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 @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}
}
|
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 @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}
}
|
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 @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 @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 @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 @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 @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}
}
|
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 @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 @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 @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 @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 @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}
}
|
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 @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 @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 @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 @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 @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}
}
|
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 @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 @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 @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}
}
|
