},
journal = {New Biotechnology},
volume = {60},
number = {C},
pages = {44--51},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2020
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Wu, Ling Juan; Lee, Seoungjun ; Park, Sungshic ; Eland, Lucy E; Wipat, Anil ; Holden, Séamus ; Errington, Jeff Geometric principles underlying the proliferation of a model cell system Journal Article Nature Communications, 11 (1), 2020. Links | BibTeX | Tags: @article{Wu2020,
title = {Geometric principles underlying the proliferation of a model cell system},
author = { Ling Juan Wu and Seoungjun Lee and Sungshic Park and Lucy E. Eland and Anil Wipat and Séamus Holden and Jeff Errington},
doi = {10.1038/s41467-020-17988-7},
year = {2020},
date = {2020-12-01},
journal = {Nature Communications},
volume = {11},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Vasileva, Mariia; Shmarov, Fedor ; Zuliani, Paolo Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes Inproceedings 2020 18th ACM-IEEE International Conference on Formal Methods and Models for System Design (MEMOCODE), pp. 1–11, Jaipur, India, 2020. Links | BibTeX | Tags: @inproceedings{Vasileva2020,
title = {Probabilistic Reachability for Uncertain Stochastic Hybrid Systems via Gaussian Processes},
author = { Mariia Vasileva and Fedor Shmarov and Paolo Zuliani},
url = {http://dx.doi.org/10.1109/MEMOCODE51338.2020.9315182},
doi = {10.1109/MEMOCODE51338.2020.9315182},
year = {2020},
date = {2020-12-01},
booktitle = {2020 18th ACM-IEEE International Conference on Formal Methods and Models for System Design (MEMOCODE)},
pages = {1--11},
address = {Jaipur, India},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
|
Sidiq, Karzan R; Chow, Man W; Zhao, Zhao ; Daniel, Richard A Alanine Metabolism in Bacillus subtilis Journal Article Molecular Microbiology, 2020. Links | BibTeX | Tags: @article{Sidiq2020,
title = {Alanine Metabolism in Bacillus subtilis},
author = { Karzan R. Sidiq and Man W. Chow and Zhao Zhao and Richard A. Daniel},
doi = {10.1111/mmi.14640},
year = {2020},
date = {2020-11-01},
journal = {Molecular Microbiology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wipat, Anil The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering Journal Article Frontiers in Bioengineering and Biotechnology, 8 (1009), pp. 15, 2020. Links | BibTeX | Tags: @article{Wipat2020b,
title = {The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering},
author = { Anil Wipat},
url = {http://dx.doi.org/10.3389/fbioe.2020.01009},
year = {2020},
date = {2020-09-01},
journal = {Frontiers in Bioengineering and Biotechnology},
volume = {8},
number = {1009},
pages = {15},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
McLaughlin, James Alastair; Beal, Jacob ; Mısırlı, Göksel ; Grünberg, Raik ; Bartley, Bryan A; Scott-Brown, James ; Vaidyanathan, Prashant ; Fontanarrosa, Pedro ; Oberortner, Ernst ; Wipat, Anil ; Gorochowski, Thomas E; Myers, Chris J The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering Journal Article Frontiers in Bioengineering and Biotechnology, 8 , 2020. Links | BibTeX | Tags: @article{McLaughlin2020,
title = {The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering},
author = { James Alastair McLaughlin and Jacob Beal and Göksel Mısırlı and Raik Grünberg and Bryan A. Bartley and James Scott-Brown and Prashant Vaidyanathan and Pedro Fontanarrosa and Ernst Oberortner and Anil Wipat and Thomas E. Gorochowski and Chris J. Myers},
doi = {10.3389/fbioe.2020.01009},
year = {2020},
date = {2020-09-01},
journal = {Frontiers in Bioengineering and Biotechnology},
volume = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Franco, Maria A; Krasnogor, Natalio ; Bacardit, Jaume Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification Journal Article IEEE Computational Intelligence Magazine, 15 (3), pp. 28–46, 2020. Links | BibTeX | Tags: @article{Franco2020,
title = {Automatic Tuning of Rule-Based Evolutionary Machine Learning via Problem Structure Identification},
author = { Maria A. Franco and Natalio Krasnogor and Jaume Bacardit},
doi = {10.1109/MCI.2020.2998232},
year = {2020},
date = {2020-08-01},
journal = {IEEE Computational Intelligence Magazine},
volume = {15},
number = {3},
pages = {28--46},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Koch, Birgit; Callaghan, Melanie M; Tellechea‐Luzardo, Jonathan ; Seeger, Ami Y; Dillard, Joseph P; Krasnogor, Natalio Protein interactions within and between two F‐type type IV secretion systems Journal Article Molecular Microbiology, 2020. Links | BibTeX | Tags: @article{Koch2020,
title = {Protein interactions within and between two F‐type type IV secretion systems},
author = { Birgit Koch and Melanie M. Callaghan and Jonathan Tellechea‐Luzardo and Ami Y. Seeger and Joseph P. Dillard and Natalio Krasnogor},
doi = {10.1111/mmi.14582},
year = {2020},
date = {2020-08-01},
journal = {Molecular Microbiology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Torelli, Emanuela; Kozyra, Jerzy ; Shirt-Ediss, Ben ; Piantanida, Luca ; Voïtchovsky, Kislon ; Krasnogor, Natalio Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami Journal Article ACS Synthetic Biology, 9 (7), pp. 1682–1692, 2020. Links | BibTeX | Tags: @article{Torelli2020,
title = {Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami},
author = { Emanuela Torelli and Jerzy Kozyra and Ben Shirt-Ediss and Luca Piantanida and Kislon Voïtchovsky and Natalio Krasnogor},
doi = {10.1021/acssynbio.0c00009},
year = {2020},
date = {2020-07-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {7},
pages = {1682--1692},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Kaiser, Marcus Computational models and fundamental constraints can inform the design of synthetic connectomes Journal Article Physics of Life Reviews, 33 (C), pp. 16–18, 2020. Links | BibTeX | Tags: @article{Kaiser2020,
title = {Computational models and fundamental constraints can inform the design of synthetic connectomes},
author = { Marcus Kaiser},
doi = {10.1016/j.plrev.2019.08.003},
year = {2020},
date = {2020-07-01},
journal = {Physics of Life Reviews},
volume = {33},
number = {C},
pages = {16--18},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wipat, Anil Codon optimisation for maximising gene expression in multiple species and microbial consortia Journal Article Biorxiv, Preprint only (Preprint only), pp. 14, 2020. Links | BibTeX | Tags: @article{Wipat2020,
title = {Codon optimisation for maximising gene expression in multiple species and microbial consortia},
author = { Anil Wipat},
url = {http://dx.doi.org/10.1101/2020.06.30.177766},
year = {2020},
date = {2020-07-01},
journal = {Biorxiv},
volume = {Preprint only},
number = {Preprint only},
pages = {14},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Jiang, Shouyong; Wang, Yong ; Kaiser, Marcus ; Krasnogor, Natalio NIHBA: a network interdiction approach for metabolic engineering design Journal Article Bioinformatics, 36 (11), pp. 3482–3492, 2020. Links | BibTeX | Tags: @article{Jiang2020,
title = {NIHBA: a network interdiction approach for metabolic engineering design},
author = { Shouyong Jiang and Yong Wang and Marcus Kaiser and Natalio Krasnogor},
doi = {10.1093/bioinformatics/btaa163},
year = {2020},
date = {2020-06-01},
journal = {Bioinformatics},
volume = {36},
number = {11},
pages = {3482--3492},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Jiang, Shouyong; Li, Hongru ; Guo, Jinglei ; Zhong, Mingjun ; Yang, Shengxiang ; Kaiser, Marcus ; Krasnogor, Natalio AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation Journal Article Information Sciences, 515 (C), pp. 365–387, 2020. Links | BibTeX | Tags: @article{Jiang2020a,
title = {AREA: An adaptive reference-set based evolutionary algorithm for multiobjective optimisation},
author = { Shouyong Jiang and Hongru Li and Jinglei Guo and Mingjun Zhong and Shengxiang Yang and Marcus Kaiser and Natalio Krasnogor},
doi = {10.1016/j.ins.2019.12.011},
year = {2020},
date = {2020-04-01},
journal = {Information Sciences},
volume = {515},
number = {C},
pages = {365--387},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Taylor, Ken; Woods, Simon Reflections on the practice of Responsible (Research and) Innovation in synthetic biology Journal Article New Genetics and Society, 39 (2), pp. 127–147, 2020. Links | BibTeX | Tags: @article{Taylor2020,
title = {Reflections on the practice of Responsible (Research and) Innovation in synthetic biology},
author = { Ken Taylor and Simon Woods},
doi = {10.1080/14636778.2019.1709431},
year = {2020},
date = {2020-04-01},
journal = {New Genetics and Society},
volume = {39},
number = {2},
pages = {127--147},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Mısırlı, Göksel; Beal, Jacob ; Gorochowski, Thomas E; Stan, Guy-Bart ; Wipat, Anil ; Myers, Chris J SBOL Visual 2 Ontology Journal Article ACS Synthetic Biology, 9 (4), pp. 972–977, 2020. Links | BibTeX | Tags: @article{Misirli2020,
title = {SBOL Visual 2 Ontology},
author = { Göksel Mısırlı and Jacob Beal and Thomas E. Gorochowski and Guy-Bart Stan and Anil Wipat and Chris J. Myers},
doi = {10.1021/acssynbio.0c00046},
year = {2020},
date = {2020-04-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {4},
pages = {972--977},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Tellechea-Luzardo, Jonathan; Winterhalter, Charles ; Widera, Paweł ; Kozyra, Jerzy ; de Lorenzo, Víctor ; Krasnogor, Natalio Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering Journal Article ACS Synthetic Biology, 9 (3), pp. 536–545, 2020. Links | BibTeX | Tags: @article{Tellechea-Luzardo2020,
title = {Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering},
author = { Jonathan Tellechea-Luzardo and Charles Winterhalter and Paweł Widera and Jerzy Kozyra and Víctor de Lorenzo and Natalio Krasnogor},
doi = {10.1021/acssynbio.9b00400},
year = {2020},
date = {2020-03-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {3},
pages = {536--545},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wipat, Anil SBOL Visual 2 Ontology Journal Article ACS Synthetic Biology, 9 (4), pp. 6, 2020. Links | BibTeX | Tags: @article{Wipat2020a,
title = {SBOL Visual 2 Ontology},
author = { Anil Wipat},
url = {http://dx.doi.org/10.1021/acssynbio.0c00046},
year = {2020},
date = {2020-03-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {4},
pages = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wipat, Anil ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL) Journal Article ACS Synthetic Biology, 9 (4), pp. 5, 2020. Links | BibTeX | Tags: @article{Wipat2020c,
title = {ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)},
author = { Anil Wipat},
url = {http://dx.doi.org/10.1021/acssynbio.9b00470},
year = {2020},
date = {2020-03-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {4},
pages = {5},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Riaz-Bradley, Amber; James, Katherine ; Yuzenkova, Yulia High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors Journal Article Nucleic Acids Research, 48 (3), pp. 1341–1352, 2020. Links | BibTeX | Tags: @article{Riaz-Bradley2020,
title = {High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors},
author = { Amber Riaz-Bradley and Katherine James and Yulia Yuzenkova},
doi = {10.1093/nar/gkz1130},
year = {2020},
date = {2020-02-01},
journal = {Nucleic Acids Research},
volume = {48},
number = {3},
pages = {1341--1352},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Little, Bethany; Alshabrawy, Ossama ; Stow, Daniel ; Ferrier, Nicol I; McNaney, Roisin ; Jackson, Daniel G; Ladha, Karim ; Ladha, Cassim ; Ploetz, Thomas ; Bacardit, Jaume ; Olivier, Patrick ; Gallagher, Peter ; O'Brien, John T Deep learning-based automated speech detection as a marker of social functioning in late-life depression Journal Article Psychological Medicine, pp. 1–10, 2020. Links | BibTeX | Tags: @article{Little2020,
title = {Deep learning-based automated speech detection as a marker of social functioning in late-life depression},
author = { Bethany Little and Ossama Alshabrawy and Daniel Stow and I. Nicol Ferrier and Roisin McNaney and Daniel G. Jackson and Karim Ladha and Cassim Ladha and Thomas Ploetz and Jaume Bacardit and Patrick Olivier and Peter Gallagher and John T. O'Brien},
doi = {10.1017/S0033291719003994},
year = {2020},
date = {2020-01-01},
journal = {Psychological Medicine},
pages = {1--10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Shmarov, Fedor; Soudjani, Sadegh ; Paoletti, Nicola ; Bartocci, Ezio ; Lin, Shan ; Smolka, Scott A; Zuliani, Paolo Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems Journal Article IEEE Access, 8 , pp. 180825–180843, 2020. Links | BibTeX | Tags: @article{Shmarov2020,
title = {Automated Synthesis of Safe Digital Controllers for Sampled-Data Stochastic Nonlinear Systems},
author = { Fedor Shmarov and Sadegh Soudjani and Nicola Paoletti and Ezio Bartocci and Shan Lin and Scott A. Smolka and Paolo Zuliani},
doi = {10.1109/ACCESS.2020.3028476},
year = {2020},
date = {2020-01-01},
journal = {IEEE Access},
volume = {8},
pages = {180825--180843},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Crowther, Matthew; Grozinger, Lewis ; Pocock, Matthew ; Taylor, Christopher P D; McLaughlin, James A; Mısırlı, Göksel ; Bartley, Bryan A; Beal, Jacob ; Goñi-Moreno, Angel ; Wipat, Anil ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL) Journal Article ACS Synthetic Biology, 9 (4), pp. 962–966, 2020. Links | BibTeX | Tags: @article{Crowther2020,
title = {ShortBOL: A Language for Scripting Designs for Engineered Biological Systems Using Synthetic Biology Open Language (SBOL)},
author = { Matthew Crowther and Lewis Grozinger and Matthew Pocock and Christopher P. D. Taylor and James A. McLaughlin and Göksel Mısırlı and Bryan A. Bartley and Jacob Beal and Angel Goñi-Moreno and Anil Wipat},
doi = {10.1021/acssynbio.9b00470},
year = {2020},
date = {2020-01-01},
journal = {ACS Synthetic Biology},
volume = {9},
number = {4},
pages = {962--966},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Alameer, Ali; Kyriazakis, Ilias ; Dalton, Hillary A; Miller, Amy L; Bacardit, Jaume Automatic recognition of feeding and foraging behaviour in pigs using deep learning Journal Article Biosystems Engineering, 197 (C), pp. 91–104, 2020. Links | BibTeX | Tags: @article{Alameer2020,
title = {Automatic recognition of feeding and foraging behaviour in pigs using deep learning},
author = { Ali Alameer and Ilias Kyriazakis and Hillary A. Dalton and Amy L. Miller and Jaume Bacardit},
doi = {10.1016/j.biosystemseng.2020.06.013},
year = {2020},
date = {2020-01-01},
journal = {Biosystems Engineering},
volume = {197},
number = {C},
pages = {91--104},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2019
|
Wipat, Anil Communicating Structure and Function in Synthetic Biology Diagrams Journal Article ACS Synthetic Biology, 8 (8), pp. 8, 2019. Links | BibTeX | Tags: @article{Wipat2019,
title = {Communicating Structure and Function in Synthetic Biology Diagrams},
author = { Anil Wipat},
url = {http://dx.doi.org/10.1021/acssynbio.9b00139},
year = {2019},
date = {2019-07-01},
journal = {ACS Synthetic Biology},
volume = {8},
number = {8},
pages = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Hallinan, Jennifer S; Wipat, Anil ; Kitney, Richard ; Woods, Simon ; Taylor, Ken ; Goñi-Moreno, Angel Future-proofing synthetic biology: educating the next generation Journal Article Engineering Biology, 3 (2), pp. 25–31, 2019. Links | BibTeX | Tags: @article{Hallinan2019,
title = {Future-proofing synthetic biology: educating the next generation},
author = { Jennifer S. Hallinan and Anil Wipat and Richard Kitney and Simon Woods and Ken Taylor and Angel Goñi-Moreno},
doi = {10.1049/enb.2019.0001},
year = {2019},
date = {2019-06-01},
journal = {Engineering Biology},
volume = {3},
number = {2},
pages = {25--31},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wade, Yana; Daniel, Richard A; Leak, David J Heterologous microcompartment assembly in Bacillaceae: Establishing the components necessary for scaffold formation Journal Article ACS Synthetic Biology, 8 (7), pp. 1642–1654, 2019. Links | BibTeX | Tags: @article{Wade2019,
title = {Heterologous microcompartment assembly in Bacillaceae: Establishing the components necessary for scaffold formation},
author = { Yana Wade and Richard A. Daniel and David J. Leak},
doi = {10.1021/acssynbio.9b00155},
year = {2019},
date = {2019-06-01},
journal = {ACS Synthetic Biology},
volume = {8},
number = {7},
pages = {1642--1654},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Schumacher, Julia; Peraza, Luis R; Firbank, Michael ; Thomas, Alan J; Kaiser, Marcus ; Gallagher, Peter ; O’Brien, John T; Blamire, Andrew M; Taylor, John-Paul Dysfunctional brain dynamics and their origin in Lewy body dementia Journal Article Brain, 142 (6), pp. 1767–1782, 2019. Links | BibTeX | Tags: @article{Schumacher2019,
title = {Dysfunctional brain dynamics and their origin in Lewy body dementia},
author = { Julia Schumacher and Luis R Peraza and Michael Firbank and Alan J Thomas and Marcus Kaiser and Peter Gallagher and John T O’Brien and Andrew M Blamire and John-Paul Taylor},
doi = {10.1093/brain/awz069},
year = {2019},
date = {2019-06-01},
journal = {Brain},
volume = {142},
number = {6},
pages = {1767--1782},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Wipat, Anil Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks Journal Article Biorxiv, Preprint only (Preprint only), pp. 9, 2019. Links | BibTeX | Tags: @article{Wipat2019a,
title = {Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks},
author = { Anil Wipat},
url = {http://dx.doi.org/10.1101/646539},
year = {2019},
date = {2019-05-01},
journal = {Biorxiv},
volume = {Preprint only},
number = {Preprint only},
pages = {9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Jiang, Shouyong; Kaiser, Marcus ; Yang, Shengxiang ; Kollias, Stefanos ; Krasnogor, Natalio A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization Journal Article IEEE Transactions on Cybernetics, pp. 1–13, 2019. Links | BibTeX | Tags: @article{Jiang2019,
title = {A Scalable Test Suite for Continuous Dynamic Multiobjective Optimization},
author = { Shouyong Jiang and Marcus Kaiser and Shengxiang Yang and Stefanos Kollias and Natalio Krasnogor},
doi = {10.1109/TCYB.2019.2896021},
year = {2019},
date = {2019-01-01},
journal = {IEEE Transactions on Cybernetics},
pages = {1--13},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
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}
}
|
Cowton, Jake; Kyriazakis, Ilias ; Bacardit, Jaume Automated Individual Pig Localisation, Tracking And Behaviour Metric Extraction Using Deep Learning Journal Article IEEE Access, pp. 1–1, 2019. Links | BibTeX | Tags: @article{Cowton2019,
title = {Automated Individual Pig Localisation, Tracking And Behaviour Metric Extraction Using Deep Learning},
author = { Jake Cowton and Ilias Kyriazakis and Jaume Bacardit},
doi = {10.1109/ACCESS.2019.2933060},
year = {2019},
date = {2019-01-01},
journal = {IEEE Access},
pages = {1--1},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Grozinger, Lewis; Amos, Martyn ; Gorochowski, Thomas E; Carbonell, Pablo ; Oyarzún, Diego A; Stoof, Ruud ; Fellermann, Harold ; Zuliani, Paolo ; Tas, Huseyin ; Goñi-Moreno, Angel Pathways to cellular supremacy in biocomputing Journal Article Nature Communications, 10 (1), 2019. Links | BibTeX | Tags: @article{Grozinger2019,
title = {Pathways to cellular supremacy in biocomputing},
author = { Lewis Grozinger and Martyn Amos and Thomas E. Gorochowski and Pablo Carbonell and Diego A. Oyarzún and Ruud Stoof and Harold Fellermann and Paolo Zuliani and Huseyin Tas and Angel Goñi-Moreno},
doi = {10.1038/s41467-019-13232-z},
year = {2019},
date = {2019-01-01},
journal = {Nature Communications},
volume = {10},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Naylor, Jonathan; Fellermann, Harold ; Krasnogor, Natalio Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations Journal Article Bioinformatics, 35 (19), pp. 3859–3860, 2019. Links | BibTeX | Tags: @article{Naylor2019,
title = {Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations},
author = { Jonathan Naylor and Harold Fellermann and Natalio Krasnogor},
doi = {10.1093/bioinformatics/btz131},
year = {2019},
date = {2019-01-01},
journal = {Bioinformatics},
volume = {35},
number = {19},
pages = {3859--3860},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Goetzfried, Marisa A; Vogele, Kilian ; Mückl, Andrea ; Kaiser, Marcus ; Holland, Nolan B; Simmel, Friedrich C; Pirzer, Tobias Periodic Operation of a Dynamic DNA Origami Structure Utilizing the Hydrophilic–Hydrophobic Phase‐Transition of Stimulus‐Sensitive Polypeptides Journal Article Small, 15 (45), pp. 1903541, 2019. Links | BibTeX | Tags: @article{Goetzfried2019,
title = {Periodic Operation of a Dynamic DNA Origami Structure Utilizing the Hydrophilic–Hydrophobic Phase‐Transition of Stimulus‐Sensitive Polypeptides},
author = { Marisa A. Goetzfried and Kilian Vogele and Andrea Mückl and Marcus Kaiser and Nolan B. Holland and Friedrich C. Simmel and Tobias Pirzer},
doi = {10.1002/smll.201903541},
year = {2019},
date = {2019-01-01},
journal = {Small},
volume = {15},
number = {45},
pages = {1903541},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Sinha, Nishant; Wang, Yujiang ; Dauwels, Justin ; Kaiser, Marcus ; Thesen, Thomas ; Forsyth, Rob ; Taylor, Peter Neal Computer modelling of connectivity change suggests epileptogenesis mechanisms in idiopathic generalised epilepsy Journal Article NeuroImage: Clinical, 21 (C), pp. 101655, 2019. Links | BibTeX | Tags: @article{Sinha2019,
title = {Computer modelling of connectivity change suggests epileptogenesis mechanisms in idiopathic generalised epilepsy},
author = { Nishant Sinha and Yujiang Wang and Justin Dauwels and Marcus Kaiser and Thomas Thesen and Rob Forsyth and Peter Neal Taylor},
doi = {10.1016/j.nicl.2019.101655},
year = {2019},
date = {2019-01-01},
journal = {NeuroImage: Clinical},
volume = {21},
number = {C},
pages = {101655},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Beal, Jacob; Nguyen, Tramy ; Gorochowski, Thomas E; Goñi-Moreno, Angel ; Scott-Brown, James ; McLaughlin, James Alastair ; Madsen, Curtis ; Aleritsch, Benjamin ; Bartley, Bryan ; Bhakta, Shyam ; Bissell, Mike ; Hair, Sebastian Castillo ; Clancy, Kevin ; Luna, Augustin ; Novère, Nicolas Le ; Palchick, Zach ; Pocock, Matthew ; Sauro, Herbert ; Sexton, John T; Tabor, Jeffrey J; Voigt, Christopher A; Zundel, Zach ; Myers, Chris ; Wipat, Anil Communicating Structure and Function in Synthetic Biology Diagrams Journal Article ACS Synthetic Biology, 8 (8), pp. 1818–1825, 2019. Links | BibTeX | Tags: @article{Beal2019,
title = {Communicating Structure and Function in Synthetic Biology Diagrams},
author = { Jacob Beal and Tramy Nguyen and Thomas E. Gorochowski and Angel Goñi-Moreno and James Scott-Brown and James Alastair McLaughlin and Curtis Madsen and Benjamin Aleritsch and Bryan Bartley and Shyam Bhakta and Mike Bissell and Sebastian Castillo Hair and Kevin Clancy and Augustin Luna and Nicolas Le Novère and Zach Palchick and Matthew Pocock and Herbert Sauro and John T. Sexton and Jeffrey J. Tabor and Christopher A. Voigt and Zach Zundel and Chris Myers and Anil Wipat},
doi = {10.1021/acssynbio.9b00139},
year = {2019},
date = {2019-01-01},
journal = {ACS Synthetic Biology},
volume = {8},
number = {8},
pages = {1818--1825},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2018
|
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}
}
|
Keasar, Chen; McGuffin, Liam J; Wallner, Björn ; Chopra, Gaurav ; Adhikari, Badri ; Bhattacharya, Debswapna ; Blake, Lauren ; Bortot, Leandro Oliveira ; Cao, Renzhi ; Dhanasekaran, B K; Dimas, Itzhel ; Faccioli, Rodrigo Antonio ; Faraggi, Eshel ; Ganzynkowicz, Robert ; Ghosh, Sambit ; Ghosh, Soma ; Giełdoń, Artur ; Golon, Lukasz ; He, Yi ; Heo, Lim ; Hou, Jie ; Khan, Main ; Khatib, Firas ; Khoury, George A; Kieslich, Chris ; Kim, David E; Krupa, Pawel ; Lee, Gyu Rie ; Li, Hongbo ; Li, Jilong ; Lipska, Agnieszka ; Liwo, Adam ; Maghrabi, Ali Hassan A; Mirdita, Milot ; Mirzaei, Shokoufeh ; Mozolewska, Magdalena A; Onel, Melis ; Ovchinnikov, Sergey ; Shah, Anand ; Shah, Utkarsh ; Sidi, Tomer ; Sieradzan, Adam K; Ślusarz, Magdalena ; Ślusarz, Rafal ; Smadbeck, James ; Tamamis, Phanourios ; Trieber, Nicholas ; Wirecki, Tomasz ; Yin, Yanping ; Zhang, Yang ; Bacardit, Jaume ; Baranowski, Maciej ; Chapman, Nicholas ; Cooper, Seth ; Defelicibus, Alexandre ; Flatten, Jeff ; Koepnick, Brian ; Popović, Zoran ; Zaborowski, Bartlomiej ; Baker, David ; Cheng, Jianlin ; Czaplewski, Cezary ; Delbem, Alexandre Cláudio Botazzo ; Floudas, Christodoulos ; Kloczkowski, Andrzej ; Ołdziej, Stanislaw ; Levitt, Michael ; Scheraga, Harold ; Seok, Chaok ; Söding, Johannes ; Vishveshwara, Saraswathi ; Xu, Dong ; Crivelli, Silvia N An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 Journal Article Scientific Reports, 8 (1), 2018. Links | BibTeX | Tags: @article{Keasar2018,
title = {An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12},
author = { Chen Keasar and Liam J. McGuffin and Björn Wallner and Gaurav Chopra and Badri Adhikari and Debswapna Bhattacharya and Lauren Blake and Leandro Oliveira Bortot and Renzhi Cao and B. K. Dhanasekaran and Itzhel Dimas and Rodrigo Antonio Faccioli and Eshel Faraggi and Robert Ganzynkowicz and Sambit Ghosh and Soma Ghosh and Artur Giełdoń and Lukasz Golon and Yi He and Lim Heo and Jie Hou and Main Khan and Firas Khatib and George A. Khoury and Chris Kieslich and David E. Kim and Pawel Krupa and Gyu Rie Lee and Hongbo Li and Jilong Li and Agnieszka Lipska and Adam Liwo and Ali Hassan A. Maghrabi and Milot Mirdita and Shokoufeh Mirzaei and Magdalena A. Mozolewska and Melis Onel and Sergey Ovchinnikov and Anand Shah and Utkarsh Shah and Tomer Sidi and Adam K. Sieradzan and Magdalena Ślusarz and Rafal Ślusarz and James Smadbeck and Phanourios Tamamis and Nicholas Trieber and Tomasz Wirecki and Yanping Yin and Yang Zhang and Jaume Bacardit and Maciej Baranowski and Nicholas Chapman and Seth Cooper and Alexandre Defelicibus and Jeff Flatten and Brian Koepnick and Zoran Popović and Bartlomiej Zaborowski and David Baker and Jianlin Cheng and Cezary Czaplewski and Alexandre Cláudio Botazzo Delbem and Christodoulos Floudas and Andrzej Kloczkowski and Stanislaw Ołdziej and Michael Levitt and Harold Scheraga and Chaok Seok and Johannes Söding and Saraswathi Vishveshwara and Dong Xu and Silvia N. Crivelli},
doi = {10.1038/s41598-018-26812-8},
year = {2018},
date = {2018-12-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
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 = {2018-09-01},
journal = {bioRxiv},
volume = {415042v2},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
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 = {2018-08-01},
journal = {Life},
volume = {8},
number = {3},
pages = {33},
keywords = {},
pubstate = {},
tppubtype = {article}
}
|
Jiang, Shouyong; Kaiser, Marcus ; Wan, Shuzhen ; Guo, Jinglei ; Yang, Shengxiang ; Krasnogor, Natalio An Empirical Study of Dynamic Triobjective Optimisation Problems Inproceedings 2018 IEEE Congress on Evolutionary Computation (CEC), pp. 1–8, Rio de Janeiro, 2018. Links | 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},
doi = {10.1109/CEC.2018.8477667},
year = {2018},
date = {2018-07-01},
booktitle = {2018 IEEE Congress on Evolutionary Computation (CEC)},
pages = {1--8},
address = {Rio de Janeiro},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
|
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 FAIM Workshop on AI for Sythetic Biology 2, 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 = {FAIM Workshop on AI for Sythetic Biology 2},
pages = {1--6},
address = {Stockholm, Sweden},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
|
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}
}
|
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}
}
|
Jiang, Shouyong; Kaiser, Marcus ; Guo, Jinglei ; Yang, Shengxiang ; Krasnogor, Natalio Less detectable environmental changes in dynamic multiobjective optimisation Inproceedings Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '18, pp. 673–680, Kyoto, Japan, 2018. Links | 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},
doi = {10.1145/3205455.3205521},
year = {2018},
date = {2018-01-01},
booktitle = {Proceedings of the Genetic and Evolutionary Computation Conference on - GECCO '18},
pages = {673--680},
address = {Kyoto, Japan},
keywords = {},
pubstate = {},
tppubtype = {inproceedings}
}
|
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}
}
|
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}
}
|
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 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}
}
|
