Publications

Publications

You can also access our individual websites (via the Members page) for further information about our research and lists of our publications.

Search or filter publications

Filter by type:

Filter by publication type

Filter by year:

to

Results

  • Showing results for:
  • Reset all filters

Search results

  • Conference paper
    Branch T, Barahona M, Ying L, 2014,

    Kinetics of the Interconversion Between Two Physiologically Important Copper-Bound Amyloid-Beta Species

    , 58th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 682A-682A, ISSN: 0006-3495
  • Conference paper
    Branch T, Evans M, Barahona M, Ying Let al., 2014,

    Kinetics of Metal Amyloid-Beta Binding and Efficacy of Ligands Targeting Metal Amyloid-Beta Interactions

    , 58th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 39A-39A, ISSN: 0006-3495
  • Journal article
    Amor B, Yaliraki SN, Woscholski R, Barahona Met al., 2014,

    Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection

    , MOLECULAR BIOSYSTEMS, Vol: 10, Pages: 2247-2258, ISSN: 1742-206X
  • Journal article
    Schumacher J, Behrends V, Pan Z, Brown DR, Heydenreich F, Lewis MR, Bennett MH, Razzaghi B, Komorowski M, Barahona M, Stumpf MPH, Wigneshweraraj S, Bundy JG, Buck Met al., 2013,

    Nitrogen and Carbon Status Are Integrated at the Transcriptional Level by the Nitrogen Regulator NtrC In Vivo

    , MBIO, Vol: 4, ISSN: 2150-7511
  • Journal article
    Thomas P, Straube AV, Timmer J, Fleck C, Grima Ret al., 2013,

    Signatures of nonlinearity in single cell noise-induced oscillations

    , JOURNAL OF THEORETICAL BIOLOGY, Vol: 335, Pages: 222-234, ISSN: 0022-5193
  • 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
  • Journal article
    Wang B, Barahona M, Buck M, Schumacher Jet al., 2013,

    Rewiring cell signalling through chimaeric regulatory protein engineering

    , BIOCHEMICAL SOCIETY TRANSACTIONS, Vol: 41, Pages: 1195-1200, ISSN: 0300-5127
  • Journal article
    Thomas P, Matuschek H, Grima R, 2013,

    How reliable is the linear noise approximation of gene regulatory networks?

    , BMC Genomics, Vol: 14, ISSN: 1471-2164

    BackgroundThe linear noise approximation (LNA) is commonly used to predict how noise is regulated and exploited at the cellular level. These predictions are exact for reaction networks composed exclusively of first order reactions or for networks involving bimolecular reactions and large numbers of molecules. It is however well known that gene regulation involves bimolecular interactions with molecule numbers as small as a single copy of a particular gene. It is therefore questionable how reliable are the LNA predictions for these systems.ResultsWe implement in the software package intrinsic Noise Analyzer (iNA), a system size expansion based method which calculates the mean concentrations and the variances of the fluctuations to an order of accuracy higher than the LNA. We then use iNA to explore the parametric dependence of the Fano factors and of the coefficients of variation of the mRNA and protein fluctuations in models of genetic networks involving nonlinear protein degradation, post-transcriptional, post-translational and negative feedback regulation. We find that the LNA can significantly underestimate the amplitude and period of noise-induced oscillations in genetic oscillators. We also identify cases where the LNA predicts that noise levels can be optimized by tuning a bimolecular rate constant whereas our method shows that no such regulation is possible. All our results are confirmed by stochastic simulations.ConclusionThe software iNA allows the investigation of parameter regimes where the LNA fares well and where it does not. We have shown that the parametric dependence of the coefficients of variation and Fano factors for common gene regulatory networks is better described by including terms of higher order than LNA in the system size expansion. This analysis is considerably faster than stochastic simulations due to the extensive ensemble averaging needed to obtain statistically meaningful results. Hence iNA is well suited for performing computationall
  • Book chapter
    Delvenne J-C, Schaub MT, Yaliraki S, Barahona Met al., 2013,

    The stability of a graph partition: A dynamics-based framework for community detection

    , Dynamics On and Of Complex Networks, Volume 2, Editors: Mukherjee, Choudhury, Peruani, Ganguly, Mitra, Publisher: Springer, Pages: 221-242, ISBN: 978-1-4614-6728-1

    Recent years have seen a surge of interest in the analysis of complexnetworks, facilitated by the availability of relational data and theincreasingly powerful computational resources that can be employed for theiranalysis. Naturally, the study of real-world systems leads to highly complexnetworks and a current challenge is to extract intelligible, simplifieddescriptions from the network in terms of relevant subgraphs, which can provideinsight into the structure and function of the overall system. Sparked by seminal work by Newman and Girvan, an interesting line of researchhas been devoted to investigating modular community structure in networks,revitalising the classic problem of graph partitioning. However, modular or community structure in networks has notoriously evadedrigorous definition. The most accepted notion of community is perhaps that of agroup of elements which exhibit a stronger level of interaction withinthemselves than with the elements outside the community. This concept hasresulted in a plethora of computational methods and heuristics for communitydetection. Nevertheless a firm theoretical understanding of most of thesemethods, in terms of how they operate and what they are supposed to detect, isstill lacking to date. Here, we will develop a dynamical perspective towards community detectionenabling us to define a measure named the stability of a graph partition. Itwill be shown that a number of previously ad-hoc defined heuristics forcommunity detection can be seen as particular cases of our method providing uswith a dynamic reinterpretation of those measures. Our dynamics-based approachthus serves as a unifying framework to gain a deeper understanding of differentaspects and problems associated with community detection and allows us topropose new dynamically-inspired criteria for community structure.
  • 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

This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.

Request URL: http://wwwtest.imperial.ac.uk:80/respub/WEB-INF/jsp/search-t4-html.jsp Request URI: /respub/WEB-INF/jsp/search-t4-html.jsp Query String: id=219&limit=10&page=14&respub-action=search.html Current Millis: 1759570333624 Current Time: Sat Oct 04 10:32:13 BST 2025