381 results found
Coghlan A, Kitney R, 2016, Tiny but mighty, NEW SCIENTIST, Vol: 230, Pages: 7-7, ISSN: 0262-4079
Sainz de Murieta I, Bultelle M, Kitney RI, 2016, Toward the First Data Acquisition Standard in Synthetic Biology., ACS Synth Biol
This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.
Bultelle MA, Sainz De Murieta I, Kitney RI, 2015, Introducing synbis - The synthetic biology information system, Pages: 838-842
Kelwick R, Kopniczky M, Bower I, et al., 2015, A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli, PLOS ONE, Vol: 10, ISSN: 1932-6203
Sainz De Murieta I, Bultelle MA, Kitney RI, 2015, A dicom extension supporting data acquisition in synthetic biology, Pages: 948-951
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
Tay D, Poh CL, Van Reeth E, et al., 2015, The Effect of Sample Age and Prediction Resolution on Myocardial Infarction Risk Prediction, IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS, Vol: 19, Pages: 1178-1185, ISSN: 2168-2194
Wong A, Wang H, Poh CL, et al., 2015, Layering genetic circuits to build a single cell, bacterial half adder, BMC Biology, Vol: 13, ISSN: 1741-7007
Background: Gene regulation in biological systems is impacted by the cellular and genetic context-dependenteffects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations ofengineering biology from an architectural point of view, with the aim of compiling a set of engineering solutionsfor overcoming failure modes during the development of complex, synthetic genetic circuits.Results: Using a synthetic biology approach that is supported by computational modelling and rigorouscharacterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements togenerate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in asingle cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls thattriggered genetic context-dependent effects, including 5′ UTR interferences and uncontrolled switch-on behaviourof the supercoiled σ54 promoter. In particular, the presence of seven consecutive hairpins immediately downstreamof the promoter transcription start site severely impeded gene expression.Conclusions: As synthetic biology moves forward with greater focus on scaling the complexity of engineeredgenetic circuits, studies which thoroughly evaluate failure modes and engineering solutions will serve as importantreferences for future design and development of synthetic biological systems. This work describes a representativecase study for the debugging of genetic context-dependent effects through principles elucidated herein, therebyproviding a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.
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.
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
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
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
Tay D, Poh CL, Kitney RI, 2013, An Evolutionary Data-Conscious Artificial Immune Recognition System, 15th Genetic and Evolutionary Computation Conference (GECCO), Publisher: ASSOC COMPUTING MACHINERY, Pages: 1101-1108
© 2012 by Imperial College Press. All rights reserved. Synthetic Biology — A Primer gives a broad overview of the emerging field of synthetic biology and the foundational concepts on which it is built. It will be of interest to final year undergraduates, postgraduates and established researchers who are interested in learning about this exciting new field. 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 utilises a conceptual framework of engineering and systematic design to build new biological systems by integrating robustly characterised biological parts into an existing system through the use of extensive mathematical modelling. The ‘bottom-up’ approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch. Exemplars of cutting-edge applications designed using synthetic biology principles are presented, including the production of novel biofuels from renewable feedstocks, microbial synthesis of pharmaceuticals and fine chemicals, and the design and implementation of biosensors to detect infections and environmental waste. The book also uses the Internationally Genetically Engineered Machine (iGEM) competition to illustrate the power of synthetic biology as an innovative research and training science. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences in synthetic biology research.
Kitney R, Freemont P, 2012, Synthetic biology - the state of play, FEBS LETTERS, Vol: 586, Pages: 2029-2036, ISSN: 0014-5793
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
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
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, ISSN: 2041-1723
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, Publisher: SPRINGER, Pages: 1377-1380, ISSN: 1680-0737
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
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
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
Kitney RI, 2009, Synthetic Biology, ISBN: 9781903496442
Kitney RI, 2009, Synthetic Biology: scope, applications and implications, Synthetic biology: scope, applications and implications, Publisher: The Royal Academy of Engineering
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 CL, 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.
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, Pages: 289-292, ISSN: 1680-0737
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
Akhtar S, Poh CL, Kitney RI, 2007, An MRI derived articular cartilage visualization framework, OSTEOARTHRITIS AND CARTILAGE, Vol: 15, Pages: 1070-1085, ISSN: 1063-4584
Chi Y, Kitney R, Cashman P, 2007, Automatic Cartilage Detection in MR Image sets using CDSG Snake, World Congress on Medical Physics and Biomedical Engineering, Publisher: SPRINGER-VERLAG BERLIN, Pages: 2398-2402, ISSN: 1680-0737
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