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2023

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.

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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.

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Partridge, Natalie

Research Briefing - Governing synthetic biology: A food policy approach Technical Report

Newcastle University (1), 2023.

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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.

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2022

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.

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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.

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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.

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Tellechea-Luzardo, J; Hobbs, L

Versioning biological cells for trustworthy cell engineering Journal Article

Nature Communications, 13 (765), pp. 12, 2022.

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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.

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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.

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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.

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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).

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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.

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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.

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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.).

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Sidiq, Karzan R; Chow, Man W; Zhao, Zhao ; Daniel, Richard A

Alanine Metabolism in Bacillus subtilis Journal Article

Molecular Microbiology, 2020.

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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.

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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.

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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.

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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.

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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.

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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.

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Wipat, Anil

Codon optimisation for maximising gene expression in multiple species and microbial consortia Journal Article

Biorxiv, Preprint only (Preprint only), pp. 14, 2020.

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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.

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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.

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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.

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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.

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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.

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Wipat, Anil

SBOL Visual 2 Ontology Journal Article

ACS Synthetic Biology, 9 (4), pp. 6, 2020.

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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.

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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.

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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.

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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.

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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.

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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.

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2019

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.

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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.

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Wipat, Anil

Communicating Structure and Function in Synthetic Biology Diagrams Journal Article

ACS Synthetic Biology, 8 (8), pp. 8, 2019.

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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.

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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.

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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.

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Wipat, Anil

Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks Journal Article

Biorxiv, Preprint only (Preprint only), pp. 9, 2019.

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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.

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86 entries « 1 of 2 »