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2021

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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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

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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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.

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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.

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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.

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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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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Markovitch, Omer; Krasnogor, Natalio

Predicting species emergence in simulated complex pre-biotic networks Journal Article

PLOS ONE, 13 (2), pp. e0192871, 2018.

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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.

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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.

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McLaughlin, James Alastair; Myers, Chris J; Zundel, Zach ; Mısırlı, Göksel ; Zhang, Michael ; Ofiteru, Irina Dana ; Goñi-Moreno, Angel ; Wipat, Anil

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology Journal Article

ACS Synthetic Biology, 2018.

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Jiang, Shouyong; Yang, Shengxiang ; Yao, Xin ; Tan, Kay Chen ; Kaiser, Marcus ; Krasnogor, Natalio

Benchmark Problems for CEC2018 Competition on Dynamic Multiobjective Optimisation Technical Report

Newcastle University (-), 2018.

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Shirt-Ediss, Ben; Krasnogor, Natalio ; Fellermann, Harold

The fittest, the common, and the dullest: Selection dynamics of exact autocatalytic replicators Inproceedings

The 2018 Conference on Artificial Life, pp. 370–371, Tokyo, Japan, 2018.

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Torres, Marina; Jiang, Shouyong ; Pelta, David ; Kaiser, Marcus ; Krasnogor, Natalio

Strain Design as Multiobjective Network Interdiction Problem: A Preliminary Approach Incollection

Advances in Artificial Intelligence, pp. 273–282, Springer International Publishing, 2018.

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68 entries « 1 of 2 »