Publications
419 results found
Sainz de Murieta Fuentes I, bultelle M, kitney, 2015, A DICOM Extension Supporting Data Acquisition in Synthetic Biology, Synthetic Biology: Engineering, Evolution & Design (SEED)
bultelle, Sainz de Murieta Fuentes I, kitney RI, 2015, Introducing Synbis – the Synthetic Biology Information System, Synthetic Biology: Engineering, Evolution & Design (SEED)
Tay D, Poh CL, Kitney RI, 2015, A novel neural-inspired learning algorithm with application to clinical risk prediction, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 54, Pages: 305-314, ISSN: 1532-0464
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- Citations: 15
Kelwick R, Kopniczky M, Bower I, et al., 2015, A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered <i>Escherichia coli</i>, PLOS ONE, Vol: 10, ISSN: 1932-6203
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- Citations: 8
Baldwin G, Bayer T, Dickinson R, et al., 2015, Synthetic biology - a primer, ISBN: 9781783268801
Synthetic Biology - A Primer (Revised Edition) presents an updated overview of the field of synthetic biology and the foundational concepts on which it is built. This revised edition includes new literature references, working and updated URL links, plus some new figures and text where progress in the field has been made. The book introduces readers to fundamental concepts in molecular biology and engineering and then explores the two major themes for synthetic biology, namely ‘bottom-up’ and ‘top-down’ engineering approaches. ‘Top-down’ engineering uses a conceptual framework of systematic design and engineering principles focused around the Design-Build-Test cycle and mathematical modelling. The ‘bottom-up’ approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch exploring the fundamental basis of living systems. Examples of cutting-edge applications designed using synthetic biology principles are presented, including: the production of novel, microbial synthesis of pharmaceuticals and fine chemicals the design and implementation of biosensors to detect infections and environmental waste. The book also describes the Internationally Genetically Engineered Machine (iGEM) competition, which brings together students and young researchers from around the world to carry out summer projects in synthetic biology. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences into synthetic biology research. Final year undergraduates, postgraduates and established researchers interested in learning about the interdisciplinary field of synthetic biology will benefit from this up-to-date primer on synthetic biology.
Casini A, Christodoulou G, Freemont PS, et al., 2014, R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences, ACS SYNTHETIC BIOLOGY, Vol: 3, Pages: 525-528, ISSN: 2161-5063
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- Citations: 47
Luboz V, Kyaw-Tun J, Sen S, et al., 2014, Real-time stent and balloon simulation for stenosis treatment, VISUAL COMPUTER, Vol: 30, Pages: 341-349, ISSN: 0178-2789
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- Citations: 7
Tay D, Poh CL, Goh C, et al., 2014, A biological continuum based approach for efficient clinical classification, JOURNAL OF BIOMEDICAL INFORMATICS, Vol: 47, Pages: 28-38, ISSN: 1532-0464
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- Citations: 6
Dickinson RJ, Kitney RI, 2014, Information driven care pathways and procedures, IFMBE Proceedings, Vol: 41, Pages: 1322-1325, ISSN: 1680-0737
The paper addresses the issue of the implementation of care pathways in electronic form. Within the National Health Service (NHS) of England, Care Pathways are becoming increasingly important. These are typically provided by the Department of Health. The Pathways provided are in the form of paper-based schema. They either have to be implemented via paper forms or, as presented here, in electronic form. In addition, care pathways must be seen in the context of the TModel of health care which comprises the care continuum and the biological continuum. The two care pathways which had been chosen as exemplars are myocardial infarction and stroke. However, the objective of the paper is not to discuss the specific care pathways in detail, but, rather, to describe technology which has been developed for their electronic implementation. The result of this implementation is that all the data and information acquired from the implementation of the care pathway is stored in a single clinical information system (CIS), which has incorporated in it the SQL database. Another important element of the system which has been developed is the ability to display data and information in terms of two dashboards (i.e. single screens which show the most important information). The two dashboards display clinical information (the point of care dashboard) and management information (the management dashboard). © Springer International Publishing Switzerland 2014.
Tay D, Poh CL, Goh C, et al., 2013, An Evolutionary Data-Conscious Artificial Immune Recognition System, 15th Genetic and Evolutionary Computation Conference (GECCO), Pages: 1101-1108
Kelay T, Kesavan S, Collins RE, et al., 2013, Techniques to aid the implementation of novel clinical information systems: A systematic review, INTERNATIONAL JOURNAL OF SURGERY, Vol: 11, Pages: 783-791, ISSN: 1743-9191
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- Citations: 1
Yang X, Han R, Guo Y, et al., 2012, Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA, Bmc Bioinformatics, Vol: 13, ISSN: 1471-2105
Kitney R, Freemont P, 2012, Synthetic biology - the state of play, FEBS LETTERS, Vol: 586, Pages: 2029-2036, ISSN: 0014-5793
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- Citations: 51
Wang B, Kitney RI, Joly N, et al., 2011, Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology, Nature Communications, Vol: 2:508
Modular and orthogonal genetic logic gates are essential for building robust biologically based digital devices to customize cell signalling in synthetic biology. Here we constructed an orthogonal AND gate in Escherichia coli using a novel hetero-regulation module from Pseudomonas syringae. The device comprises two co-activating genes hrpR and hrpS controlled by separate promoter inputs, and a σ54-dependent hrpL promoter driving the output. The hrpL promoter is activated only when both genes are expressed, generating digital-like AND integration behaviour. The AND gate is demonstrated to be modular by applying new regulated promoters to the inputs, and connecting the output to a NOT gate module to produce a combinatorial NAND gate. The circuits were assembled using a parts-based engineering approach of quantitative characterization, modelling, followed by construction and testing. The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts.
MacDonald JT, Barnes C, Kitney RI, et al., 2011, Computational design approaches and tools for synthetic biology, INTEGRATIVE BIOLOGY, Vol: 3, Pages: 97-108, ISSN: 1757-9694
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- Citations: 58
Poh CL, Cui LC, Kitney RI, 2010, Modeling biological systems in Laplace Domain for Synthetic Biology Design, WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING, Pages: 1377-1380, ISSN: 1680-0737
Gulati S, Rouilly V, Niu X, et al., 2009, Opportunities for microfluidic technologies in synthetic biology, JOURNAL OF THE ROYAL SOCIETY INTERFACE, Vol: 6, ISSN: 1742-5689
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- Citations: 54
Heimann T, van Ginneken B, Styner MA, et al., 2009, Comparison and Evaluation of Methods for Liver Segmentation From CT Datasets, IEEE TRANSACTIONS ON MEDICAL IMAGING, Vol: 28, Pages: 1251-1265, ISSN: 0278-0062
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- Citations: 716
Poh C-L, Kitney RI, Akhtar S, 2009, Web-Based Multilayer Viewing Interface for Knee Cartilage, IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, Vol: 13, Pages: 546-553, ISSN: 1089-7771
Poh C-L, Kitney RI, Akhtar S, 2009, Web-based multilayer viewing interface for knee cartilage., IEEE Trans Inf Technol Biomed, Vol: 13, Pages: 546-553
Many adults suffer from osteoarthritis (OA) with the majority of people over 65 showing radiographic evidence of the disease. To carry out effective diagnosis and treatment, it is necessary to understand the progression of cartilage loss and study the effectiveness of therapeutic interventions. Hence, it is important to have accurate, fast diagnosis of the disease. In this paper, we describe a Web-based user interface that enables the direct viewing of 2-D and 3-D image data from the visceral and tissue levels of the biological continuum (i.e., the continuum comprising systems, viscera, tissue, cells, proteins, and genes)--while preserving geometric integrity. This is achieved despite the fact that the data are from different modalities (i.e., magnetic resonance (MR) and light microscopy). The user interface was tested using image data acquired from a study of articular cartilage thickness in the porcine knee. The interface allows the clinician to view both MR and light microscopy images in an integrated manner-with the information linked geometrically.
Kitney RI, 2009, Synthetic Biology: scope, applications and implications, Synthetic biology: scope, applications and implications, Publisher: The Royal Academy of Engineering
Delakis I, Xanthis C, Kitney RI, 2009, Assessment of the limiting spatial resolution of an MRI scanner by direct analysis of the edge spread function, MEDICAL PHYSICS, Vol: 36, Pages: 1637-1642, ISSN: 0094-2405
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- Citations: 4
Wang B, Kitney R, Buck M, et al., 2009, The Design and Construction of a Set of Modular Synthetic BioLogic Devices for Programming Cells, World Congress on Medical Physics and Biomedical Engineering, Publisher: Springer Berlin Heidelberg, Pages: 289-292
Modularity is an essential property for rationally engineered standard parts and devices. This principle is now being extended to biological based parts and devices for programming cells. However, the design principles and building blocks which are currently in Synthetic Biology are somewhat limited. In addition, it is important to explore the underlying mechanisms of existing, natural biological systems in order to utilise them in designing novel genetic circuit modules. In this paper, we will describe a set of modular synthetic biological parts and devices that are based in rational design. Particularly, a modular tight-controlled and hypersensitive genetic circuit with digital logic AND function is rationally designed and engineered. They use a sigma factor 54( σ 54 ) dependent hetero-regulation module in the hrp (hypersensitive response and pathogenicity) gene regulatory system for Type III secretion in Pseudomonas syringae . Their inputs and outputs are both promoters and thus do not rely on specific inducible promoters and could drive various cellular responses. It shows that the hrp system has significant potential for building a range of biological parts and devices with good performance and flexibility.
Noirhomme Q, Kitney RI, Macq B, 2008, Single-trial EEG source reconstruction for brain-computer interface, IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, Vol: 55, Pages: 1592-1601, ISSN: 0018-9294
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- Citations: 43
Kitney RI, Freemont PS, Rouilly V, 2007, Engineering a molecular predation oscillator, IET Synthetic Biology, Vol: 1, Pages: 68-70, ISSN: 1752-1394
The paper addresses the problem of designing and building a stable molecular based oscillator which can be controlled in terms of both amplitude and frequency. A study of previous oscillators of this type showed that they are inherently unstable. To overcome this problem a design was chosen which is based on Lotka-Voltera dynamics. An important aspect of the work was the use of what we term the Engineering Cycle; that is, the cycle of system specification, design, modelling, implementation, and testing and validation. The Lotka-Voltera dynamic, in the context of a predation oscillator, amounts to a predator-prey approach. This is the basis of the oscillator design. The oscillator was designed and detailed modelling undertaken to establish the modes of the dynamic; how it could be tuned for stability; and how to control its amplitude and frequency. The biological implementation of the design was undertaken using a number of BioBricks from the MIT registry (http://parts.mit.edu/registry/ index.php/Main_Page), together with a number of parts which we designed and built. © 2007 The Institution of Engineering and Technology.
Delakis I, Hammad O, Kitney RI, 2007, Wavelet-based de-noising algorithm for images acquired with parallel magnetic resonance imaging (MRI), PHYSICS IN MEDICINE AND BIOLOGY, Vol: 52, Pages: 3741-3751, ISSN: 0031-9155
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- Citations: 37
Poh C-L, Kitney RI, Shrestha RBK, 2007, Addressing the future of clinical information systems - Web-based multilayer visualization, IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, Vol: 11, Pages: 127-140, ISSN: 1089-7771
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- Citations: 14
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