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• Journal article
  Yeung HO, Foerster A, Bebeacua C, Niwa H, Ewens C, McKeown C, Zhang X, Freemont PSet al., 2014,

  Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy

  , Open Biology, Vol: 4, ISSN: 2046-2441

  The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes.

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• Journal article
  Luboz V, Kyaw-Tun J, Sen S, Kneebone R, Dickinson R, Kitney R, Bello Fet 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
• Journal article
  Cai Y, Ellis T, 2014,

  The Sixth International Meeting on synthetic Biology (SB6.0) Special Issue Editorial

  , ACS SYNTHETIC BIOLOGY, Vol: 3, Pages: 107-107, ISSN: 2161-5063
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• Journal article
  Tay D, Poh CL, Goh C, Kitney RIet 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
• Journal article
  Reeve B, Hargest T, Gilbert C, Ellis Tet al., 2014,

  Predicting translation initiation rates for designing synthetic biology.

  , Frontiers in Bioengineering and Biotechnology, Vol: 2, Pages: 1-1, ISSN: 2296-4185

  In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5'-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

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• Journal article
  Pan W, Sootla A, Stan G-B, 2014,

  Distributed Reconstruction of Nonlinear Networks: An ADMM Approach

  , IFAC PAPERSONLINE, Vol: 47, Pages: 3208-3213, ISSN: 2405-8963
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  • Citations: 1
• Journal article
  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.

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• Conference paper
  Algar RJR, Ellis T, Stan G-B, 2014,

  Modelling essential interactions between synthetic genes and their chassis cell

  , 53rd IEEE Annual Conference on Decision and Control (CDC), Publisher: IEEE, Pages: 5437-5444, ISSN: 0743-1546
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  • Citations: 12
• Journal article
  Reeve B, Sanderson T, Ellis T, Freemont Pet al., 2014,

  How Synthetic Biology Will Reconsider Natural Bioluminescence and Its Applications

  , BIOLUMINESCENCE: FUNDAMENTALS AND APPLICATIONS IN BIOTECHNOLOGY, VOL 2, Vol: 145, Pages: 3-30, ISSN: 0724-6145
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  • Citations: 10
• Journal article
  Casini A, MacDonald JT, De Jonghe J, Christodoulou G, Freemont PS, Baldwin GS, Ellis Tet al., 2013,

  One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

  , Nucleic Acids Research, Vol: 42, ISSN: 1362-4962

  Overlap-directed DNA assembly methods allowmultiple DNA parts to be assembled together inone reaction. These methods, which rely onsequence homology between the ends of DNAparts, have become widely adopted in syntheticbiology, despite being incompatible with a key principleof engineering: modularity. To answer this, wepresent MODAL: a Modular Overlap-DirectedAssembly with Linkers strategy that brings modularityto overlap-directed methods, allowing assemblyof an initial set of DNA parts into a variety ofarrangements in one-pot reactions. MODAL isaccompanied by a custom software tool thatdesigns overlap linkers to guide assembly,allowing parts to be assembled in any specifiedorder and orientation. The in silico design of syntheticorthogonal overlapping junctions allows formuch greater efficiency in DNA assembly for avariety of different methods compared with usingnon-designed sequence. In tests with three differentassembly technologies, the MODAL strategy givesassembly of both yeast and bacterial plasmids,composed of up to five DNA parts in the kilobaserange with efficiencies of between 75 and 100%.It also seamlessly allows mutagenesis to beperformed on any specified DNA parts duringthe process, allowing the one-step creation of constructlibraries valuable for synthetic biologyapplications.

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• Journal article
  O'Clery N, Yuan Y, Stan G-B, Barahona Met al., 2013,

  Observability and coarse graining of consensus dynamics through the external equitable partition

  , PHYSICAL REVIEW E, Vol: 88, ISSN: 1539-3755
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  • Citations: 48
• Journal article
  Brucoli F, Hawkins RM, James CH, Jackson PJM, Wells G, Jenkins TC, Ellis T, Kotecha M, Hochhauser D, Hartley JA, Howard PW, Thurston DEet al., 2013,

  An Extended Pyrrolobenzodiazepine-Polyamide Conjugate with Selectivity for a DNA Sequence Containing the ICB2 Transcription Factor Binding Site

  , JOURNAL OF MEDICINAL CHEMISTRY, Vol: 56, Pages: 6339-6351, ISSN: 0022-2623
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  • Citations: 25
• Journal article
  Arpino JAJ, Hancock EJ, Anderson J, Barahona M, Stan G-BV, Papachristodoulou A, Polizzi Ket al., 2013,

  Tuning the dials of Synthetic Biology

  , Microbiology-Sgm, Vol: 159, Pages: 1236-1253, ISSN: 1465-2080
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• Journal article
  Wright O, Stan G-B, Ellis T, 2013,

  Building-in biosafety for synthetic biology

  , MICROBIOLOGY-SGM, Vol: 159, Pages: 1221-1235, ISSN: 1350-0872
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  • Citations: 82
• Journal article
  Wu M, Su R-Q, Li X, Ellis T, Lai Y-C, Wang Xet al., 2013,

  Engineering of regulated stochastic cell fate determination

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 10610-10615, ISSN: 0027-8424
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  • Citations: 69
• Journal article
  MacDonald JT, Kelley LA, Freemont PS, 2013,

  Validating a Coarse-Grained Potential Energy Function through Protein Loop Modelling

  , PLOS One, Vol: 8, ISSN: 1932-6203

  Coarse-grained (CG) methods for sampling protein conformational space have the potential to increase computational efficiency by reducing the degrees of freedom. The gain in computational efficiency of CG methods often comes at the expense of non-protein like local conformational features. This could cause problems when transitioning to full atom models in a hierarchical framework. Here, a CG potential energy function was validated by applying it to the problem of loop prediction. A novel method to sample the conformational space of backbone atoms was benchmarked using a standard test set consisting of 351 distinct loops. This method used a sequence-independent CG potential energy function representing the protein using -carbon positions only and sampling conformations with a Monte Carlo simulated annealing based protocol. Backbone atoms were added using a method previously described and then gradient minimised in the Rosetta force field. Despite the CG potential energy function being sequence-independent, the method performed similarly to methods that explicitly use either fragments of known protein backbones with similar sequences or residue-specific /-maps to restrict the search space. The method was also able to predict with sub-Angstrom accuracy two out of seven loops from recently solved crystal structures of proteins with low sequence and structure similarity to previously deposited structures in the PDB. The ability to sample realistic loop conformations directly from a potential energy function enables the incorporation of additional geometric restraints and the use of more advanced sampling methods in a way that is not possible to do easily with fragment replacement methods and also enable multi-scale simulations for protein design and protein structure prediction. These restraints could be derived from experimental data or could be design restraints in the case of computational protein design. C++ source code is available for download from http://www.sbg.

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• Journal article
  Yuan Y, Stan G-B, Shi L, Barahona M, Goncalves Jet al., 2013,

  Decentralised minimum-time consensus

  , AUTOMATICA, Vol: 49, Pages: 1227-1235, ISSN: 0005-1098
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  • Citations: 88
• Journal article
  Chappell J, Jensen K, Freemont PS, 2013,

  Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology

  , Nucleic Acids Research, Vol: 41, Pages: 3471-3481, ISSN: 0305-1048

  A bottleneck in our capacity to rationally and predictably engineer biological systems is the limited number of well-characterized genetic elements from which to build. Current characterization methods are tied to measurements in living systems, the transformation and culturing of which are inherently time-consuming. To address this, we have validated a completely in vitro approach for the characterization of DNA regulatory elements using Escherichia coli extract cell-free systems. Importantly, we demonstrate that characterization in cell-free systems correlates and is reflective of performance in vivo for the most frequently used DNA regulatory elements. Moreover, we devise a rapid and completely in vitro method to generate DNA templates for cell-free systems, bypassing the need for DNA template generation and amplification from living cells. This in vitro approach is significantly quicker than current characterization methods and is amenable to high-throughput techniques, providing a valuable tool for rapidly prototyping libraries of DNA regulatory elements for synthetic biology.

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• Journal article
  Cehovin A, Simpson PJ, McDowell MA, Brown DR, Noschese R, Pallett M, Brady J, Baldwin GS, Lea SM, Matthews SJ, Pelicic Vet al., 2013,

  Specific DNA recognition mediated by a type IV pilin

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 3065-3070, ISSN: 0027-8424
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  • Citations: 112
• Journal article
  Papadimitriou KI, Stan G-B, Drakakis EM, 2013,

  Systematic computation of non-linear cellular and molecular dynamics with low-power cytomimetic circuits: A simulation study

  , PLoS ONE, Vol: 8, ISSN: 1932-6203

  This paper presents a novel method for the systematic implementation of low-power microelectronic circuits aimed at computing nonlinear cellular and molecular dynamics. The method proposed is based on the Nonlinear Bernoulli Cell Formalism (NBCF), an advanced mathematical framework stemming from the Bernoulli Cell Formalism (BCF) originally exploited for the modular synthesis and analysis of linear, time-invariant, high dynamic range, logarithmic filters. Our approach identifies and exploits the striking similarities existing between the NBCF and coupled nonlinear ordinary differential equations (ODEs) typically appearing in models of naturally encountered biochemical systems. The resulting continuous-time, continuous-value, low-power CytoMimetic electronic circuits succeed in simulating fast and with good accuracy cellular and molecular dynamics. The application of the method is illustrated by synthesising for the first time microelectronic CytoMimetic topologies which simulate successfully: 1) a nonlinear intracellular calcium oscillations model for several Hill coefficient values and 2) a gene-protein regulatory system model. The dynamic behaviours generated by the proposed CytoMimetic circuits are compared and found to be in very good agreement with their biological counterparts. The circuits exploit the exponential law codifying the low-power subthreshold operation regime and have been simulated with realistic parameters from a commercially available CMOS process. They occupy an area of a fraction of a square-millimetre, while consuming between 1 and 12 microwatts of power. Simulations of fabrication-related variability results are also presented.

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