2023
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Huang, Yiming; Wipat, Anil ; Bacardit, Jaume Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains Journal Article Biotechnology and Bioengineering, 2023. Links | BibTeX | Tags: @article{Huang2023a,
title = {Transcriptional biomarker discovery toward building a load stress reporting system for engineered Escherichia coli strains},
author = { Yiming Huang and Anil Wipat and Jaume Bacardit},
doi = {10.1002/bit.28567},
year = {2023},
date = {2023-10-01},
journal = {Biotechnology and Bioengineering},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Huang, Yiming; Sinha, Nishant ; Wipat, Anil ; Bacardit, Jaume A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis Journal Article Synthetic and Systems Biotechnology, 8 (1), pp. 97–106, 2023. Links | BibTeX | Tags: @article{Huang2023,
title = {A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis},
author = { Yiming Huang and Nishant Sinha and Anil Wipat and Jaume Bacardit},
doi = {10.1016/j.synbio.2022.12.001},
year = {2023},
date = {2023-03-01},
journal = {Synthetic and Systems Biotechnology},
volume = {8},
number = {1},
pages = {97--106},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Partridge, Natalie Research Briefing - Governing synthetic biology: A food policy approach Technical Report Newcastle University (1), 2023. Links | BibTeX | Tags: @techreport{Partridge2023,
title = {Research Briefing - Governing synthetic biology: A food policy approach},
author = { Natalie Partridge},
url = {http://dx.doi.org/10.5281/zenodo.10804432},
year = {2023},
date = {2023-03-01},
number = {1},
institution = {Newcastle University},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
|
Shirt-Ediss, Ben; Connolly, Jordan ; Elezgaray, Juan ; Torelli, Emanuela ; Navarro, Silvia Adriana ; Bacardit, Jaume ; Krasnogor, Natalio Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists Journal Article Computational and Structural Biotechnology Journal, 21 (C), pp. 3615–3626, 2023. Links | BibTeX | Tags: @article{Shirt-Ediss2023,
title = {Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists},
author = { Ben Shirt-Ediss and Jordan Connolly and Juan Elezgaray and Emanuela Torelli and Silvia Adriana Navarro and Jaume Bacardit and Natalio Krasnogor},
doi = {10.1016/j.csbj.2023.07.011},
year = {2023},
date = {2023-01-01},
journal = {Computational and Structural Biotechnology Journal},
volume = {21},
number = {C},
pages = {3615--3626},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2022
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Torelli, Emanuela; Shirt-Ediss, Benjamin ; Navarro, Silvia A; Manzano, Marisa ; Vizzini, Priya ; Krasnogor, Natalio Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing Journal Article bioRxiv, 2022.07.20.500791v1 , 2022. Links | BibTeX | Tags: @article{Torelli2022,
title = {Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing},
author = { Emanuela Torelli and Benjamin Shirt-Ediss and Silvia A. Navarro and Marisa Manzano and Priya Vizzini and Natalio Krasnogor},
doi = {10.1101/2022.07.20.500791},
year = {2022},
date = {2022-07-01},
journal = {bioRxiv},
volume = {2022.07.20.500791v1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Huang, Yiming; Sinha, Nishant ; Wipat, Anil ; Bacardit, Jaume A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis Journal Article bioRxiv, 2022.06.20.496894v1 , 2022. Links | BibTeX | Tags: @article{Huang2022,
title = {A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis},
author = { Yiming Huang and Nishant Sinha and Anil Wipat and Jaume Bacardit},
doi = {10.1101/2022.06.20.496894},
year = {2022},
date = {2022-06-01},
journal = {bioRxiv},
volume = {2022.06.20.496894v1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Jiang, Shouyong; Otero-Muras, Irene ; Banga, Julio R; Wang, Yong ; Kaiser, Marcus ; Krasnogor, Natalio OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production Journal Article ACS Synthetic Biology, 11 (4), pp. 1531–1541, 2022. Links | BibTeX | Tags: @article{Jiang2022,
title = {OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production},
author = { Shouyong Jiang and Irene Otero-Muras and Julio R. Banga and Yong Wang and Marcus Kaiser and Natalio Krasnogor},
doi = {10.1021/acssynbio.1c00610},
year = {2022},
date = {2022-04-01},
journal = {ACS Synthetic Biology},
volume = {11},
number = {4},
pages = {1531--1541},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Tellechea-Luzardo, J; Hobbs, L Versioning biological cells for trustworthy cell engineering Journal Article Nature Communications, 13 (765), pp. 12, 2022. Links | BibTeX | Tags: @article{Tellechea-Luzardo2022,
title = {Versioning biological cells for trustworthy cell engineering},
author = { J Tellechea-Luzardo and L Hobbs},
url = {http://dx.doi.org/10.1038/s41467-022-28350-4},
year = {2022},
date = {2022-01-01},
journal = {Nature Communications},
volume = {13},
number = {765},
pages = {12},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Li, Bowen; Mackenzie, Neil ; Shirt-Ediss, Ben ; Krasnogor, Natalio ; Zuliani, Paolo Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking Inproceedings 28th International Conference on DNA Computing and Molecular Programming (DNA 28), pp. 1–22, Dagstuhl, Germany, 2022. Links | BibTeX | Tags: @inproceedings{Li2022,
title = {Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking},
author = { Bowen Li and Neil Mackenzie and Ben Shirt-Ediss and Natalio Krasnogor and Paolo Zuliani},
url = {https://doi.org/10.4230/LIPIcs.DNA.28.5},
year = {2022},
date = {2022-01-01},
booktitle = {28th International Conference on DNA Computing and Molecular Programming (DNA 28)},
pages = {1--22},
address = {Dagstuhl, Germany},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
|
2021
|
Lopiccolo, Annunziata; Shirt-Ediss, Ben ; Torelli, Emanuela ; Olulana, Abimbola Feyisara Adedeji ; Castronovo, Matteo ; Fellermann, Harold ; Krasnogor, Natalio A last-in first-out stack data structure implemented in DNA Journal Article Nature Communications, 12 (1), 2021. Links | BibTeX | Tags: @article{Lopiccolo2021,
title = {A last-in first-out stack data structure implemented in DNA},
author = { Annunziata Lopiccolo and Ben Shirt-Ediss and Emanuela Torelli and Abimbola Feyisara Adedeji Olulana and Matteo Castronovo and Harold Fellermann and Natalio Krasnogor},
doi = {10.1038/s41467-021-25023-6},
year = {2021},
date = {2021-12-01},
journal = {Nature Communications},
volume = {12},
number = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Guyet, Aurelie; Alofi, Amirah ; Daniel, Richard Insights into the role of lipoteichoic acids in Bacillus subtilis- a new function for MprF Journal Article Biorxiv, N/A (N/A), pp. 1, 2021. Links | BibTeX | Tags: @article{Guyet2021,
title = {Insights into the role of lipoteichoic acids in Bacillus subtilis- a new function for MprF},
author = { Aurelie Guyet and Amirah Alofi and Richard Daniel},
url = {http://dx.doi.org/10.1101/2021.12.12.472321},
year = {2021},
date = {2021-12-01},
journal = {Biorxiv},
volume = {N/A},
number = {N/A},
pages = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Mısırlı, Göksel; Yang, Bill ; James, Katherine ; Wipat, Anil Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits Journal Article ACS Synthetic Biology, 10 (12), pp. 3304–3315, 2021, (Portabolomics paper). Links | BibTeX | Tags: @article{Msrl2021,
title = {Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits},
author = { Göksel Mısırlı and Bill Yang and Katherine James and Anil Wipat},
doi = {10.1021/acssynbio.1c00157},
year = {2021},
date = {2021-12-01},
journal = {ACS Synthetic Biology},
volume = {10},
number = {12},
pages = {3304--3315},
note = {Portabolomics paper},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Velázquez, Elena; Al-Ramahi, Yamal ; Tellechea-Luzardo, Jonathan ; Krasnogor, Natalio ; de Lorenzo, Víctor Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection Journal Article ACS Synthetic Biology, 10 (10), pp. 2552–2565, 2021. Links | BibTeX | Tags: @article{Velazquez2021,
title = {Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection},
author = { Elena Velázquez and Yamal Al-Ramahi and Jonathan Tellechea-Luzardo and Natalio Krasnogor and Víctor de Lorenzo},
doi = {10.1021/acssynbio.1c00199},
year = {2021},
date = {2021-10-01},
journal = {ACS Synthetic Biology},
volume = {10},
number = {10},
pages = {2552--2565},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Konur, Savas; Mierla, Laurentiu ; Fellermann, Harold ; Ladroue, Christophe ; Brown, Bradley ; Wipat, Anil ; Twycross, Jamie ; Dun, Boyang Peter ; Kalvala, Sara ; Gheorghe, Marian ; Krasnogor, Natalio Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation Journal Article ACS Synthetic Biology, 10 (8), pp. 1931–1945, 2021. Links | BibTeX | Tags: @article{Konur2021,
title = {Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation},
author = { Savas Konur and Laurentiu Mierla and Harold Fellermann and Christophe Ladroue and Bradley Brown and Anil Wipat and Jamie Twycross and Boyang Peter Dun and Sara Kalvala and Marian Gheorghe and Natalio Krasnogor},
doi = {10.1021/acssynbio.1c00143},
year = {2021},
date = {2021-08-01},
journal = {ACS Synthetic Biology},
volume = {10},
number = {8},
pages = {1931--1945},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Partridge, Natalie Towards greater transparency: Digital opportunities to promote traceability in genetic engineering. Technical Report Newcastle University (1), 2021, (This Policy Brief is an output from the N8 AgriFood Food Systems Policy Hub. It is one of a collection produced by participants on the Rapid Evidence Synthesis Training (REST) programme. REST was delivered through a collaboration between the University of Leeds, Newcastle University and the N8 AgriFood Programme, supported by Research England QR-SPF funds from the University of Leeds and the University of York.). Links | BibTeX | Tags: @techreport{Partridge2021,
title = {Towards greater transparency: Digital opportunities to promote traceability in genetic engineering.},
author = { Natalie Partridge},
url = {http://dx.doi.org/10.5281/zenodo.5343358},
year = {2021},
date = {2021-08-01},
number = {1},
institution = {Newcastle University},
note = {This Policy Brief is an output from the N8 AgriFood Food Systems Policy Hub. It is one of a collection produced by participants on the Rapid Evidence Synthesis Training (REST) programme. REST was delivered through a collaboration between the University of Leeds, Newcastle University and the N8 AgriFood Programme, supported by Research England QR-SPF funds from the University of Leeds and the University of York.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}
|
Mitchell, Anca Manuela; Gogulancea, Valentina ; Smith, Wendy ; Wipat, Anil ; Ofiţeru, Irina Dana Recombinant Protein Production with Escherichia coli in Glucose and Glycerol Limited Chemostats Journal Article Applied Microbiology, 1 (2), pp. 239–254, 2021. Links | BibTeX | Tags: @article{Mitchell2021,
title = {Recombinant Protein Production with Escherichia coli in Glucose and Glycerol Limited Chemostats},
author = { Anca Manuela Mitchell and Valentina Gogulancea and Wendy Smith and Anil Wipat and Irina Dana Ofiţeru},
doi = {10.3390/applmicrobiol1020018},
year = {2021},
date = {2021-07-01},
journal = {Applied Microbiology},
volume = {1},
number = {2},
pages = {239--254},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
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}
}
|
Callaghan, Melanie M; Koch, Birgit ; Hackett, Kathleen T; Klimowicz, Amy K; Schaub, Ryan E; Krasnogor, Natalio ; Dillard, Joseph P Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System Journal Article Frontiers in Microbiology, 12 , 2021. Links | BibTeX | Tags: @article{Callaghan2021,
title = {Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System},
author = { Melanie M. Callaghan and Birgit Koch and Kathleen T. Hackett and Amy K. Klimowicz and Ryan E. Schaub and Natalio Krasnogor and Joseph P. Dillard},
doi = {10.3389/fmicb.2021.784483},
year = {2021},
date = {2021-01-01},
journal = {Frontiers in Microbiology},
volume = {12},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
Choo, Siew Woh; Mohammed, Waleed K; Mutha, Naresh V R; Rostami, Nadia ; Ahmed, Halah ; Krasnogor, Natalio ; Tan, Geok Yuan Annie ; Jakubovics, Nicholas S Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis Journal Article Applied and Environmental Microbiology, 87 (22), 2021. Links | BibTeX | Tags: @article{Choo2021,
title = {Transcriptomic Responses to Coaggregation between Streptococcus gordonii and Streptococcus oralis},
author = { Siew Woh Choo and Waleed K. Mohammed and Naresh V. R. Mutha and Nadia Rostami and Halah Ahmed and Natalio Krasnogor and Geok Yuan Annie Tan and Nicholas S. Jakubovics},
doi = {10.1128/AEM.01558-21},
year = {2021},
date = {2021-01-01},
journal = {Applied and Environmental Microbiology},
volume = {87},
number = {22},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
2020
|
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
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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 = {2019-12-01},
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 = {2019-10-01},
journal = {Bioinformatics},
volume = {35},
number = {19},
pages = {3859--3860},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
|
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}
}
|
