Publications, conference contributions and awards

Search for publications, conference contributions and awards by year (BCCS PhD researcher shown in bold):

2015

Journal articles
Dunleavy, A. J., Wiesner, K., Yamamoto, R., & Royall, C. P. (2015). Mutual information reveals multiple structural relaxation mechanisms in a model glass former. Nature Communications6.
Cowley, D. J., Johnson, O. T. & Pocock, M. J. O. (2015). Using electric network theory to model the spread of oak processionary moth, Thaumetopoea processionea, in urban woodland patches. Landscape Ecology.
Giuggioli, L., McKetterick, T. J., Holderied, M. (2015) Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats. PLoS Computational Biology 11(3): e1004089
Conference contributions
Venturi, E., Matyjaszkiewicz, A., O'Brien, F., Nishi, M., Takeshima, H., & Sitsapesan, R. (2014) Critical role of TRIC-channels: What can be revealed by single-channel studies? in: Proceedings of The Physiological Society, Proc Physiol Soc 31, SA064. 

 

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2014

Journal articles

Aldersley, A., Champneys, A., Homer, M. and Robert, D. (2014) 'Time-frequency composition of mosquito flight tones obtained using Hilbert spectral analysis', The Journal of the Acoustical Society of America, 136(4), 1982-1989.

Hunt, E. R., O'Shea-Wheller, T., Albery, G. F., Bridger, T. H., Gumn, M., & Franks, N. R. (2014). Ants show a leftward turning bias when exploring unknown nest sites. Biology letters10(12), 20140945.

Jordan, T., Partridge, J. and Roberts, N. (2014) 'Disordered animal multilayer reflectors and the localization of light', Journal of The Royal Society Interface, 11(101), 20140948.

Lawson, D. J. and Oak, N. (2014) 'Apparent strength conceals instability in a model for the collapse of historical states', PloS one, 9(5), e96523.

McKetterick, T. J. and Giuggioli, L. (2014) 'Exact dynamics of stochastic linear delayed systems: Application to spatiotemporal coordination of comoving agents', Physical Review E, 90(4), 042135.

Oates, M. E., Stahlhacke, J., Vavoulis, D. V., Smithers, B., Rackham, O. J., Sardar, A. J., Zaucha, J., Thurlby, N., Fang, H. and Gough, J. (2014) 'The SUPERFAMILY 1.75 database in 2014: a doubling of data', Nucleic acids research, gku1041.

O'Brien, F., Venturi, E., Galfrè, E., Matyjaszkiewicz, A., Yamazaki, D., Nishi, M., Takeshima, H. and Sitsapesan, R. (2014) 'H+ Inhibits TRIC-B Channels Derived from Mouse TRIC-A Knockout Tissue', Biophysical Journal, 106(2), 763a.

Onslow, A. C., Jones, M. W. and Bogacz, R. (2014) 'A Canonical Circuit for Generating Phase-Amplitude Coupling', PloS one, 9(8), e102591.

Sardar, A. J., Oates, M. E., Fang, H., Forrest, A. R., Kawaji, H., Gough, J. and Rackham, O. J. (2014) 'The Evolution of Human Cells in Terms of Protein Innovation', Molecular biology and evolution, 31(6), mst139.

Silk, H., Demirel, G., Homer, M. and Gross, T. (2014) 'Exploring the adaptive voter model dynamics with a mathematical triple jump', New Journal of Physics, 16(9), 093051.

Slowinski, P., Rooke, M. D. B. and Tanaseva-Atanasova, K. (2014) 'Kinematic Characteristics of Motion in the Mirror Game'.

Zaucha, J., Stahlhacke, J., Oates, M. E., Thurlby, N., Rackham, O. J., Fang, H., Smithers, B. and Gough, J. (2014) 'A Proteome Quality Index', Environmental microbiology.

Zienkiewicz, A., Barton, D. W., Porfiri, M. and di Bernardo, M. (2014) 'Data-driven stochastic modelling of zebrafish locomotion', Journal of Mathematical Biology, 1-25.

Conference contributions

McGovern, P., Lawry, J., Rossiter, J. and Leonards, U. (2014) Conceptual spaces and language games for an artificial fingertip, Sensors, 2014 IEEE,  332-335.

Kempton, L., Herrmann, G. and di Bernardo, M. (2014) Adaptive Weight Selection for Optimal Consensus Performance. in: Proceedings of the 53rd IEEE Conference on Decision and Control, Los Angeles, USA.

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2013

Journal articles

Fang, H., Oates, M. E., Pethica, R. B., Greenwood, J. M., Sardar, A. J., Rackham, O. J. L., Donoghue, P. C. J., Stamatakis, A., de Lima Morais, D. A. and Gough, J. (2013) 'A daily-updated tree of (sequenced) life as a reference for genome research', Sci. Rep., 3.

Giuggioli, L., Potts, J. R., Rubenstein, D. I. and Levin, S. A. (2013) 'Stigmergy, collective actions, and animal social spacing', Proceedings of the National Academy of Sciences, 110(42), 16904-16909.

Jordan, T., Partridge, J. and Roberts, N. (2013) 'Suppression of Brewster delocalization anomalies in an alternating isotropic-birefringent random layered medium', Physical Review B, 88(4), 041105.

Klix, C. L., Murata, K.-i., Tanaka, H., Williams, S. R., Malins, A. and Royall, C. P. (2013) 'Novel kinetic trapping in charged colloidal clusters due to self-induced surface charge organization', Scientific reports, 3.

Malins, A., Eggers, J. and Royall, C. P. (2013) 'Investigating isomorphs with the topological cluster classification', The Journal of chemical physics, 139(23), 234505.

Malins, A., Eggers, J., Royall, C. P., Williams, S. R. and Tanaka, H. (2013) 'Identification of long-lived clusters and their link to slow dynamics in a model glass former', The Journal of chemical physics, 138(12), 12A535.

Malins, A., Williams, S. R., Eggers, J. and Royall, C. P. (2013) 'Identification of structure in condensed matter with the topological cluster classification', The Journal of chemical physics, 139(23), 234506.

Mills, H., Ganesh, A. and Colijn, C. (2013) 'Pathogen spread on coupled networks: effect of host and network properties on transmission thresholds', Journal of theoretical biology, 320, 47-57.

Mills, H. L., Cohen, T. and Colijn, C. (2013) 'Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: A model-based analysis', Science translational medicine, 5(180), 180ra49-180ra49.

Mills, H. L., White, E., Colijn, C., Vickerman, P. and Heimer, R. (2013) 'HIV transmission from drug injectors to partners who do not inject, and beyond: modelling the potential for a generalized heterosexual epidemic in St. Petersburg, Russia', Drug and alcohol dependence, 133(1), 242-247.

Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., Dunker, A. K. and Gough, J. (2013) 'D2P2: database of disordered protein predictions', Nucleic acids research, 41(D1), D508-D516.

Potts, J. R., Harris, S. and Giuggioli, L. (2013) 'Quantifying behavioral changes in territorial animals caused by sudden population declines', The American Naturalist, 182(3), E73-E82.

Robinson, K., Fyson, N., Cohen, T., Fraser, C. and Colijn, C. (2013) 'How the dynamics and structure of sexual contact networks shape pathogen phylogenies', PLoS computational biology, 9(6), e1003105.

Silk, H., Demirel, G., Homer, M. and Gross, T. (2013) 'Exploring network dynamics with a mathematical triple jump', arXiv preprint arXiv:1302.2743.

Venturi, E., Matyjaszkiewicz, A., Pitt, S. J., Tsaneva-Atanasova, K., Nishi, M., Yamazaki, D., Takeshima, H. and Sitsapesan, R. (2013) 'TRIC-B channels display labile gating: evidence from the TRIC-A knockout mouse model', Pflugers Arch, 465(8), 1135-48.

Vincent, T. L., Green, P. J. and Woolfson, D. N. (2013) 'LOGICOIL—Multi-state prediction of coiled-coil oligomeric state', Bioinformatics, 29(1), 69-76.

Vincent, T. L., Woolfson, D. N. and Adams, J. C. (2013) 'Prediction and analysis of higher-order coiled-coils: Insights from proteins of the extracellular matrix, tenascins and thrombospondins', The international journal of biochemistry & cell biology, 45(11), 2392-2401.

Awards
McKetterick, Thomas Awarded a grant by the Institute of Mathematics and its Applications (IMA) for an extended research trip to work with Professor Nitant Kenkre at the University of New Mexico on the project "The statistical mechanics of epidemics in territorial animals" - see BCCS student awarded IMA grant for more details.
Taylor, Richard Awarded second place for his talk entitled "The evolutionary history of plant microRNAs" at the South West RNA Club seminar in Cardiff - see BCCS student awarded second place for more details.

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2012

Journal articles

Fletcher, J. M., Boyle, A. L., Bruning, M., Bartlett, G. J., Vincent, T. L., Zaccai, N. R., Armstrong, C. T., Bromley, E. H. C., Booth, P. J., Brady, R. L., Thomson, A. R. and Woolfson, D. N. (2012) 'A Basis Set of de Novo Coiled-Coil Peptide Oligomers for Rational Protein Design and Synthetic Biology', ACS Synthetic Biology, 1(6), 240-250.

Fyson, N., De Bie, T. and Cristianini, N. (2012) 'The NetCover algorithm for the reconstruction of causal networks', Neurocomputing, 96, 19-28.

Giuggioli, L., Potts, J. R. and Harris, S. (2012) 'Predicting oscillatory dynamics in the movement of territorial animals', Journal of The Royal Society Interface, 9(72), 1529-1543.

Gorochowski, T. E., di Bernardo, M. and Grierson, C. S. (2012) 'Using Aging to Visually Uncover Evolutionary Processes on Networks', Visualization and Computer Graphics, IEEE Transactions on, 18(8), 1343-1352.

Gorochowski, T. E., Matyjaszkiewicz, A., Todd, T., Oak, N., Kowalska, K., Reid, S., Tsaneva-Atanasova, K. T., Savery, N. J., Grierson, C. S. and di Bernardo, M. (2012) 'BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology', PloS one, 7(8), e42790.

Irving, T., Blyuss, K., Colijn, C. and Trotter, C. (2012) 'Modelling meningococcal meningitis in the African meningitis belt', Epidemiology and infection, 140(05), 897-905.

Jordan, T. M., Partridge, J. C. and Roberts, N. W. (2012) 'Non-polarizing broadband multilayer reflectors in fish', Nat Photon, 6(11), 759-763.

Mills, H., Colijn, C., Vickerman, P., Leslie, D., Hope, V. and Hickman, M. (2012) 'Respondent driven sampling and community structure in a population of injecting drug users, Bristol, UK', Drug and alcohol dependence, 126(3), 324-332.

Pavlides, A., John Hogan, S. and Bogacz, R. (2012) 'Improved conditions for the generation of beta oscillations in the subthalamic nucleus–globus pallidus network', European Journal of Neuroscience, 36(2), 2229-2239.

Potts, J. R., Harris, S. and Giuggioli, L. (2012) 'Territorial Dynamics and Stable Home Range Formation for Central Place Foragers', PloS one, 7(3), e34033.

Purcell, O., Grierson, C. S., Bernardo, M. and Savery, N. J. (2012) 'Temperature dependence of ssrA-tag mediated protein degradation', J. Biol. Eng, 6(10), 10.

Robinson, K., Cohen, T. and Colijn, C. (2012) 'The dynamics of sexual contact networks: Effects on disease spread and control', Theoretical population biology, 81(2), 89-96.

Speck, T., Malins, A. and Royall, C. P. (2012) 'First-Order Phase Transition in a Model Glass Former: Coupling of Local Structure and Dynamics', Physical Review Letters, 109(19), 195703.

Talbot, C., Jordan, T. M., Roberts, N. W., Collin, S. P., Marshall, N. J. and Temple, S. E. (2012) 'Corneal microprojections in coleoid cephalopods', Journal of Comparative Physiology A, 198(12), 849-856.

Conference contributions

Cartlidge, J., Szostek, C., De Luca, M. and Cliff, D. (2012) Too Fast Too Furious-Faster Financial-market Trading Agents Can Give Less Efficient Markets, 4th International Conference on Agents and Artificial Intelligence (ICAART),  126-135.

Jordan, T. M., Roberts, N. W. and Partridge, J. C. (2012) An omnidirectional broadband mirror design inspired by biological multilayer reflectors, Proc. SPIE 8339, Bioinspiration, Biomimetics, and Bioreplication 2012,  83390G-83390G-7.

McVicar, M. and De Bie, T. (2012) CCA and a multi-way extension for investigating common components between audio, lyrics and tags, Proceedings of the 9th international symposium on computational music modeling and retrieval (CMMR),  53-68.

Awards
Rackham, Owen and Sardar, Adam Both researchers were awarded the "Science, Technology, Engineering and Mathematics (STEM) University Department of the Year" title for their outreach work in the Bristol, Bath and Somerset region - see STEM award for University researchers for more details.
Potts, Jonathan Awarded a Worldwide Universities Network (WUN) Research Mobility Programme fund of £1,900 to work with Professor Mark Lewis at the University of Alberta on models of territory formation in Amazonian bird flocks to understand the impact of resources and memory on movement - see WUN award for complexity sciences student for more details.
Aldersley, Andrew Won best poster at Student Conference for Complexity Sciences (SCCS) in Cheltenham for his work "The swarm and the mosquito: Information transfer, co-operation and decision-making in a group" - you can learn more about this research from Issue 6 of the BCCS newsletters.

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2011

Journal articles

Aldersley, A., Murray, S. J. and Cornell, S. E. (2011) 'Global and regional analysis of climate and human drivers of wildfire', Science of the Total Environment, 409(18), 3472-3481.

Armstrong, C. T., Vincent, T. L., Green, P. J. and Woolfson, D. N. (2011) 'SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences', Bioinformatics, 27(14), 1908-1914.

De Luca, M., Szostek, C., Cartlidge, J. and Cliff, D. (2011) 'Studies on interactions between human traders and Algorithmic Trading Systems', UK Government Foresight Project.

Giuggioli, L., Potts, J. R. and Harris, S. (2011) 'Brownian walkers within subdiffusing territorial boundaries', Physical Review E, 83(6), 061138.

Giuggioli, L., Potts, J. R. and Harris, S. (2011) 'Animal interactions and the emergence of territoriality', PLoS computational biology, 7(3), e1002008.

Malins, A., Williams, S. R., Eggers, J., Tanaka, H. and Royall, C. P. (2011) 'The effect of inter-cluster interactions on the structure of colloidal clusters', Journal of Non-Crystalline Solids, 357(2), 760-766.

Mills, H., Cohen, T. and Colijn, C. (2011) 'Modelling the performance of isoniazid preventive therapy for reducing tuberculosis in HIV endemic settings: the effects of network structure', Journal of The Royal Society Interface, 8(63),

Ni, Y., Mcvicar, M., Santos-Rodriguez, R. and De Bie, T. (2011) 'Harmony progression analyzer for mirex 2011'.

Ni, Y., Mcvicar, M., Santos-Rodriguez, R. and De Bie, T. (2011) 'Meta-song evaluation for chord recognition', arXiv preprint arXiv:1109.0420.

Ni, Y., Santos-Rodríguez, R., Mcvicar, M. and De Bie, T. (2011) 'Hit song science once again a science?'.

Onslow, A. C., Bogacz, R. and Jones, M. W. (2011) 'Quantifying phase–amplitude coupling in neuronal network oscillations', Progress in biophysics and molecular biology, 105(1), 49-57.

Pocock, M. J., Johnson, O. and Wasiuk, D. (2011) 'Succinctly assessing the topological importance of species in flower–pollinator networks', Ecological Complexity, 8(3), 265-272.

Purcell, O., di Bernardo, M., Grierson, C. S. and Savery, N. J. (2011) 'A multi-functional synthetic gene network: a frequency multiplier, oscillator and switch', PloS one, 6(2), e16140.

Yoshizumi, A., Fletcher, J. M., Yu, Z., Persikov, A. V., Bartlett, G. J., Boyle, A. L., Vincent, T. L., Woolfson, D. N. and Brodsky, B. (2011) 'Designed coiled coils promote folding of a recombinant bacterial collagen', Journal of Biological Chemistry, 286(20), 17512-17520.

Conference contributions

McVicar, M., Freeman, T. and De Bie, T. (2011) Mining the Correlation between Lyrical and Audio Features and the Emergence of Mood, The 12th International Society for Music Information Retrieval Conference (ISMIR),  783-788.

Rooke, E., Bardy, B. and Tsaneva-Atanasova, K. (2011) Toward a synergetic model of postural coordination dynamics, BIO Web of Conferences, EDP Sciences, 00077.

Snowsill, T. M., Fyson, N., De Bie, T. and Cristianini, N. (2011) Refining causality: who copied from whom?, Proceedings of the 17th ACM SIGKDD international conference on Knowledge discovery and data mining, ACM, 466-474.

Book section

Fyson, N., De Bie, T. and Cristianini, N. (2011) 'Reconstruction of causal networks by set covering' in Adaptive and Natural Computing Algorithms,Springer, 196-205.

Awards
Sardar, Adam Won the outstanding poster award at the prestigious Intelligent Systems for Molecular Biology (ISMB) conference for his work on horizontal gene transfer and its impact on the tree of life - see BCCS student wins prestigious poster prize for more details.

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2010

Journal articles

Flaounas, I. N., Fyson, N. and Cristianini, N. (2010) Predicting relations in news-media content among EU countries, 2nd International Workshop on Cognitive Information Processing (CIP), IEEE, 269-274.

Gorochowski, T. E., di Bernardo, M. and Grierson, C. S. (2010) A Dynamical Approach to the Evolution of Complex Networks, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS).

de Lima Morais, D. A., Fang, H., Rackham, O. J., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2010) 'SUPERFAMILY 1.75 including a domain-centric gene ontology method', Nucleic acids research, 39(Database issue).

DeLellis, P., Bernardo, M., Gorochowski, T. E. and Russo, G. (2010) 'Synchronization and control of complex networks via contraction, adaptation and evolution', Circuits and Systems Magazine, IEEE, 10(3), 64-82.

Flaounas, I., Turchi, M., Ali, O., Fyson, N., De Bie, T., Mosdell, N., Lewis, J. and Cristianini, N. (2010) 'The structure of the EU mediasphere', PloS one, 5(12), e14243.

Gorochowski, T. E., di Bernardo, M. and Grierson, C. S. (2010) 'Evolving enhanced topologies for the synchronization of dynamical complex networks', Physical Review E, 81(5), 056212.

McVicar, M. and De Bie, T. (2010) 'Exploiting online resources to improve chord recognition accuracy'.

Purcell, O., Savery, N. J., Grierson, C. S. and di Bernardo, M. (2010) 'A comparative analysis of synthetic genetic oscillators', Journal of The Royal Society Interface, 7(52), rsif20100183.

Rackham, O. J., Madera, M., Armstrong, C. T., Vincent, T. L., Woolfson, D. N. and Gough, J. (2010) 'The evolution and structure prediction of coiled coils across all genomes', Journal of molecular biology, 403(3), 480-493.

Rackham, O. J., Tsaneva-Atanasova, K., Ganesh, A. and Mellor, J. R. (2010) 'A Ca2+-based computational model for NMDA receptor-dependent synaptic plasticity at individual post-synaptic spines in the hippocampus', Frontiers in synaptic neuroscience, 2.

Taffs, J., Malins, A., Williams, S. R. and Royall, C. P. (2010) 'A structural comparison of models of colloid–polymer mixtures', Journal of Physics: Condensed Matter, 22(10), 104119.

Conference contributions

Flaounas, I. N., Fyson, N. and Cristianini, N. (2010) Predicting relations in news-media content among EU countries, 2nd International Workshop on Cognitive Information Processing (CIP), IEEE, 269-274.

Gorochowski, T. E., di Bernardo, M. and Grierson, C. S. (2010) A Dynamical Approach to the Evolution of Complex Networks, Proceedings of the 19th International Symposium on Mathematical Theory of Networks and Systems (MTNS).

Book section

Musselle, C. J. (2010) 'Insights into the antigen sampling component of the dendritic cell algorithm' in Artificial Immune Systems,Springer, 88-101.

Awards
Rackham, Owen Chosen to lead a nationwide campaign communicating the impact of science, engineering and maths on everyday lives as part of NOISE (New Outlooks in Science & Engineering), a project funded by the Engineering and Physical Sciences Research Council (EPSRC) - see Phd student to become voice for UK science and engineering for more details.
Gorochowski, Tom Won best poster for the Computational Methods and Tools session at the International Conference on Systems Biology. His work focussed on understanding the dynamic and networked structure of complex systems, and how this evolves over time - see PhD student wins award at International Conference on Systems Biology for more details.

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2009

Journal articles

Malins, A., Williams, S. R., Eggers, J., Tanaka, H. and Royall, C. P. (2009) 'Geometric frustration in small colloidal clusters', Journal of Physics: Condensed Matter, 21(42), 425103.

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