Publications

The first cohort of students will be admitted in 2014. Information about publications arising from SynBio students will therefore be added in due course. However, the SynBio programme has been split out of the very successful LSI, DTP, SysBio and SABS-IDC programmes, which have been running in the Rex Richards Building from 2003. Publications from all students are listed below. We hope that yours will soon be added to this growing list!

ProgrammeIntake YearFirst NameLast NamePublication
DTP2012JacobGalsonGalson, J.D., Pollard, A.J., Trück, J. & Kelly, D.F. Studying the antibody repertoire after vaccination: Practical applications. Trends in Immunology 35, 319-331 (2014).
LSI2010FedericoGarza de LeonStephan Uphoff; Rodrigo Reyes-Lamothe; Federico Garza de Leon; David J Sherratt; Achillefs N Kapanidis. Single-molecule DNA repair in live bacteria. PNAS
LSI2006LoukasMoutsianasDemographic history and rare allele sharing among human populations S Gravel, BM Henn, RN Gutenkunst, AR Indap, GT Marth, AG Clark, F Yu, RA … Proceedings of the National Academy of Sciences 108 (29), 11983
LSI2006LoukasMoutsianasThe 1000 Genomes Project Consortium. 2010. A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073. PMID: 20981092
LSI2006LoukasMoutsianasThe International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58. PMID: 20811451
LSI2006AfidalinaTumianThe 1000 Genomes Project Consortium, "A map of human genome variation from population-scale sequencing", Nature 467, 7319 (2010), pp. 1061-1073.
LSI2006LoukasMoutsianasGenetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Stephen Sawcer, Garrett Hellenthal, Matti Pirinen, CC Spencer, Nikolaos A Patsopoulos, Loukas Moutsianas, Alexander Dilthey, Zhan Su etc Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Nature 476 pp 214-219 (2011)
LSI2006LoukasMoutsianasDurbin, R et al - 'A map of human genome variation from population-scale sequencing' - Nature (2010) Volume: 467, Issue: 7319, Publisher: Nature, Pages: 1061-1073
LSI2006AfidalinaTumianDurbin, R et al - 'A map of human genome variation from population-scale sequencing' - Nature (2010) Volume: 467, Issue: 7319, Publisher: Nature, Pages: 1061-1073
LSI2005EleniGiannoulatouThe Wellcome Trust Case Control Consortium 'Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls' Nature 464, 713-720 (1 April 2010)
LSI2004AvigailAgamBinnaz Yalcin*, Kim Wong*, Avigail Agam*, Martin Goodson* et al., Sequence-based characterization of structural variation in the mouse genome Nature 2011, 477 (7364), 326-329
LSI2004ZhanSuThe Wellcome Trust Case Control Consortium Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls Nature 464, 713-720 (1 April 2010)
LSI2003AdamAuton‘Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication’. Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, et al, Nature [2010, 464(7290):898-902]
LSI2003AdamAutonThe International HapMap Consortium. A second generation human haplotype map of over 311 million SNPs. Nature 449, 851-861. 2007
LSI2003AdamAutonJ. Novembre, T. Johnson, K. Bryc, Z. Kutalik, A.R. Boyko, A. Auton, A. Indap, K.S. King, S. Bergmann, M.R. Nelson, M. Stephens and C.D. Bustamante, "Genes mirror geography within Europe", Nature, August 2008.
LSI2012MichaelBoemoPhosphoesterase [Caenorhabditis brenneri]. Boemo, M., Mead, J., NCBI, June 29, 2009.
LSI2012MichaelBoemoWagh K, Bhatia A, Alexe G, Reddy A, Ravikumar V, Seiler M, Boemo M, Yao M, Cronk L, Naqvi A, Ganesan S, Levine AJ, Bhanot G (2012) Lactase Persistence and Lipid Pathway Selection in the Maasai. PLoS ONE 7(9): e44751. doi:10.1371/journal.pone.0044751
LSI2011ThaddeusAidA novel computer-based system for personalised aphasia therapy, 2011 Biennial International Conference of the British Aphasiology Society, Reading. I presented my research from my undergraduate degree on how to help enable tele-therapy for people with aph
LSI2011ThaddeusAidTrees, Glorious Tree part 2, Doctoral Training Centre, University of Oxford. I was invited back to give an updated talk on my research.
LSI2011ThaddeusAidTrees, glorious trees, Doctoral Training Centre, University of Oxford. I presented a talk about my research project to other PhD students as part of the DTC’s research seminars.
LSI2011ThaddeusAid'Hiding in the Trees: Positive Selection In Humans' at Science Oxford! Live (4 October 2012)
LSI2011JackMillerJ. M. A. Ashbourn, J. J. Miller, V. Reumers, V. Baekelandt and L. Geris, A mathematical model of adult subventricular neurogenesis, Interface Journal of the Royal Society 2012 (http://rsif.royalsocietypublishing.org/content/9/75/2414)
LSI2011LinusSchumacherMicrosoft Research Prize
LSI2011SiyingWangA local sensitivity analysis method for developing biological models with identifiable parameters: application to L-type Calcium channel modelling A. Sher‚ K. Wang‚ A. Wathen‚ G. Mirams‚ D. Abramson and D. Gavaghan 2012 IEEE Sixth International Conferenc
LSI2011SiyingWangCardiac electrophysiological imaging systems scalable for high-throughput drug testing Peter Lee*‚ Ken Wang*‚ ChristopherE. Woods‚ Ping Yan‚ Peter Kohl‚ Paul Ewart‚ LeslieM. Loew‚ DerekA. Terrar and Christian Bollensdorff Pflügers Archiv − European Jour
LSI2011SiyingWangA Local Sensitivity Analysis Method for Developing Biological Models with Identifiable Parameters: Application to Cardiac Ionic Channel Modelling A. Sher‚ K. Wang‚ A. Wathen‚ P.J. Maybank‚ G.R. Mirams‚ D. Abramson‚ D. Noble and D.J. Gavaghan Future Gener
LSI2011SiyingWangMinimum information about a cardiac electrophysiology experiment (MICEE): Standardised reporting for model reproducibility‚ interoperability‚ and data sharing T.A. Quinn‚ S. Granite‚ M.A. Allessie‚ C. Antzelevitch‚ C. Bollensdorff‚ G. Bub‚ R.A.B. Burton‚
LSI2011SiyingWangComparison of functional parameter measured from tissue slices and whole-heart Ken Wang, Peter Lee, David Gavaghan , Peter Kohl, Christian Bollensdorff Biophysics Society 57th annual meeting 2013
LSI2011SiyingWangAction potential duration maps in cardiac ventricular tissue slices depends mainly on stimulation site Ken Wang, Peter Lee, David Gavaghan , Peter Kohl, Christian Bollensdorff Biophysics Society 56th Annual meeting 2012
LSI2011DianaDi PaoloDynamics of the Bacterial Flagellar Motor through super-resolution microscopy and electroporation, id2 Conference UCL
LSI2011JackMillerA. Van Schepdael, J. M.A. Ashbourn, R. Beard, J. J. Miller & L. Geris. Mechanisms of cell migration in the adult brain: modelling subventricular neurogenesis. Computer Methods in Biomechanics and Biomedical Engineering
LSI2011LinusSchumacherSchumacher, L, Woolley, T, Baker, R. Noise-induced temporal dynamics in Turing systems. April 2013 issue of Physical Review E (Vol.87, No.4)
LSI2011LinusSchumacherNoise-induced temporal dynamics in Turing systems, id2 Conference UCL
LSI2010Anna MariaFrangouFrangou, A., Ladle, R. J., Malhado, A. C. M., Whittaker, R. J. Wildlife in a Warming World (2010). A World of Science (UNESCO publication).
LSI2010Anna MariaFrangouDunbar, R. I. M., Baron, R., Frangou, A., Pearce, E., van Leeuwen, E. J. C., Stow, J., Partridge, G., MacDonald, I., Barra, V., van Vugt, M. Social laughter is correlated with an elevated pain threshold (2011). Proceedings of the Royal Society B.
LSI2010LiangXuL. Xu, A. Georgieva, et al. (2012). Detection and Analysis of Pattern Readjustment in Fetal Heart Rate Signal. MEDSIP 12. Liverpool, UK.
LSI2010Anna MariaFrangouFrangou, A. M., Ladle, R. J., Malhado, A. C. M., & Whittaker, R. J., (2010) ‘Wildlife in a warming world’, in UNESCO’s ‘A World of Science’.
LSI2010DeweiJiaDNA origami, F1-ATPase, and bacterial flagella motor: towards a controllable nanomachine construction, id2 Conference UCL
LSI2010DeweiJiaStudy of a hybrid system of F1-ATPase and DNA nanostructures, id2 Conference UCL
LSI2010Richard PaulMasonR.P. Mason and A. Papachristodoulou. 'Dynamic Edge Adaptation in Delayed Oscillator Networks. Proc of the 51st IEEE Conference on Decision and Control, Maui, HI, 2012.
LSI2009RichardFranzeseFranzese, Richard: 'Barefoot and shod biomechanics of running in trained distance runners', University of Verona, July 2012
LSI2009JamieHillJamie R Hill, Sebastian Kelm, Jiye Shi, Charlotte M Deane Environment Specific Substitution Tables Improve Membrane Protein Alignment Bioinformatics, 2011, 27:i15-i23 (doi: 10.1093/bioinformatics/btr230)
LSI2009JamieHillJamie R. Hill, Charlotte M. Deane P-T: improving membrane protein alignment for structure prediction ioinformatics (2013) 29 (1): 54-61 (doi: 10.1093/bioinformatics/bts640)
LSI2009JamieHillPatent application: GB 1219196.1
LSI2009PeterLeeSara Dutta, Martin J. Bishop, Pras Pathmanathan, Peter Lee, Peter Kohl, T. Alexander Quinn, Blanca Rodríguez: Interpreting Optical Mapping Recordings in the Ischemic Heart: A Combined Experimental and Computational Investigation. FIMH 2011: 20-27
LSI2009PeterLeeTeaching Evolution in a Historical Context: From the Wisdom of the Ancient Greeks to Genetic Algorithms. Ferrari, F., Lee, P., Taylor, R.S. (2010) In M. Ferrari & R. Taylor, Epistemology and Science Education: Understanding the Evolution vs. Intelligent D
LSI2009PeterLeeCardiac MEC and Arrhythmias 2010 (Plus poster) Single-Camera Multi-Parametric Optical Mapping During Local Excitation of Isolated Rat Heart and Tissue Slices. Lee, P., Bollensdorff, C., Kohl, P, Lee, P., Bollensdorff, C., Wuskell, J.P., Loew, L.M., Kohl,
LSI2009SofiaPiltzSIAM Student Travel Award
LSI2009SofiaPiltzLinacre House Trust Travel Grant
LSI2009PeterLeeInterlaced optical force-fluorescence measurements for single molecule biophysics. Brau,R.R., Tarsa, P.B., Ferrer, J.M., Lee, P., Lang, M.J.Biophysical Journal 91: 1069-1077.
LSI2009PeterLeeTemporal pixel multiplexing for simultaneous high-speed high-resolution imaging. Bub,G., Tecza, M., Helmes, M., Lee, P., Kohl, P , Nature Methods 7: 209-211.
LSI2009PeterLeeNorthern Cardiovascular Research Group Meeting (Plus poster) Regional impact-induced arrhythmia in isolated rabbit heart visualised by optical mapping. Quinn, T.A., Lee, P., Bub, G., Epstein, A., Kohl, P.
LSI2009PeterLeeInterpreting optical mapping recordings in the ischemic heart. A combined experimental and computational investigation. Dutta, S., Bishop, M.J., Pathmanathan, P., Lee, P., Kohl, P., Quinn, T.A., Rodriguez, B. Lecture Notes in Computer Science 2011; 6666/2
LSI2009PeterLeeSingle-sensor system for spatially-resolved, continuous and multi-parametric optical mapping of cardiac tissue, Lee, P., Bollensdorff, C., Quinn, T.A., Wuskell, J.P., Loew, L.M., Kohl, P. Heart Rhythm. 2011 Sep; 8(9):1482-91. doi: 10.1016/j.hrthm.2011.03.
LSI2009PeterLeeBiophysical Society 55th Annual Meeting 2011 (Plus poster) Single-Camera Multi-Parametric Optical Mapping during Local Excitation of Isolated Rat Heart. Lee, P., Bollensdorff, C., Wuskell, J.P., Loew, L.M., Kohl, P.
LSI2009RobertZeldin‘High throughput metalo-protein analysis by microPIXE’ and the British Crystallographic Association Spring meeting
LSI2009Mohamad AzimAnsariDingle K. E.; Didelot, X.; Ansari, M. A.; Eyre, D. W.; Vaughan, A.; Griffiths, D.; Ip, C. L. C.; Batty, E. M.; Bowden, R.; Jolley, K. A.; Hood, D. W.; Fawley, W. N.; Walker, A. S.; Peto, T. E. A.; Wilcox, M.; Crook, D. W. Recombinational switching of the Clostridium difficile S-layer and a novel glycosylation gene cluster revealed by large scale whole genome sequencing. Journal of Infectious Diseases, 207:675-686, 2013.
LSI2009Mohamad AzimAnsariDidelot, X.; Eyre, D. W.; Cule, M.; Ip, C. L. C.; Ansari, M. A.; Griffiths, G.; Vaughan, A; O'Connor, L.; Golubchik, T; Batty, E. M.; Piazza, P.; Wilson, D. J.; Bowden, R.; Donnelly, P. J; Dingle, K. E.; Wilcox, M; Walker, A. S.; Crook, D. W.; Peto, T. E. A.; Harding, R. M. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biology, 13:R118,2012.
LSI2009DuncanPalmerFryer HR, Frater J, Duda A, Palmer D, Phillips RE and McLean AR (2012). Cytotoxic TLymphocyte
Escape Mutations Identified by HLA Association Favor Those Which Escape and
Revert Rapidly. J. Virology. 86 (16): 8568-8580.
LSI2009RobertZeldinElemental analysis of proteins by Proton Induced X-ray Emission (microPIXE). Elspeth F. Garman, Oliver B. Zeldin. Book chapter in “Present and future methods for biomolecular crystallography”, Springer, 2013.
LSI2009RobertZeldinTalk selected for presentation at Biochemistry DPhil symposium, Laboratory of Molecular Biophysics Seminar Series, University of Oxford, 2012.
LSI2009RobertZeldinOliver B. Zeldin, Markus Gerstel, Elspeth F. Garman. Modelling Dose Profiles in 3D: Quantifying and optimising strategies for the minimisation of radiation damage. Journal of Synchrotron Radiation, 20(1), 49-57 (2013)
LSI2009RobertZeldinSelected Poster for Oral Presentation, Gordon Research Conference on Diffraction Methods in Structural Biology, ME, USA, 2012.
LSI2009RobertZeldinDivisional Funding in Enterprise Skills Award, University of Oxford, 2012.
LSI2009RobertZeldinBest Talk by a Young Crystallographer, British Crystallographic Association Spring Meeting, Keele, 2011.
LSI2008ChristopherArthursRapid Reliable Results: Accurate Cardiac Simulations Without the Wait (presented at SIAM Life Sciences 2010)
LSI2008ChristopherArthursC. Arthurs‚ M. Bishop and D. Kay, Efficient Simulation of Cardiac Electrical Propagation using High Order Finite Elements Journal of Computational Physics. Vol. 231. Pages 3946−3962. 2012.
LSI2008BrianChuangChuang, B. et al., “Understanding Ultrasound Elastography : Image Registration of Breast Cancer Histopathology and Ultrasound Elastography Images”, IEEE ISBI conference 2010, Rotterdam
LSI2008EoinHyde“Determination of fluid-related parameters for poroelastic modelling of myocardial perfusion” 4th Cardiac Physiome conference.
LSI2008EoinHydeThe Cardiac Physiome: Multi-scale and Multi-physics Mathematical Modelling Applied to the Heart - 2009
LSI2008EoinHydeDeveloping a continuum model of perfusion” 3rd Cardiac Physiome conference.
LSI2008EoinHyde“Determination of complex absorbing potentials from the electron self-energy” - Henderson, T.M., Fagas, G., Hyde, E. & Greer, J.C. (J.Chem.Phys., 2006)
LSI2008GabrielVillarSumeet Agarwal, Gabriel Villar and Nick S. Jones. High Throughput Network Analysis (extended abstract). In Machine Learning in Systems Biology (MLSB), Proceedings of the Fourth International Workshop, Edinburgh, Scotland, October 2010
LSI2008GabrielVillarGabriel Villar, Sumeet Agarwal and Nick S. Jones. High Throughput Network Analysis (extended abstract). In Proceedings of the Workshop on Analysis of Complex NEtworks (ACNE), ECML PKDD, Barcelona, Spain, September 2010
LSI2008GabrielVillarPrize for performance in Collections in Physics at Keble College
LSI2008GabrielVillarPrizes awarded by the Physics tutors of Keble College, Oxford, for essays: Review of laser propulsion technology, and Quantum dynamics of wave packets in one spatial dimension.
LSI2008GabrielVillarData Connection prize for best use of software in an Mphys project
LSI2008CiaraDangerfieldC.E. Dangerfield, J.V. Ross, and M.J. Keeling, “Integrating stochasticity and network structure into an epidemic model,” vol. 6, Sep. 2009, pp. 761-774.
LSI2008GabrielVillarVillar, G., Doye, J. P. K., Wilber, A. W., and Williamson, A. J. Modelling the self-assembly of tetrameric protein complexes. Poster presented at the conference Physics Meets Biology, University of Oxford (2008).
LSI2008CiaraDangerfieldLife Science Interface Doctoral Training Centre Short Project Award, 2009
LSI2008GabrielVillarVillar, G., Wilber, A. W., Williamson, A. J., Thiara, P., Doye, J. P. K., Louis, A. A., Jochum, M. N., Lewis, A. C. F., and Levy, E. D. Self-assembly and evolution of homomeric protein complexes. Phys. Rev. Lett. 102, 118106 (2009)
LSI2008CiaraDangerfield"Stochastic models and simulation of ion channel dynamics", 10th International Conference on Computational Science (ICCS), 31 May - 2 June, University of Amsterdam, The Netherlands
LSI2008CiaraDangerfieldC.E. Dangerfield, D. Kay, and K. Burrage, “Stochastic models and simulation of ion channel dynamics,” Procedia Computer Science, vol. 1, May. 2010, pp. 1587-1596.
LSI2008ClaireLucasAn Anatomical Model of the Cerebral Vasculature and the Autoregulation of Cerebral Blood Flow, 6th World Congress of Biomechanics (WCB 2010). August 1-6, 2010 Singapore
LSI2008IvorSimpsonI Simpson, J Schnabel, A Groves, J Andersson, M Woolrich A Bayesian approach to non-rigid registration with adaptive regularisation.Proc. Human Brain Mapping 2010.
LSI2008GabrielVillarVillar, G. Evolving a DNA oscillator. Poster presented at the DTC Annual Conference, University of Oxford (2010).
LSI2008GabrielVillarVillar, G., Heron, A.J. and Bayley, H. Formation of droplet networks that function in aqueous environments. Nature Nanotechnol. 6, 803–808 (2011).
LSI2008GabrielVillarApplication: Multisomes: encapsulated droplet networks
LSI2008CiaraDangerfieldC. E. Dangerfield, D. Kay, and K. Burrage, Comparison of Continuous and Discrete Stochastic Ion Channel Models, Proceedings of Annual International Conference of the IEEE, 704-707, 2011
LSI2008CiaraDangerfieldC.E. Dangerfield, Keeping perspective: The mathematics behind the response to an epidemic, New Collection, vol.6, 2010.
LSI2008CiaraDangerfieldC. E. Dangerfield‚ D. Kay‚ S. Macnamara and K. Burrage, A Boundary Preserving Numerical Algorithm for the Wright−Fisher Model with Mutation, BIT Num. Math. DOI (10.1007/s10543-011-0351-3), 2011
LSI2008MandeepGillModules for Reusable and Collaborative Modelling of Biological Mathematical Systems - 21ST IEEE International WETICE Conference (WETICE-2012)
LSI2008MandeepGillModular Mathematical Modelling of Biological Systems - Symposium on Theory of Modeling and Simulation (TMS'12)
LSI2008MandeepGillAbstraction in Physiological Modelling Languages - Symposium on Theory of Modeling and Simulation (TMS'13)
LSI2008MandeepGillFounding member of 2 web-based startups, one in Oxford, one in London. Both early stages with independent funding at present
LSI2008GabrielVillarApplication: Droplet assembly by 3D printing
LSI2007JamesAndersonJ. Anderson, A. Teixeira, H. Sandberg and A. Papachristodoulou. ‘Dynamical System Decomposition Using Dissipation Inequalities. 50th IEEE Conference on Decision and Control and European Control Conference 2011
LSI2007JamesAndersonJ. Anderson, Y.-C. Chang and A. Papachristodoulou. Model Decomposition and Reduction Tools for Large-Scale Networks in Systems Biology. Automatica, Vol 47.6 pp 1165-1174 (2011)
LSI2007JamesAndersonSymposium on Trends in Networked Systems and Cooperative Control (Poster presentation)
LSI2007JamesAnderson11th International Conference on Systems Biology (poster presentation)
LSI2007JamesAndersonFrontiers of Multidisciplinary Research: Mathematics, Engineering and Biology (Poster presentation)
LSI2007JamesAndersonRobust Synthetic Biology Workshop 209,2010 (Poster presentation)
LSI2007ThomasDoel'Pulmonary lobe segmentation from CT images using fissureness, airways, vessels and multilevel B-splines', Doel, T.; Matin, T.N.; Gleeson, F.V.; Gavaghan, D.J.; Grau, V., IEEE International Symposium on Biomedical Imaging, p1491-4 , 2012
LSI2007ThomasDoelGauldie, Mayne, Mital, Doel & Cruickshank. Determining a viewpoint for navigating a virtual camera through a biological object with a lumen. US 7853058
LSI2007Sara-JaneDunnS-J. Dunn, I. Näthke, P. Appleton, H. Byrne, D.J. Gavaghan and J.M. Osborne, A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the
BasementMembrane and Actin Basket (in preparation)
LSI2007Sara-JaneDunnS-J. Dunn, A.G. Fletcher, S.J. Chapman, D.J. Gavaghan and J.M. Osborne, (under review) Modelling the Role of the Basement Membrane in the Colonic Epithelium, submitted to Journal of Theoretical Biology
LSI2007Sara-JaneDunnLandahl travel award (Society of Mathematical Biology)
LSI2007LukeHeatonF. Davidson, G. Boswell, M. Fischer, L. Heaton, D. Hofstadler, M.
Roper, 2011, Mathematical modelling of fungal growth and function, IMA Fungus 2: 33-37.
LSI2007LukeHeatonL. L. M. Heaton, B. Obara, V. Grau, N. S Jones, T. Nakagaki, L.
Boddy, M. D. Fricker, 2012, Analysis of fungal networks, Fungal Biol.
Rev. 26: 12-29.
LSI2007LukeHeaton"Transport in growing fungal networks" at International Conference on Systems Biology, Edinburgh ICC, October 2010.
LSI2007LukeHeaton"Transport in growing fungal networks" at The Biology of Fungi, IMC9, Edinburgh ICC, August 2010.
LSI2007LukeHeaton"Transport in growing fungal networks" at Transport Networks in Nature and Technology, Institut des Systemes Complexes, Paris, June 2010.
LSI2007LukeHeaton"Transport in growing fungal networks" at Pattern formation: The inspiration of Alan Turing, University of Oxford, March 2012.
LSI2007SamuelHuguenyHugueny S, Clifton DA, and Tarassenko L. Probabilistic patient monitoring with multivariate, multimodal extreme value theory. Biomedical Engineering Systems and Technologies, Communications in Computer Science, 2011 (invited paper).
LSI2007SamuelHuguenyClifton DA, Hugueny S, and Tarassenko L. Novelty Detection with Multivariate Extreme Value Statistics. Journal of Signal Processing Systems, 2010 (invited paper).
LSI2007SamuelHuguenyBest Paper Award at the 3rd International Conference on Bio-inspired Systems and Signal Processing.
LSI2007SamuelHuguenyAbbey-Santander Academic Travel Awards.
LSI2007GabrielRosser“Frontiers of multidisciplinary research: mathematics, engineering and biology”, Exeter: September 2010
LSI2007GabrielRosserWood, T., Yates, C. A., Wilkinson, D., and Rosser, G. (2011). “Visual tracking of bacteria using the Gaussian Mixture Probability Hypothesis Density Filter”. IEEE T. Circuits. Syst. For Video Technology, 22:702-713.
LSI2007GabrielRosserRosser, G., Fletcher, A. G., Baker, R. E., and Maini, P. K. “The effect of sampling rate on observations of a correlated random walk.”. In preparation, manuscript available upon request
LSI2007GabrielRosserRosser, G., Wilkinson, D., Fletcher, A. G., Baker, R. E., Yates, C. A., Armitage, J. P., and Maini, P. K. “Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides”. Under review at PLoS Comp. Biol..
LSI2007GabrielRosserSt Anne's College Travel Award 2009
LSI2007GabrielRosserSt Anne's College Travel Award 2010
LSI2007AaronSmithTrichas G, Smith AM, White N, Wilkins V, Watanabe T, et al. (2012) Multi-Cellular Rosettes in the Mouse Visceral Endoderm Facilitate the Ordered Migration of Anterior Visceral Endoderm Cells. PLoS Biol 10(2): e1001256. doi:10.1371/journal.pbio.1001256
LSI2007JamesAndersonV. M. Becerra, S. J. Nasuto, J. Anderson, M. Ceriotti, C. Bombardelli. "Search space pruning and global optimization of multiple gravity assist trajectories with deep space manoeuvres." In Proceedings of IEEE Congress on Evolutionary Computation 2007, pp.
LSI2007JamesAndersonM. Vasile, M. Ceriotti, V.M. Becerra, S.J. Nasuto and J. Anderson, "Global trajectory optimization: Can we prune the solution space when cosidering deep space maneuvres?" Final Report, Ariadna id:06/4101,Contract no:20273/06/NL/HE, European Space Agency,
LSI2007ThomasDoelMicrosoft Research European Science Initiative award for best first year research project at the Oxford LSI DTC
LSI2007SamuelHuguenyHierarchical detection of multiple organs using boosted features. International Conference on Computer Analysis of Images and Patterns, 2007.
LSI2007AaronSmithP. Blondel, D. Fang, A.M. Smith and N. Jayasundere, "High-frequency bistatic imaging of pround targets - Influence of target orientation and target type." Proceedings of the Second International Conference on Underwater Acoustic Measurements: Technologies
LSI2007JemPearsonR.H.C. Tan, J.M. Pearson, Y. Zheng, P.B. Wyatt, and W.P. Gillin, “Evidence for erbium-erbium energy migration in erbium(III) bis(perfluoro-p-tolyl)phosphinate,” Applied Physics Letters, vol. 92, 2008, p. 103303.
LSI2007JemPearsonY. Zheng, J. Pearson, R.H.C. Tan, W.P. Gillin, and P.B. Wyatt, “Erbium bis(pentafluorophenyl)phosphinate: a new hybrid material with unusually long-lived infrared luminescence,” Journal of Materials Science: Materials in Electronics, vol. 20, 2008, pp. 43
LSI2007JamesAndersonJ.Anderson and A. Papachristodoulou, "A Decomposition/Synchronization Scheme for Formulating and Solving Optimization Problems." In Proc. 1st IFAC workshop on distributed estimation and control in networked systems, 2009.
LSI2007KatzarynaBlochInternational Workshop in Network Biology “Understanding Metabolic and Protein Interactions”, Ohio State University, USA
LSI2007ThomasDoelAmerican Thoracic Society International Conference, San Diego, USA
Assessing the Relative Influence of Branching Structure on Pulmonary Blood Flow with Computational Models
LSI2007ThomasDoelPresenatation at International Union of Physiological Sciences 2009, Kyoto, Japan
LSI2007ThomasDoelT. Doel, K. S. Burrowes, J. P. Whiteley, V. Grau and D. J. Gavaghan. 'Assessing the Relative Influence of Branching Structure on Pulmonary Blood Flow with Computational Models. American Thoracic Society International Conference 2009, San Diego. 15-20 May
LSI2007ThomasDoelInternational Union of Physiological Sciences 2009, Kyoto, Japan
Assessing the Relative Influence of Vascular Branching Structure on Pulmonary Blood Flow Distribution via Computational Models
LSI2007ThomasDoelVice-Chancellor's Interdisciplinary Research Forum on Integrated Quantatitive Biosciences, Oxford, UK
Assessment of lung disease by combining functional imaging with personalised computational modelling
LSI2007ThomasDoelBritish Science Festival Perspectives poster competition. Breath of Life
LSI2007ThomasDoelFinalist, 2009 Perspectives poster competition (British Science Festival). British Science Association
LSI2007JemPearsonI. Hernández, R.H.C. Tan, J.M. Pearson, P.B. Wyatt, and W.P. Gillin, “Nonradiative De-excitation Mechanisms in Long-Lived Erbium(III) Organic Compounds ErxY1-x[(p-CF3-C6F4)2PO2]3,” The Journal of Physical Chemistry B, vol. 113, May. 2009, pp. 7474-7481.
LSI2007SusannePfeiferAnne Goriely, Ruth M S Hansen, Indira B Taylor, Inge A Olesen, Grete Krag Jacobsen, Simon J McGowan, Susanne P Pfeifer, Gilean A T McVean, Ewa Rajpert-De Meyts, and Andrew O M Wilkie. Activating mutations in FGFR3 and HRAS reveal a shared genetic origin f
LSI2007Anna TundeSzilagyiT. Szilágyi, Sir M. Brady, "Reliable structural information from multi-scale decomposition with the Mellor-Brady Filter", SPIE, San Diego, 2nd - 6th August
LSI2007Anna TundeSzilagyiT. Szilágyi, M. Verhoek, A. Noble, “Detecting early response to therapy in liver cancer treatment: 3D metastases segmentation using graph-cuts with a modified prior”, Medical Image Understanding and Analysis, London, 14th -15th July
LSI2007Anna TundeSzilagyiT. Szilágyi, Sir M. Brady, T. Brunner, N. Joshi, "Local phase significance estimated with uncertainties to detect fibrotic regions from in vivo pancreatic cancer images", Medical Image Understanding and Analysis, London, 14th -15th July
LSI2007Anna TundeSzilagyiT. Szilágyi, Sir M. Brady, "Feature extraction from cancer images using local phase congruency: a reliable source of image descriptors", International Symposium on Biomedical Imaging, Boston, 28th June-1st July
LSI2007JamesAndersonInvited Session Chair, IEEE Conference on Decision and Control, Atlanta, Georgia, 2010, for the session "Distributed network analysis, control and optimization"
LSI2007JamesAndersonJ.Anderson and A. Papachristodoulou, "A network decomposition approach for efficient sum-of-squares based analysis." In Proc. 2010 American Control Conference 2009.
LSI2007JamesAndersonJ. Anderson and A. Papachristodoulou. "Dynamical System Decomposition for Efficient, Sparse Analysis." In Proceedings of the 49th IEEE Conference on Decision and Control, Atlanta GA, 2010.
LSI2007JamesAndersonA. Papachristodoulou, Y.-C. Chang, E. August and J. Anderson. Structured Model Reduction for Dynamical Networked Systems. In Proceedings of the 49th IEEE Conference on Decision and Control, Atlanta GA, 2010.
LSI2007JamesAndersonJ.Anderson and A. Papachristodoulou, "Input-Output Systems Analysis Using Sum of Squares Programming: A Decomposition Approach." In Proc. Of the 19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.
LSI2007JamesAnderson"Dynamic Decomposition", COXIC, Complexity Oxford Imperial College, Institute for Mathematical Sciences, Imperial College, London, 21 April 2010
LSI2007JamesAnderson"Input-Output Systems Analysis Using Sum of Squares Programming: A Decomposition Approach", 19th International Symposium on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010. Part of the invited session "Real Algebraic Geometry and Appl
LSI2007CourtneyBishopC.A. Bishop, D. Merhof, J. Declerck and M. Jenkinson, "Evaluation of four hippocampal segmentation methods for healthy and pahtological subjects, The Organization of Human Brain Mapping, Barcelona, June 2010
LSI2007CourtneyBishopC.A. Bishop, M. Jenkinson, J. Declerck, and D. Merhof, "Evaluation of hippocampal segmentation methods for healthy and pathological subjects." Eurographics Workshop on Visual Computing for Biology and Medicine, Leipzig, July 2010
LSI2007CourtneyBishopA.C Tziortzi, G Douaud, P. Shotbolt, C. Bishop, G. Searle, M. Larouelle, E.A. Rabiner, M Jenkinson, R.N Gunn. "A combined diffusion tensor imaging (DTI) and [11C]-(+)-PHNO positron emission tomography (PET) study to quantify dopamine D3/D2 receptors in pa
LSI2007KatzarynaBlochDoctoral Training Centre Conference, University of Warwick, UK Poster presentation: “Bioenergetic changes in tumour spheroids during growth”
LSI2007Sara-JaneDunnPresented research at 'Scientific Advances in Colorectal Cancer', hosted by Astra-Zeneca, University of Nottingham, 2010
LSI2007Sara-JaneDunnMathematical Modelling of Cancer Growth and Treatment Summer School and Workshop, University of Dundee
LSI2007Sara-JaneDunnPresented research at the InternationalWorkshop on Cancer Modelling Hosted by the Korea Advanced Institute of Science and Technology, Daejeon, South
Korea
LSI2007Sara-JaneDunnContributed talk given at the Annual Meeting of the Society of Mathematical Biology, Rio de Janeiro, Brazil
LSI2007Sara-JaneDunnS.-J. Dunn and J.P. Whiteley, “Modeling Alveolar Volume Changes During Periodic Breathing in Heterogeneously Ventilated Lungs,” Annals of Biomedical Engineering, vol. 38, 2010, pp. 2988-2999.
LSI2007Sara-JaneDunnFirst prize for the best presentation at the Computing Laboratory Dphil conference, 2010
LSI2007LukeHeatonL. L. M Heaton, E Lopez, P. K Maini, M. D Fricker, N. S Jones, 2010, Growth-inducedmass
ows in fungal networks, Proc. Roy. Soc. B. 277: 3265-3274.
LSI2007SamuelHuguenyProbabilistic patient monitoring using extreme value theory. Third International Conference on Bio-inspired Systems and Signal Processing, 2010
LSI2007SamuelHuguenyNovelty Detection with Multivariate Extreme Value Statistics, Journal of Signal Processing Systems, 2010
LSI2007SamuelHuguenyWilliam James Award awarded annually by the IET to “the student whose PhD research shows the most potential to contribute toward the development and improvement of the biomedical engineering field”.
LSI2007SamuelHuguenyBest Paper Award at the 3rd International Conference on Bio-inspired Systems and Signal Processing
LSI2007GabrielRosserWood TM, Yates CA, Wilkinson D, Rosser G. Simplified multitarget tracking using the PHD filter for microscopic data. Circuits and Systems for Video Technology, IEEE Transactions, Volume: 22 , Issue: 5, pp 702-713
LSI2007GabrielRosserDelalez NJ, Wadhams GH, Rosser G, Xue Q, Brown MT, Dobbie IM, Berry RM, Leake MC, Armitage JP. Signal-dependent turnover of the bacterial flagellar switch protein FliM. Proc Natl Acad Sci U S A 2010 Jun 22;107(25):11347-51
LSI2007Anna TundeSzilagyiR. Ali, T. Szilágyi, K. Hussien, M. Christlieb, Borivoj Vojnovic, Sir M. Brady, "Automatic nucleus segmentation of adherent cells from brightfield microscopy images", British Machine Vision Association and Society for Pattern Recognition Symposium, London
LSI2007Anna TundeSzilagyiT. Szilágyi, A.K. Harvey, Sir M. Brady, L. Cochlin, N. Joshi, "Quantitative analysis of tendon ECM damage using MRI", International Symposium on Biomedical Imaging, Rotterdam, Netherlands, 14 -17 April
LSI2007Anna TundeSzilagyiA.K. Harvey, T. Szilágyi, Sir M. Brady, M. Thompson, N. Joshi, " Curvatures with uncertainties derived in conformal space to characterize tendon microstructure", International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), Buen
LSI2007CourtneyBishop(submitted) C.A. Bishop, D. Merhof, J. Declerck, M. Jenkinson and the Alzheimer's Disease Neuroimaging Initiative (ADNI), "Accounting for changes in data and labeling protocol: improving atlas-based hippocampal segmentation." The Organization of Human Bra
LSI2007CourtneyBishopC.A. Bishop, M. Jenkinson, J. Andersson, J. Declerck, and D. Merhof, “Novel Fast Marching for Automated Segmentation of the Hippocampus (FMASH): Method and validation on clinical data,” NeuroImage, vol. 55, Apr. 2011, pp. 1009-1019.
LSI2007LukeHeatonL. L. M Heaton, E Lopez, P. K Maini, M. D Fricker, N. S Jones, 2012, Advection, diffusion and delivery over a network, Phys. Rev. E
86: 021905.
LSI2007SamuelHuguenyUnderstanding Vital-Sign Abnormalities in Critical Care Patients, 30th International Symposium on Intensive Care and Emergency Medicine, 2010
LSI2007SamuelHuguenyProbabilistic patient monitoring with multivariate, multimodal extreme value theory, Biomedical Engineering Systems and Technologies, Communications in Computer Science, 2011 (invited paper)
LSI2007AaronSmithA. Smith, R. Baker, D. Kay and P. Maini, "Incorporating chemical signalling factors into cell based models of growing epithelial tissues." Journal of Mathematical Biology 2012 Sep;65(3):441-63. doi: 10.1007/s00285-011-0464-y. Epub 2011 Sep 7.
LSI2007Anna TundeSzilagyiR. Ali, M. Gooding, T. Szilágyi , B. Vojnovic, M. Christlieb, Sir M. Brady, "Automatic segmentation of adherent biological cell boundaries and nuclei from brightfield microscopy images", Machine Vision and Applications
LSI2007Anna TundeSzilagyiR. Ali, T. Szilágyi , M. Gooding, M. Christlieb, Sir M. Brady, "On the use of low pass filters for image processing with inverse Laplacian models", Journal for Mathematcial Imaging and Vision
LSI2007JamesAndersonJ. Anderson and A. Papachristodoulou. A Decomposition Technique for Nonlinear Dynamical System Analysis. IEEE Transactions on Automatic Control 57(6):1516-1521, June 2012
LSI2007GabrielRosserTM Wood, CA Yates, DA Wilkinson, G Rosser - Simplified Multitarget Tracking Using the PHD Filter for Microscopic Video Data
LSI2007JamesAndersonJ. Anderson and A. Papachristodoulou, "On validation and invalidation of biological models", BMC Bioinformatics, 2009, 10:132 doi:10.1186/1471-2105-10-132
LSI2007JamesAnderson12.J. Anderson and A. Papachristodoulou. On Validation and Invalidation of Biological Models. BMC Bioinformatics 2009, 10:132
LSI2007SamuelHuguenyS. Hugueny, D. Clifton, and L. Tarassenko. Novelty detection with multivariate extreme value theory, part II: Analytical approach for unimodal estimation. Proceedings of IEEE Workshop on Machine Learning in Signal Processing, 2009.
LSI2007SamuelHuguenyD. Clifton, S. Hugueny, and L. Tarassenko. Novelty detection with multivariate extreme value theory, part I: Numerical approach for multimodal estimation. Proceedings of IEEE Workshop on Machine Learning in Signal Processing, 2009
LSI2007SamuelHuguenyD. Clifton, S. Hugueny, and L. Tarassenko. A comparison of approaches to multivariate extreme value theory for novelty detection. Proceedings of IEEE Workshop on Statistical Signal Processing, 2009.
LSI2007SusannePfeiferAdam Auton⋆, Adi Fledel-Alon⋆, Susanne Pfeifer⋆, Oliver Venn⋆, Laure Ségurel, Teresa Street, Ellen Leffler, Rory Bowden, Ivy Aneas, John Broxholme, Peter Humburg, Zamin Iqbal, Gerton Lunter, Julian Maller, Ryan Hernandez, Cord Melton, Aarti Venkat, Marcelo A. Nobrega, Ronald Bontrop, Simon Myers, Peter Donnelly, Molly Przeworski⋄, and Gil McVean⋄ ‘A Fine-Scale Chimpanzee Genetic Map from Population Sequencing’
LSI2007SusannePfeiferSociety for Molecular Biology and Evolution Walter Fitch symposium laureate
LSI2007SusannePfeiferSummer Institute Statistical Genetics Scholarship
LSI2006BartuAhiska‘Adaptive cloud based app streaming’ (13/458,618)
LSI2006BartuAhiskaApplication (US/PCT)
LSI2006BartuAhiska‘Data reduction techniques for processing wide-angle video’ (8,238,695); ‘Automatically expanding the zoom capability of wide-angle video camera’ (7,990,422);
LSI2006SimonLiS Li, C Buehnemann, B Hassan, JA Noble - Segmentation of Cell Clumps for Quantitative Analysis
LSI2006SimonLiBritish Machine Vision Association one day technical meeting on microscopy image analysis for biomedical applications- Oral presentation (April 2010).
LSI2006SimonLiQuantitative Imaging for Systems Biology- Joint oral presentation (December 2009)
LSI2006SimonLiPGBIOMED Conference- Oral presentation (July 2009)
LSI2006SimonLiBritish Society for Cell Biology Conference- Poster presentation (April 2009)
LSI2006SimonLiIEEE International Symposium on Biological Imaging- Poster presentation (March 2011)
LSI2006LoukasMoutsianasBerlin, International Congress of Genetics, July 2008What affects siRNA efficacy? A systematic Monte Carlo approach on a combined dataset offers novel insights.
Moutsianas L., Klingelhoefer J, Holmes C.
LSI2006LoukasMoutsianasCold Spring Harbor, NY, Genome Informatics, October 2009 - An imputation-based analysis of fine-mapping the association of the Major Histocompatibility Complex with Multiple Sclerosis - Loukas Moutsianas, Alexander Dilthey, Stephen Leslie, Gil McVean, the
LSI2006LoukasMoutsianasPhiladelphia, PA, American Society of Human Genetics, November 2008 - Modelling mutation and error in SNP data as a per-site uncertainty rate L. Moutsianas and G. McVean
LSI2006LoukasMoutsianasGenetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat. Genet.42: 985-990. PMID: 20953190
LSI2006LoukasMoutsianasSurakka, I., Kristiansson, K., Anttila, V., Inouye, M., Barnes, C., Moutsianas, L., Salomaa, V., Daly, M., Palotie, A., Peltonen, L., et al. 2010. Founder population-specific HapMap panel increases power in GWA studies through improved imputation accurac
LSI2006LoukasMoutsianasHosking, F. J., Leslie, S., Dilthey, A., Moutsianas, L., Wang, Y., Dobbins, S. E., Papaemmanuil, E., Sheridan, E., Kinsey, S. E., Lightfoot, T., et al. 2010. MHC variation and risk of childhood B-cell precursor acute lymphoblastic leukaemia. Blood. PMID:
LSI2006MichalPlotkowiakM P. Plotkowiak, K Burrowes, J Wolber, R J.O. Davies, F V. Gleeson, and D Gavaghan: Hyperpolarized Gas MRI For COPD Assessment Automated Regional Image Analysis And Computational Simulations, American Journal of Respiratory and Critical Care Medicine
LSI2006GarethStevensonLeveraging e-Science infrastructure for electrochemical research, Peachey, T., Mashkina, E., Lee, C., Enticott, C., Abramson, D., Bond, A., Elton, D., Gavaghan, D., Stevenson, G., Kennedy, G., “Leveraging e-Science Infrastructure for Electrochemistry Rese
LSI2006GarethStevensonTheoretical and experimental investigation of surface-confined two-center metalloproteins by large-amplitude Fourier transformed ac voltammetry, Chong-Yong Lee, Gareth P. Stevenson, Alison Parkin, Maxie M. Roessler, Ruth E. Baker, Kathryn Gillow, David J.
LSI2006GarethStevensonTheoretical Analysis of the Two-Electron Transfer Reaction and Experimental Studies with Surface-Confined Cytochrome c Peroxidase Using Large-Amplitude Fourier Transformed AC Voltammetry, Gareth P. Stevenson, Chong-Yong Lee, Gareth F. Kennedy, Alison Park
LSI2006GarethStevensonDesigner based Fourier transformed voltammetry: A multi-frequency, variable amplitude, sinusoidal waveform, Yongjun Tan, Gareth P. Stevenson, Ruth E. Baker, Darrell Elton, Kathryn Gillow, Jie Zhang, Alan M. Bond, David J. Gavaghan; Journal of Electroanaly
LSI2006GarethStevensonAccess to enhanced differences in Marcus–Hush and Butler–Volmer electron transfer theories by systematic analysis of higher order AC harmonics, Gareth P. Stevenson, Ruth E. Baker, Gareth F. Kennedy, Alan M. Bond, David J. Gavaghan and Kathryn Gillow, Phys
LSI2006GarethStevensonY Tan, GP Stevenson, RE Baker, D Elton, K Gillow, J Zhang, AM Bond, DJ Gavaghan - Designer based Fourier transformed voltammetry: A multi-frequency, variable amplitude, sinusoidal waveform
LSI2006GarethStevensonC-Y Lee, GP Stevenson, A Parkin, MM Roessler, RE Baker, K Gillow, DJ Gavaghan, FA Armstrong, AM Bond - Theoretical and experimental investigation of surface-confined two-center metalloproteins by large-amplitude Fourier transformed AC voltammetry
LSI2006GarethStevensonEPSRC PhD Plus Postdoc
LSI2006AfidalinaTumianA.Tumian and S.Myers, Rapid, lineage-specific losses of particular degenerate motifs have occurred genome-wide, throughout the history of great apes, The Biology of Genomes, 2012.
LSI2006ShelleyWickhamL. Poladian, M. Large, W. Padden, K. H. Lee, S. Wickham, and N. Beeton, "Is the photonic crystal in the butterflies T. imperialis and P. sesostris optimal?," in Conference on Lasers and Electro-Optics/International Quantum Electronics Conference and Photo
LSI2006ShelleyWickhamShelley Wickham, Maryanne C.J Large, Leon Poladian and Lars S Jermiin: Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours, J. R. Soc. Interface 22 February 2006 vol. 3 no. 6 99-109
LSI2006ShelleyWickhamM. Large, S. Wickham, Hayes J and L. Poladian: Insights from nature: Optical biomimetics
LSI2006RobertCrawfordK Lymperopoulos, M Heilemann, LC Hwang, R Crawford, AN Kapanidis - Single-molecule DNA biosensors for transcription-factor detection
LSI2006MichalPlotkowiakM Plotkowiak, B Rodriguez, G Plank, J E. Schneider, D Gavaghan, P Kohl and V Grau High Performance Computer Simulations of Cardiac Electrical Function Based on High Resolution MRI Datasets Computational Science – ICCS 2008 Lecture Notes in Computer Scien
LSI2006MichalPlotkowiakM Plotkowiak, K Burrowes, J Wolber, C Buckley, R Davies, F Gleeson, D Gavaghan and V Grau Relationship between structural changes and hyperpolarized gas magnetic resonance imaging in chronic obstructive pulmonary disease using computational simulations wi
LSI2006ShelleyWickhamLeon Poladian, Shelley Wickham, Kwan Lee and Maryanne C.J Large: Iridescence from photonic crystals and its suppression in butterfly scales,J. R. Soc. Interface 6 April 2009 vol. 6 no. Suppl 2 S233-S242
LSI2006RobertCrawfordR Crawford, K Lymperopoulos, JP Torella, M Heilemann, LC Hwang, SJ Holden, A Kapanidis - Single-Molecule DNA Biosensors for Quantitative Transcription Factor Detection
LSI2006RobertCrawfordK Lymperopoulos, R Crawford, JP Torella, M Heilemann, LC Hwang, SJ Holden, AN Kapanidis - Single-molecule DNA biosensors for protein and ligand detection
LSI2006JochenKlingelhoeferDavid Stoddart, Andrew J. Heron, Jochen Klingelhoefer, Ellina Mikhailova, Giovanni Maglia and Hagan Bayley ‘Nucleobase Recognition in ssDNA at the Central Constriction of the α-Hemolysin Pore’ Nano Lett., 2010, 10 (9), pp 3633–3637 American Chemical Soc
LSI2006JessicaLeitchLeitch J, Stebbins J, Zavatsky AB. ‘Subject-specific axes of the ankle joint complex.’ J Biomech. 2010 Nov 16;43(15):2923-8. Epub 2010 Aug 19.
LSI2006BenceMelykutiIstván Miklós, Bence Mélykúti, Krister Swenson 'The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths' IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(4), 763-767, 2010
LSI2006BenceMelykutiBence Mélykúti, Elias August, Antonis Papachristodoulou and Hana El-Samad 'Discriminating between rival biochemical network models: three approaches to optimal experiment design' BMC Systems Biology 2010, 4:38
LSI2006BenceMelykutiBence Mélykúti, Kevin Burrage, and Konstantinos C. Zygalakis Fast stochastic simulation of biochemical reaction systems by alternative formulations of the chemical Langevin equation J. Chem. Phys. 132, 164109 vol 132 issue 16
LSI2006BeatrizMendozaE. Jayne Wallace, Robert S. G. D'Rozario, Beatriz Mendoza Sanchez and Mark S. P. Sansom A multiscale simulation study of carbon nanotube interactions with designed amphiphilic peptide helices. Nanoscale, 2010, 2, 967-975
LSI2006AfidalinaTumianS. Myers, R. Bowden, A. Tumian, R E. Bontrop, C. Freeman, T S. MacFie, G. McVean and P. Donnelly - Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination Science 12 February 2010: Vol. 327 no. 5967 pp. 876-879
LSI2006LindaGrossLC Gross, OK Castell, MI Wallace – Dynamic and reversible control of 2D membrane protein concentration in a droplet interface bilayer
LSI2006LindaGrossLCM Gross, AJ Heron, S Baca, MI Wallace - Determining Membrane Capacitance by Dynamic Control of Droplet Interface Bilayer Area
LSI2006JessicaLeitchLeitch J, Stebbins J, Paolini G, Zavatsky AB. ‘Identifying gait events without a force plate during running: a comparison of methods.’ Gait Posture. 2011 Jan;33(1):130-2. Epub 2010 Nov 16.
LSI2006BeatrizMendozaZhao, Xin; Sanchez, Beatriz Mendoza: Dobson, Peter J; Grant, Patrick S: The role of nanomaterials in redox-based supercapacitors for next generation energy storage devices. Nanoscale, Volume 3, Issue 3, pp. 839-855 (2011). RSC
LSI2006LoukasMoutsianasAlexander T. Dilthey, Loukas Moutsianas, Stephen Leslie, and Gil McVean 'HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes' Bioinformatics (2011) 27(7): 968-972
LSI2006ShelleyWickhamS. F. J. Wickham, M Endo, Y Katsuda, K Hidaka, J Bath, H Sugiyama & A J. Turberfield: Direct observation of stepwise movement of a synthetic molecular transporter, Nature Nanotechnology Volume:6, Pages:166–169
LSI2006BartuAhiska‘Automatically expanding the zoom capability of wide-angle video camera’ (7,990,422)
LSI2006RafelBordasBordas, R, Gillow, K, Lou, Q, Efimov, IR, Gavaghan, D, Kohl, P, Grau, V, Rodriguez, B. Rabbit-Specific Ventricular Model of Cardiac Electrophysiological Function including Specialized Conduction System. Progress in Biophysics and Molecular Biology Vol. 107 No. 1 pp 90-100. 2011
LSI2006RafelBordasR Bordas, V Grau, RAB Burton, P Hales, JE Schneider, D Gavaghan, P Kohl, B Rodriguez - Integrated Approach for the Study of Anatomical Variability in the Cardiac Purkinje System: From High Resolution MRI to Electrophysiology Simulation
LSI2006RafelBordasDJ Gavaghan, J Pitt-Francis, P Pathmanathan, MO Bernabeu, R Bordas, J Cooper, AG Fletcher, GR Mirams, P Murray, JM Osborne, A Walter, SJ Chapman, A Garny, IMM van Leeuwen, PK Maini, B Rodriguez, SL Waters, JP Whiteley, HM Byrne - Chaste: a test-driven approach to software development for biological modelling
LSI2006RafelBordasPitt-Francis, J, Pathmanathan, P, Bernabeu, MO, Bordas, R, Cooper, J, Fletcher, AG, Mirams, GR, Murray, P, Osborne, JM, Walter, A, Chapman, SJ, Garney, A, van Leeuwen, IMM, Maini, PK, chaste: A Test-Driven Approach to Software Development for Biological Modelling. Computer Physics Communications, Vol 180, pp 2452-2471. 2009
LSI2006RafelBordasP Pathmanathan‚ MO Bernabeu‚ R Bordas‚ J Cooper‚ A Garny‚ J Pitt-Francis‚ JP Whiteley and DJ Gavaghan - A numerical guide to the solution of the bidomain equations of cardiac electrophysiology
LSI2006RobertCrawford54th Annual Meeting of the Biophysical Society, San Francisco, California. Largest international conference in my field with around 6000 attendees. Selected to deliver 1 of 8 talks in the Biotechnology session. Audience around 200. £400 travel award granted by St John’s College.
LSI2006RobertCrawfordFirst place out of ~150 entrants in the 2010 ‘Idea Idol’ competition run by Oxford
Entrepreneurs, University of Oxford. Awarded £5k cash prize for my proposed start-up company, ‘Oxford Nanosense’, aiming to detect infectious bacteria e.g. MRSA with high sensitivity, speed and at lower cost than competitors. Format: elevator pitch to judging panel and large audience in the Saïd Business School, University of Oxford.
LSI2006JochenKlingelhoeferL. Moutsianas, J.W. Klingelhoefer, C. Holmes, 'What Affects siRNA Efficacy? A systematic Monte Carlo Approach on a Combined Dataset Offers Novel Insights', XX International Congress of Genetics, Berlin, Germany, July 12 - 17, 2008.
LSI2006JochenKlingelhoeferJ. Klingelhoefer. T. Carpenter, M. Sansom. ‘Peptide Nanopores and Lipid Bilayers: Interactions by Coarse-Grained Molecular-Dynamics Simulations’. Biophysical Journal. 96:3519-3528 2009. doi:10.1016/j.bpj.2009.01.046.
LSI2006JochenKlingelhoeferJ.W. Klingelhoefer, L. Moutsianas, C. Holmes, 'Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency', Bioinformatics, 25(13):1594-1601, 2009. doi:10.1093/bioinformatics/btp284.
LSI2006JochenKlingelhoeferDL Parton, JW Klingelhoefer, MSP Sansom - Aggregation of model membrane proteins, modulated by hydrophobic mismatch, membrane curvature, and protein class
LSI2006SimonLiS Li, J Wakefield, JA Noble - Automated segmentation and alignment of mitotic nuclei for kymograph visualisation
LSI2006BenceMelykutiI. Miklos, B. Melykuti, K. Swenson, 'The Metropolized Partial Importance Sampling MCMC mixes slowly on minimum reversal rearrangement paths' IEEE/ACM Transactions on Computational Biology and Bioinformatics, 99(1), 2009. doi: 10.1109/TCBB.2009.26.
LSI2006LoukasMoutsianasL Moutsianas, A Dilthey, S Leslie, G McVean - An imputation-based analysis of fine-mapping the association of the Major Histocompatibility Complex with Multiple Sclerosis
LSI2006LoukasMoutsianasL. Moutsianas and G. McVean. ‘Modelling mutation and error in SNP data as a per-site uncertainty rate’. American Society of Human Genetics, Philadelphia, November 2008
LSI2006LoukasMoutsianasMultiple Hodgkin lymphoma–associated loci within the HLA region at chromosome 6p21. 3 L Moutsianas, V Enciso-Mora, YP Ma, S Leslie, A Dilthey, P Broderick, A … Blood 118 (3), 670-674
LSI2006LoukasMoutsianasE. van der Wath, L. Moutsianas, R. van der Wath, A. Visagie, L. Milanesi and P. Lio ‘Grid methodology for identifying co-regulated genes and transcription factor binding sites’ IEEE Transactions on Nanobioscience, Vol.6, Issue 2, June 2007, pp 162-167.
LSI2006LoukasMoutsianasIntegrating common and rare genetic variation in diverse human populations DM Altshuler, RA Gibbs, L Peltonen, E Dermitzakis, SF Schaffner, F Yu, PE Nature 467 (7311), 52
LSI2006RichardMuscat“Small Molecule Signals that Direct the Route of a Molecular Cargo” R.A. Muscat, J. Bath, A.J. Turberfield. Small 8(23), 3593-3597, 2012.
LSI2006RichardMuscat"A Programmable Molecular Robot” R.A. Muscat, J. Bath, A.J. Turberfield . Nano Letters 11(3), 982-987, 2011
LSI2006VaclavPotesilAutomated tumor delineation using joint PET/CT information SPIE 2007 February 1, 2007
LSI2006VaclavPotesilImproved Anatomical Landmark Localization in Medical Images Using Dense Matching of Graphical Models BMVC 2010
LSI2006VaclavPotesilV. Potesil ‘Statistical Lesion Characterization and Change Quantification’ SPIE Medical Imaging 2007 (joint publication with Siemens Medical Solutions USA)
LSI2006VaclavPotesilV. Potesil ‘Automatic Tumour Delineation using Joint PET-CT Information’ SPIE Medical Imaging 2007 (joint publication with Siemens Medical Solutions USA)
LSI2006VaclavPotesilImage-based normalization of FDG-PET uptake 2012 IEEE Nuclear Science Symposium and Medical Imaging Conference
LSI2006VaclavPotesilV Potesil, T Kadir, G Platsch, SM Brady - Personalization of pictorial structures for anatomical landmark localization
LSI2006VaclavPotesilLandmark Localization in CT Images Using Dense Matching of Graphical Models MIUA 2010 July 1, 2010 Best Paper Prize.
LSI2006VaclavPotesilWinner, Oxford Entrepreneurs Idea Idol 2007, 1st prize (4000GBP), Oxford University flagship business competition at the Said Business School
LSI2006VaclavPotesil3D imaging spin-off together with www.pix4d.com
LSI2006AfidalinaTumianA Tumain and S Myers. 'The effect of biased gene conversion on human sequence evolution.' EMBO Meiosis confernce, 19-23 Sept, France 2009.
LSI2005PatrickBuehlerBuhler P., Rebholz P. and Hesser J., Automatic 3D reconstruction of the coronary artery tree based on stochastic branch and bound, SPIE – International conference on Physiology, Function, and Structure from Medical Images, 2005
LSI2005PatrickBuehlerBuehler P., Everingham M., and Zisserman A., Employing Signed TV Broadcasts for Automatic Learning of British Sign Language, LREC 2010
LSI2005PatrickBuehlerWerner, G. D., Gemmell, P., Grosser, S., Hamer, R., & Shimeld, S. M. Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Marine Biotechnology, 1-14
LSI2005PatrickBuehlerBuehler P., Everingham M., Huttenlocher D.P. and Zisserman A., Upper Body Detection and Tracking in Extended Video Sequences, International Journal of Computer Vision (IJCV), 2011
LSI2005PatrickBuehlerApplication
LSI2005PatrickBuehlerApplication as first author
LSI2005PatrickBuehlerI am currently working for a US start-up company with ~20 employees
LSI2005MarkChangThe Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002. Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching". Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".
LSI2005MarkChangTraditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".
LSI2005MarkChangYo-Cheng Chang, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial N
LSI2005MarkChangYo-Cheng Chang, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July
LSI2005MarkChangYo-Cheng Chang and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.
LSI2005MarkChangYo-Cheng Chang, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Sy
LSI2005MarkChangChung-Yung Chen, Keh-Min Wu, Yo-Cheng Chang, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 200
LSI2005MarkChangHon-Wei Chen, Yo-Cheng Chang, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB),
LSI2005MarkChangYo-Cheng Chang and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.
LSI2005MarkChangChao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, Yo-Cheng Chang, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip
LSI2005MarkChangChung-Yung Chen, Keh-Ming Wu, Yo-Cheng Chang, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genom
LSI2005MarkChangYo-Cheng Chang and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)
LSI2005SusannahFlemingS Fleming, P Gill, C Jones, A van den Bruel, J Taylor, C Heneghan, M Thompson. Systematic review of the diagnostic accuracy of capillary refill time for serious illness in children. Pediatric Academic Societies Annual Meeting, May 2013.
LSI2005SusannahFlemingS Fleming, M Thompson, M Lakhanpaul. Improving measurement of vital signs in children in primary and emergency care. School of Primary Care Research Showcase, October 2012.
LSI2005SusannahFlemingH Ashdown, S Fleming, E Spencer, R Stevens, M Thompson. Assessing the accuracy of over-the-counter breathalysers. National Primary Care ACF Conference, January 2013.
LSI2005SusannahFlemingH F Ashdown, S Fleming, E Spencer, R J Stevens, M J Thompson. Assessing the accuracy of personal breathalysers. SWSAPC Annual Research Meeting, March 2013.
LSI2005SusannahFlemingS Fleming, P Gill, C Jones, A van den Bruel, J Taylor, C Heneghan, M Thompson. Systematic review of the diagnostic accuracy of capillary refill time for serious illness in children. Evidence Live, March 2013.
LSI2005SusannahFlemingS. Wilson, D. Wong, D.A. Clifton, S. Fleming, R. Way, R. Pullinger, and L. Tarassenko. Track and Trigger in an Emergency Department: an observational evaluation study. Emergency Medicine Journal 2013; 30:186-191
LSI2005SusannahFlemingC. Orphanidou, S. Fleming, S.A. Shah and L. Tarassenko. Data fusion for estimating respiratory rate from a single-channel ECG. Biomedical Signal Processing & Control. 2013; 8(1): 98-105
LSI2005SusannahFlemingSusannah Fleming, Dr Matthew Thompson, Richard Stevens, Carl Heneghan, Annette Plüddemann, Ian Maconochie, Lionel Tarassenko and David Mant ‘Normal ranges of heart rate and respiratory rate in children from birth to 18 years of age: a systematic review o
LSI2005EleniGiannoulatouEleni Giannoulatou, Christopher Yau, Stefano Collela, Jiannis Ragoussis, Christopher C. Holmes, “GenoSNP: a new genotyping algorithm for the Infinium SNP genotyping platform that uses Robust Bayesian Clustering”, Poster Presentation at the International B
LSI2005EleniGiannoulatouEleni Giannoulatou, Christopher Yau, Christopher C. Holmes, “Bayesian Mixture Model Clustering for genotyping of DNA Copy Number Variants”, Oral presentation at Greek Stochastics Alpha, Lefkada, Greece, August 2009
LSI2005EleniGiannoulatouEleni Giannoulatou and Jotun Hein, “Evolution of Metabolic Networks”, Poster presentation at the DTC Open day, Martin Wood Complex, Department of Physics, Oxford University, November 8th 2006
LSI2005EleniGiannoulatouEleni Giannoulatou, Christopher Yau, Christopher C. Holmes, “Statistical Model-based Normalisation of Illumina BeadArray SNP Data”, Poster Presentation at the Genomics of Common Diseases, Wellcome Trust Conference Centre, Hinxton, UK, 7-10 July 2007
LSI2005MiklosGyongyConstantin-C Coussios, Manish Arora, Jamie R T Collin, Ian Webb, Miklós Gyöngy, Bubble Therapy: Towards Cavitation-Enhanced HIFU Ablation and Drug Delivery, In: International Congress on Ultrasonics.
LSI2005MiklosGyongyGyongy, M. ; Arora, M. ; Noble, J.A. ; Coussios, C.C. ; Use of passive arrays for characterization and mapping of cavitation activity during HIFU exposure Ultrasonics Symposium, 2008. IUS 2008. IEEE 871
LSI2005MiklosGyongyMiklós Gyöngy, Robert Ritchie, Manish Arora, Thomas Leslie, Constantin-C Coussios, Monitoring of thermal ablation during HIFU exposure using passive cavitation mapping
LSI2005MiklosGyongyGyongy, M. ; Coussios, C.-C. ; Passive Spatial Mapping of Inertial Cavitation During HIFU Exposure, Biomedical Engineering, IEEE Transactions on Jan. 2010
Volume : 57 , Issue:1 Pg 48
LSI2005MiklosGyongyMiklós Gyöngy, Manish Arora, J Alison Noble, Constantin-C Coussios, A Passive Array Technique for Cavitation Mapping During HIFU Treatment, JOURNAL OF THE ACOUSTICAL SOCIETY OF AMERICA 123:(5) p. 3223. (2008)
LSI2005MiklosGyongyMapping and characterization of cavitation activity, patent number WO/2010/052494
LSI2005RichardMannC Armstrong, R Mann, M Collett, R Freeman, S Roberts and T Guilford. Why do pigeons form habitual routes? In: Orientation and Navigation: Birds, Humans and Other Animals. Conference of the Royal Institute of Navigation.
LSI2005RichardMannRoyal Institute of Navigation, Univ. of Reading, uk.
LSI2005RichardMannWorkshop on Synthetic Neuroethology, Univ. of Sussex, uk.
LSI2005RichardMannSwedish Meeting on Mathematics in Biology, Gothenburg Univ., sweden.
LSI2005RichardMannMaxEnt, Univ. of Mississippi, usa.
LSI2005RichardMannComplex Systems Lunch Seminar, Uppsala Univ., sweden.
LSI2005RichardMannR Freeman, R Mann, T Guilford and D Biro. Group decisions and individual differences: route fidelity predicts flight leadership in homing pigeons (Columba livia). Biology Letters.
LSI2005RichardMannMaxEnt, Chamonix, france. (poster)
LSI2005TahirMansooriGoodyer, C.E.; Grau, V.; Mansoori, T.; Schneider, J.E.; Brodlie, K.W.; Kohl, P.; 3D Visualization of Cardiac Anatomical MRI Data with Para-Cellular Resolution Engineering in Medicine and Biology Society, 2007. EMBS 2007. 29th Annual International Conferen
LSI2005TahirMansooriMansoori, T.; Plank G; Burton, R.; Schneider, J.; Kohl, P.; Gavaghan, D.; Grau, V.; An Iterative Method For Registration Of High-Resolution Cardiac Histoanatomical And MRI Images. Biomedical Imaging: From Nano to Macro, 2007. ISBI 2007. 4th IEEE Interna
LSI2005RobinRyderG. K. Nicholls and R. J. Ryder, Phylogenetic Models for Semitic Vocabulary (2011), Proceedings of the 26th International Workshop on Statistical Modelling
LSI2005RobinRyderRobert, R. Ryder, N. Chopin, Discussion on Particle Learning (2010), in Bayesian Statistics 9
LSI2005RobinRyder(Popular science article) : R. Ryder, interview with P. Pajot, L'arbre des langues indo-européennes (2011), La Recherche 450
LSI2005RobinRyderR. Ryder, G. Nicholls, Missing Data in a Stochastic Dollo Model for Cognate Data, and its Application to the Dating of Proto-Indo-European (2011), Journal of the Royal Statistical Society Series C , 60(1)
LSI2005RobinRyderJ.-M. Marin, P. Pudlo, C. Robert, R. Ryder, Approximate Bayesian Computational Methods (2011), submitted to Statistics and Computing
LSI2005RobinRyderR. J. Ryder, interview with P. Pajot, L'arbre des langues indo-européennes (2011), La Recherche 450:20-1
LSI2005RobinRyderR. J. Ryder and G. K. Nicholls, Missing data in a stochastic Dollo model for cognate data, and its application to the dating of Proto-Indo-European (2011), Journal of the Royal Statistical Society Series C (Applied Statistics) 60(1):71-92, DOI: 10.1111/j.
LSI2005RobinRyderJ.-M. Marin, P. Pudlo, C. P. Robert and R. J. Ryder, Approximate Bayesian Computational methods (2011), Statistics and Computing, arXiv: 1101.0955
LSI2005RobinRyderC. P. Robert, R. J. Ryder and N. Chopin, Discussion on Particle Learning (2010), Bayesian Statistics 9:349-50, arXiv: 1006.0554
LSI2005RobinRyderR. Ryder, J. Arbel, N. Chopin, Regression in a Thurstonian model, and application to Eurovision vote data (2011), poster at Greek Stochastics Gamma
LSI2005RobinRyder2010 Savage award honourable mention for best PhD thesis in applied Bayesian methodology, awarded by the International Society for Bayesian Analysis
LSI2005AdrianGrovesAdrian R. Groves and Robert N. Rohling ‘Two-dimensional spatial compounding with warping’ Ultrasound in Medicine & Biology, Volume 30, Issue 7, July 2004, Pages 929-942
LSI2005AdrianGrovesA.R. Groves, M.A. Chappell, M.W. Woolrich, 'Combined spatial and non-spatial prior for inference on MRI time-series', NeuroImage, 2008, 45(3): 795-809. doi:10.1016/j.neuroimage.2008.12.027.   
LSI2005MiklosGyongyStuart Faragher, Miklós Gyöngy, Mark Hodnett, Adam Shaw, and Constantin‐C. Coussios ‘Development of a tomographic cavitation sensor for quality assessment of clinical high intensity focused ultrasound systems.’ J. Acoust. Soc. Am. Volume 125, Issue 4, pp
LSI2005MiklosGyongyStuart Faragher, Miklós Gyöngy, Jamie Collin, Mark Hodnett, and Constantin‐C. Coussios ‘Design and implementation of a cylindrical array for passive mapping of cavitation fields produced by clinical high intensity focused ultrasound transducers’. J. Acou
LSI2005MiklosGyongyStuart Faragher, Miklós Gyöngy, Jamie Collin, Mark Hodnett, Andrew Hurrell, and Constantin‐C. Coussios ‘Three‐dimensional passive localization of cavitation activity for quality assessment of clinical high‐intensity focused ultrasound devices’. J. Acoust.
LSI2005RichardBranchT. Pilizota*, M. T. Brown*, M. C. Leake, R. W. Branch, R. M. Berry, J. P. Armitage. A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor. PNAS, 106(28) (2009) 11582-7.
LSI2005RichardBranchFan Bai, Richard W. Branch, Dan V. Nicolau, Jr., Teuta Pilizota, Bradley C. Steel, Philip K. Maini, and Richard M. Berry. (2010). Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch. Science 327 (5966), 685.
LSI2005RichardBranchLSI DTC Biophysics Award for best rotation project
LSI2005PatrickBuehlerBuehler, P. , Everingham, M. and Zisserman, A. Learning sign language by watching TV (using weakly aligned subtitles) Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (2009)
LSI2005PatrickBuehlerBuehler, P. , Everingham, M. , Huttenlocher, D. P. and Zisserman, A. Long Term Arm and Hand Tracking for Continuous Sign Language TV Broadcasts Proceedings of the British Machine Vision Conference (2008)
LSI2005SusannahFlemingS. Fleming, L. Tarassenko, M. Thompson and D. Mant. Non-invasive Measurement of Respiratory Rate in Children Using the Photoplethysmogram. Engineering in Medicine and Biology Society. EMBS 2008. 30th Annual International Conference of the IEEE, 1886-1889.
LSI2005SusannahFlemingS. Fleming and L. Tarassenko, 'A Comparison of Signal Processing Techniques for the Extraction of Breathing Rate from the Photoplethysmogram', Proceedings of World Academy of Science, Engineering and Technology, 24:276-280, October 2007.
LSI2005SusannahFlemingS. Fleming, L. Tarassenko, M. Thompson and D. Mant, ‘Data fusion for identification of serious illness in children’, CM2009. The Sixth International Conference on Condition Monitoring and Machinery Failure Prevention Technologies, June 2009; 138
LSI2005SusannahFlemingS. Fleming and L. Tarassenko, 'A Comparison of Signal Processing Techniques for the Extraction of Breathing Rate from the Photoplethysmogram', International Journal of Biomedical Sciences, 2(4):232-236. 2007
LSI2005SusannahFlemingS. Fleming and L. Tarassenko, 'Method and apparatus for measuring breathing rate' (patent pending)
LSI2005SusannahFlemingS. Flemming. '...or meningitis?' Runner-up prize at the British Science Festival's *perspectives* poster competition, 2009. 
LSI2005SusannahFlemingS. Fleming.  Royal Academy Research Student Development Fellowship 2008
LSI2005SusannahFlemingS. Fleming.  Institution of Engineering and Technology William James Award 2008
LSI2005EleniGiannoulatouEleni Giannoulatou, Christopher Yau, Christopher C. Holmes, “Bayesian Mixture Model Clustering for CNV Calling”, Poster Presentation at the 5th Conference of the Eastern Mediterranean Region of the International Biometric Society, Istanbul, Turkey, May 20
LSI2005AdrianGrovesA.R. Groves, M.W. Woolrich, 'Combined Spatial and Biophysical Gaussian process prior for fMRI analysis', 14th Annual Meeting of the Organization for Human Brain Mapping, 2008.
LSI2005AdrianGrovesAR Groves, MA Chappell, MW Woolrich, 'Gaussian process prior for combining spatial regularization with fixed biophysical priors', 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, June 2009.
LSI2005AdrianGrovesA. R. Groves, T. T. Liu, and M. W. Woolrich ‘Bayesian inference of multi-modal perfusion FMRI data’ 16th Meeting of the International Society for Magnetic Resonance in Medicine, ISMRM, Berlin, May 19-24th, 2007.
LSI2005AdrianGrovesAR Groves, LT Hunt, TEJ Behrens, MW Woolrich, 'Multivariate Bayesian Decoding of Multiple States', 15th Annual Meeting of the Organization for Human Brain Mapping, San Francisco, June 2009.
LSI2005AdrianGrovesA.R. Groves, M.W. Woolrich, 'Fast Bayesian nonlinear model fitting for analysis of simultaneous BOLD and ASL data', 14th Annual Meeting of the Organization for Human Brain Mapping, 2008.
LSI2005AdrianGrovesM.A. Chappell, A.R. Groves, B. Whitcher, M.W. Woolrich, 'Variational Bayesian Inference for a Nonlinear Forward Model' IEEE Trans. Sig. Proc. 57:1 223-236, 2009.
LSI2005MiklosGyongyS. Duncan, M. Gyongy ‘Using the EM algorithm to estimate the disease parameters for smallpox in 17th century London’ IEEE International Conference in Control Applications, 2006
LSI2005AnnHarveyAK Harvey, HR Cornell, PA Hulley, LE Cochlin, U Tirlapur, Z Cui, Sir M Brady, MS Thompson. Functional Imaging of Extracellular Matrix. British Society for Matrix Biology. 14-16 June, London 2009
LSI2005AnnHarveyAK Harvey, MS Thompson, HR Cornell, PA Hulley, LE Cochlin, U Tirlapur, Z Cui, Sir M Brady. Functional Imaging of Tendon for Improved Tissue Assessment. Movement Biomechanics and Sport, European Society of Biomechanics Workshop. 7-9 June, ETH Zurich 2009
LSI2005AnnHarveyT. Szilagyi, A. K. Harvey, Sir M. Brady, L. E. Cochlin, and N. Joshi (2010). Quantitative analysis of tendon ecm damage using MRI. Rotterdam, The Netherlands. IEE ISBI
LSI2005AnnHarveyA.K. Harvey, M.S. Thompson, L. Cochlin, P.A. Raju, Z. Cui, H. Cornell, P. Hulley, M. Brady, 'Functional Imaging Of Tendon' MIUA, Dundee, Scotland. 2008 (Honourable menetion for presentation)
LSI2005AnnHarveyA. K. Harvey, M. S. Thompson, Z. Cui, and Sir M. Brady (2009). Functional imaging of tendon for improved tissue assessment. ETH, Zurich, Switzerland. Proc. Move. Biomech. Sport ESB Workshop. 51-52.
LSI2005AnnHarveyG. D. Mitsis, A. K. Harvey, S. Dirckx, S. D. Mayhew, R. Rogers, I. Tracey, R. G. Wise, K. T. S. Pattinson (2008). Modeling of dynamic CO2 reactivity in the human brainstem using BOLD fMRI. Athens, Greece. IEEE Bioinf. Bioeng. 8:4696667
LSI2005AnnHarveyA. K. Harvey, T. Szilágyi, Sir M. Brady, M S. Thompson, and N. Joshi (2010). Curvatures with uncertainties derived in conformal space to characterize tendon microstructure. Buenos Aires, Argentina. IEEE EMBC.
LSI2005AnnHarveyW. Po, C. Kelly, A. K. Harvey, Q. Naseer, R. Muschel and Sir M. Brady (2010). Quantitative Analysis of Tumour Vascular Structure After Drug Treatment. Buenos Aires, Argentina. IEEE EMBC.
LSI2005AnnHarveyJ. C. W. Brooks, A. K. Harvey, K. T. S. Pattinson, M. Jenkinson, R. G. Wise (2008). Improved physiological noise modelling for brainstem functional imaging. Proc. ISMRM 16:2452.
LSI2005AnnHarveyKTS Pattinson, GD Mitsis, AK Harvey, S Jbabdi, S Dirckx, SD Mayhew, R Rogers, I Tracey, RG Wise. Determination of the human brainstem respiratory control network and its cortical connections in vivo using functional and structural imaging. NeuroImage, 200
LSI2005AnnHarveyK. T. S. Pattinson, G. D. Mitsis, A. K. Harvey, S. Jbabdi, S. Dirckx, S. D. Mayhew, D. H. Hoar, R. Rogers, I. Tracey, R. G. Wise (2008). Imaging structure and function of respiratory control in the human brainstem. Brit. J. Anaes. 100:582-583
LSI2005AnnHarveyA. K. Harvey, H. R. Cornell, P. A. Hulley, L. E. Cochlin, P. A. Raju, Z. Cui, Sir M. Brady, and M. S.Thompson (2009). Functional imaging of tendon extracellular matrix. Br. Soc. Mat. Biol. P078.
LSI2005AnnHarveyG. D. Mitsis, K. T. S. Pattinson, A. K. Harvey, S. Dirckx, S. D. Mayhew, D. H. Hoar, R. Rogers, I. Tracey, R. G. Wise (2007). Modelling of dynamic CO2 reactivity in the human brainstem using BOLD FMRI. Proc. Hum. Br. Map. 13:327. NeuroImage 36 sup. 1:327.
LSI2005AnnHarveyA. K. Harvey, M. S. Thompson, Z. Cui, and Sir M. Brady (2009). Quantitative modelling of tendon second harmonic images. London, UK. Proc. MIUA 13:259-263.
LSI2005AnnHarveyK. T. S. Pattinson, G. D. Mitsis, A. K. Harvey, S. Dirckx, S. D. Mayhew, D. H. Hoar, R. Rogers, I. Tracey, R. G. Wise (2007). Natural fluctuations in CO2 induce low frequency variation in the BOLD signal, in the human brainstem. Proc. ISMRM 15:614.
LSI2005RichardMannReece, S, Mann, R., Rezek, I., Roberts, S. Gaussian Process Segmentation of Co-Moving Animals, Bayesian Inference and Maximum Entropy Methods in Proceedings of the 30th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science an
LSI2005RichardMannMann, R., Freeman, R., Osborne, M., Garnett, R., Armstrong, C., Meade, J., Biro, D., Guilford, T., Roberts, S., Gaussian Processes for Prediction of Homing Pigeon Flight Trajectories. Bayesian Inference and Maximum Entropy Methods in Science and Engineeri
LSI2005RichardMannHart, T., Mann, R., Pettorelli, N., Coulson, T. & Trathan, P.N. Behavioural switching in a central place forager: patterns of diving behaviour in the Macaroni Penguin (Eudyptes chrysolophus). Marine Biology, 2010
LSI2005TahirMansooriT. Maharaj, B. Rodriguez, G. Plank, A. Prassl, T. Mansoori, V. Grau, P. Kohl, D.J. Gavaghan, N. Trayanova ‘Shock-induced virtual electrodes in a micro-anatomically accurate wedge model’ Annual Scientific Sessions Meeting Abstracts2007; P01-12–Heart Rhyth
LSI2005TahirMansooriT. Mansoori, V. Grau, R. Burton, G. Plank, P. Kohl and D.J. Gavaghan ‘Spatial Localization of Heterogeneous Cell Types and Fibre Orientations in Computational Cardiac Models’, ICT Review, Oxford, UK, 2006
LSI2005TahirMansooriT. Mansoori, G. Plank, R. Burton, J. Schneider, D.J. Gavaghan, P. Kohl, V. Grau ‘High Resolution Cardiac Computational Mesh Generation using MRI and Histology’ British Russian Young Scientist Workshop, Yekaterinburg, Russia, 2007.
LSI2005TahirMansooriT. Mansoori, V. Grau, P. Kohl and CCLRC Grid Applications Group ‘Collaborative Visualisation of Histo-Anatomical Computer Models of the Heart’, SuperComputing06: International Conference on High Performance Computing, Networking and Storage, Florida, USA,
LSI2005TahirMansooriG. Picton, R. Burton, T. Mansoori, P. Kohl ‘Presence of Caveolae in Rabbit Ventricular Myocytes at 0 h and 8 h after Isolation’ British Russian Young Scientist Workshop, Yekaterinburg, Russia, 2007. 
LSI2005TahirMansooriT. Mansoori ‘Physiology, Structure and Function from Medical Images of the Heart’ 15th Northern Cardiovascular Research Group Meeting, Manchester, 2007.
LSI2005RobinRyderR.J. Ryder and G.K. Nicholls, 'Modelling and fitting rate heterogeneity', 18th International Conference on Historical Linguistics, Montreal, Canada, August 2007
LSI2005RobinRyderR. Ryder ‘Reconstructing history using language structure’ at The Divergence of Languages: Mathematical Modelling and Estimation Workshop, Oxford, 2006
LSI2005RobinRyderR. J. Ryder, 'Phylogenetic methods for linguistic data', launch of the Indo-European Case and Argument Structure in a Typological Perspective project, Bergen, Norway, August 2008
LSI2005YusdiSantosoY. Santoso, L.C. Hwang, and A.N. Kapanidis. Single molecule gel electrophoresis for studying RNAP-DNA open complex dynamics. UK RNA Polymerase workshop. Bristol, April 2009.
LSI2005YusdiSantosoY. Santoso, M. Heilemann, L.C. Hwang, S. Wigneshweraraj, M. Buck, A.N. Kapanidis. Single molecule fluorescence study of the σ54-dependent transcription initiation. Biophysical Society meeting. Long Beach, February 2008.
LSI2005YusdiSantosoY. Santoso, L.C. Hwang, and A.N. Kapanidis. Single molecule gel electrophoresis:a novel method for studying biomolecular dynamics. 14th International Workshop on "Single Molecule Spectroscopy and Ultra Sensitive Analysis in the Life Sciences". Berlin, Sep
LSI2005YusdiSantosoY. Santoso, L. Le Reste, A.N. Kapanidis. Zinc-mediated Oligomerisation of DNA. 6th European Biophysics Congress. London, July 2007.
LSI2005YusdiSantosoTorella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN, Identifying molecular dynamics in single-molecule FRET experiments with Burst Variance Analysis. Biophysical Journal 2011; 100 (6), pp.1568-1577.
LSI2005YusdiSantosoSantoso Y, Torella J P, Kapanidis AN, Characterizing single-molecule FRET dynamics with Probability Distribution Analysis. ChemPhysChem 2010; 11 (10), pp 2209-2219.
LSI2005YusdiSantosoCordes T, Santoso Y, Tomescu AI, Gryte K, Hwang LC, Camara B, Wigneshweraraj S, Kapanidis AN, Sensing DNA opening in transcription using quenchable FRET. Biochemistry, 2010; 49, pp 9171-9180.
LSI2005YusdiSantosoY. Santoso, L.C. Hwang, L. Le Reste, and A.N. Kapanidis. Red light, green light: probing single molecules using alternating-laser excitation. Biochem. Soc. Trans., 36(Pt 4):738–744, Aug 2008.
LSI2005YusdiSantosoY. Santoso, C.M. Joyce, O. Potapova, L. Le Reste, J. Hohlbein, J.P. Torella, N.D.F. Grindley, and A.N. Kapanidis. Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proc. Natl. Acad. Sci. U. S. A., 107(2):715–720, 2010.
LSI2005YusdiSantosoJ.R. Thompson, A.J. Heron, Y. Santoso, M.I. Wallace. Enhanced stability and fluidity in droplet on hydrogel bilayers for measuring membrane protein diffusion. Nano Letters, 7 (12):3875–3878, 2007.doi: 10.1021/nl071943y.
LSI2005YusdiSantosoY. Santoso and A.N. Kapanidis. Probing Biomolecular Structures and Dynamics of Single Molecules Using In-Gel Alternating-Laser Excitation. Anal. Chem., 81(23):9561–9570, 2009.
LSI2005YusdiSantosoNicholas Kurti prize - Dept of Physics, Oxford (2009)
LSI2005YusdiSantosoEPA Cephalosporin scholarship - Linacre College, Oxford (2007-2009)
LSI2005DanieleSelmiD.N. Selmi, H. Attrill, R.J.C. Gilbert, A. Watts & A.J. Turberfield, “GPCR ligand binding studied by cryo-electron microscopy on DNA templates”. Under second round of review as an Article for Nature (2010)
LSI2005DanieleSelmiD.N.Selmi & A.J.Turberfield: Patent pending
LSI2005DanieleSelmiJunior Research Fellowship at St-Cross college, starting in October for 3-5 years
LSI2005NickWuProceedings of the Oxford University Computing Laboratory Student Conference 2009 Programme Co−Chairs: Lu Feng‚ John Lyle and Nicolas Wu
LSI2005NickWuTowards Formally Templated Relational Database Representations in Z
Nicolas Wu and Andrew Simpson In Proceedings of the Second International Conference on Abstract State Machines‚ Alloy‚ B and Z (ABZ 2010). Vol. 5977 of Lecture Notes in Computer Science. Pages 363−376. Springer−Verlag. 2010.
LSI2004AvigailAgamThomas M Keane, Leo Goodstadt, Petr Danecek, Michael A White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka
LSI2004AvigailAgamChristoffer Nellåker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting, The genomic landscape shaped by selection on transposable elements across 18 mouse strains, Geno
LSI2004AvigailAgamAgam A, Yalcin B, Bhomra A, Cubin M, Webber C, et al. (2010) Elusive Copy Number Variation in the Mouse Genome. PLoS ONE 5(9): e12839
LSI2004RehanAliAli R, Gooding M, Christlieb M, Brady JM, "Advanced phase-based segmentation of multiple cells with brightfield microscopy", Proceedings of the IEEE Symposium on Biomedical Imaging, May 2008, pp181-184
LSI2004RehanAliAli R, Szilagyi T, Gooding M, Hussien K, Christlieb M ,Vojnovic B, Brady JM, "Automatic nucleus segmentation of adherent cells from brightfield microscopy images", Proceedings of the BMVA Symposium on Microscopy Image Analysis, April 2010
LSI2004RehanAliAli R, Gooding M, Christlieb M, Brady JM, "Phase-based methods for segmentation and registration of brightfield microscope images of biological cells", Proceedings of the Medical Image Understanding and Analysis Conference (MIUA), Dundee, July 2008, pp159
LSI2004RehanAliOral: "Sensitivity analysis of a three compartment model used in PET tracer kinetic modelling", Ali R, Schottlander D, Brady JM, MIAS-IRC Conference, Oxford, Sept 2006
LSI2004RehanAliOral: "RNAi and Image Analysis", Ali R, RNAi2008 Conference, St. Annes College, Oxford, March 2008
LSI2004RehanAliOral: "Development and validation of a simulated human torso dynamic FHBG-PET dataset", Ali R, Schottlander D, Brady JM, MIAS-IRC PET Meeting, Manchester, Feb 2006
LSI2004RehanAliOral: Segmentation of Single Cancer Cells for the Evaluation of Morphological Evolution", Ali R, Petroudi S, Brady JM, IEEE EMBS Student Club on Cell Microscopy, Linz, Austria, May, 2006
LSI2004RehanAliAli R, Szilagyi T, Gooding M, Christlieb M, Brady JM, "On the use of low pass filters for image processing with inverse laplacian models", Journal of Mathematical Imaging and Vision Vol 43.2 pp 156-165(2012)
LSI2004RehanAliAli R, Gooding M, Szilagyi T, Christlieb M, Brady JM, "Automatic segmentation of adherent biological cell boundaries and nuclei from brightfield microscopy images", Machine Vision and Applications, DOI 10.1007/s00138-011-0337-9 (2011)
LSI2004RehanAliPoster: "PETParams: An on-line database of PET tracer studies", Ali R, Schottlander D, Brady JM, American Molecular Imaging Conference, Orlando, Florida, March, 2006
LSI2004RehanAliPoster: "Using mathematical modelling to gain new insights into how tumour cells respond to hypoxia-selective PET tracers", Ali R, Kelly C, DiSouza S, Fletcher A, Brady JM, Christlieb M, National Cancer Research Institute (NCRI), Birmingham, October 2009
LSI2004RehanAliPoster: "Using mathematical modelling to investigate the mechanisms regulating hypoxia-mediated DNA damage response", Ali R, Bencocova Z, Pires I, Fletcher A, Christlieb M, Byrne H, Brady JM, Hammond E, National Cancer Research Institute (NCRI), Birmingha
LSI2004RehanAliPoster: "Advanced microscope-based cytometry using brightfield image analysis", Ali R, Gooding M, Bentin E, Christlieb M, Brady JM, National Cancer Research Institute (NCRI), Birmingham, October 2008, supported by the Matt's Trust Fund for Cancer
LSI2004RehanAliPoster: "Phase-Based Segmenation of Cells with Brightfield Microscopy", Ali R, Gooding M, Christlieb M, Brady JM, EPSRC Student Conference in Edinburgh, June 2007
LSI2004RehanAliPoster: "Sensitivity analysis of a three compartment model used in PET tracer kinetic modelling", Ali R, Schottlander D, Yau C, Brady JM, American Molecular Imaging Conference, Orlando, Florida, March, 2006
LSI2004RehanAliPoster: "Development and validation of a simulated human torso dynamic FHBG-PET dataset", Ali R, Schottlander D, Brady JM, American Molecular Imaging Conference, Orlando, Florida, March, 2006
LSI2004RehanAliLinacre Travel Grant
LSI2004RehanAliVolcoTech Inc., director and consultant, 2012+
LSI2004RehanAliBell Biosystems Inc., consultant, 2011+
LSI2004KatherineAllenAllen, K., Joshi, N., Noble, J.A.: Tramline and NP windows estimation for enhanced unsupervised retinal vessel segmentation. In: IEEE International Symposium on Biomedical Imaging: Nano to Macro, ISBI. (2011) 1387-90. [doi: 10.1109/ISBI.2011.5872659]
LSI2004LukeBeaumontButtrick GJ, Beaumont LM, Leitch J, Yau C, Hughes JR, Wakefield JG. ‘Akt regulates centrosome migration and spindle orientation in the early Drosophila melanogaster embryo.’ J Cell Biol. 2008 Feb 11;180(3):537-48.
LSI2004KatieFisher2007: BSCB-BSDB Spring Meeting, Edinburgh. K. H. Fisher, J. R. Hughes, R. Saeed, C. Deane, J. G. Wakefield. “Identification and Investigation of Microtubule Associated Proteins using Bioinformatics.”
LSI2004KatieFisher2007: 41st American Society for Cell Biology Meeting, Washington DC. K. H. Fisher, J. R. Hughes, R. Saeed, C. Deane, J. G. Wakefield. “Identification and Investigation of Microtubule Associated Proteins using Bioinformatics.”
LSI2004KatieFisherBSCB-BSDB Spring Meeting, Warwick. Hughes, J. R*, Meireles A.M.*, Fisher K.H.*, Garcia A., Antrobus P.R., Wainman A., Zitzmann N, Deane C., Ohkura H. and Wakefield J.G. “A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis.” * Jo
LSI2004KatieFisherHughes, J. R*, Meireles A.M.*, Fisher K.H.*, Garcia A., Antrobus P.R., Wainman A., Zitzmann N, Deane C., Ohkura H. and Wakefield J.G. A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis. PLoS Biology, 2008, 6(4), e98. Joint first au
LSI2004KatieFisherPatel P.C., Fisher K.H., Yang E.C., Deane C.M., Harrison R.E. Proteomic analysis of microtubule-associated proteins during macrophage activation. Molecular and Cellular Proteomics. 2009, 8(11), 2500 – 2514. (IF: 7.4)
LSI2004KatieFisherASCB Travel grant awarded to attend conference: 41st American Society for Cell Biology Meeting, Washington DC, 2007.
LSI2004KatieFisherBSCB Travel grant awarded to attend conference: BSCB-BSDB Spring Meeting, Edinburgh, 2007.
LSI2004KatieFisherPoster prize : 2nd place – Awarded by British Society of Cell Biology (BSCB)
LSI2004AlexanderFletcherJoe Pitt-Francis, Pras Pathmanathan, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alexander G. Fletcher, Gary R. Mirams, Philip Murray, James M. Osborne, Alex Walter, S. Jon Chapman, Alan Garny, Ingeborg M.M. van Leeuwen, Philip K. Maini, Blanca Rod
LSI2004AlexanderFletcherP. Pathmanathan, J. Cooper, A.G. Fletcher, G.R. Mirams, L. Momtahan, P. Murray, J. Osborne, J. Pitt-Francis, A. Walter and S.J. Chapman (2009). A computational study of discrete mechanical tissue models. Phys. Biol., 6:036001.
LSI2004AlexanderFletcherA.G. Fletcher, C.J. Breward and S.J. Chapman (2012). Mathematical modelling of monoclonal conversion in the colonic crypt. J. Theor. Biol. 300:118-133.
LSI2004AlexanderFletcherOctober 2004: Light Senior Scholarship (St Catherine's College, University of Oxford)
LSI2004KateHibbsM. M. Knight, K. Hibbs, S. R. Roberts, D. A. Lee and D. L.Bader. Cyclic preconditioning mediates chondrocytes calcium signaling in unstrained and compressed agarose constructs. 50th Annual Meeting of the Orthopaedic Research Society, San Francisco, March
LSI2004PhillipMurrayContributed talk at Annual meeting of the Society of Mathematical Biology, San Jose.
LSI2004PhillipMurrayInvited speaker at ZIH, Technische Universitat Dresden.2007
LSI2004PhillipMurrayInvited speaker at the Center for Modelling and Simulation in the Biosciences (BIOMS), Heidelberg.
LSI2004PhillipMurrayInvited speaker at the Indian Statistical Institute, Calcutta.
LSI2004PhillipMurrayA. G. Fletcher, G. R. Mirams, P. J. Murray, A. Walter, J. W. Kang, K. H. Cho, P. K., Maini, and H. M. Byrne. Multiscale modeling of colonic crypts and early colorectal cancer. Multiscale Cancer Modeling, 2010.
LSI2004PhillipMurrayP. J. Murray, C. M. Edwards, M. J. Tindall, and P. K. Maini. From a discrete to a continuum model of cell dynamics in one dimension. Physical Review E, 80(3):031912, 2009. *Selected for the October 1, 2009 issue of Virtual Journal of Biological Physics Re
LSI2004PhillipMurrayPrize for best student presentation at the British Applied Mathematics Colloquium, Bristol.
LSI2004BenPetersDaniel Axford, Jason J. Davis, Nan Wang, Dongxu Wang, Tiantian Zhang, Jianwei Zhao, and Ben Peters ‘Molecularly Resolved Protein Electromechanical Properties’ J. Phys. Chem. B, 2007, 111 (30), pp 9062–9068
LSI2004ZhanSuBurton et al ‘Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants’ Nature Genetics 39, 1329 - 1337 (2007)
LSI2004RanjitVijayan
LSI2004RanjitVijayanVijayan, R. , Plested, A.J.R., Mayer, M.L. , Biggin, P.C. ‘Selectivity and cooperativity of modulatory ions in a neurotransmitter receptor’ Biophysical Journal
Volume 96, Issue 5, 2009, Pages 1751-1760
LSI2004RanjitVijayanVijayan, R., Sahai, M.A., Czajkowski, T., Biggin, P.C. ’ A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors’ Physical Chemistry Chemical Physics
LSI2004RanjitVijayanVijayan, R., Biggin, P.C. ‘Conformational preferences of a 14-residue fibrillogenic peptide from acetylcholinesterase’ Biochemistry Volume 49, Issue 17, 4 May 2010, Pages 3678-3684
LSI2004Chze LingWeeInteractions between a voltage sensor and a toxin via multiscale simulations. Wee CL, Gavaghan D, Sansom MS. Biophys J. 2010 Apr 21;98(8):1558-65
LSI2004Chze LingWeePrize Scholarship, Merton College
LSI2004AvigailAgamEPSRC PhD Plus Award to extend the research arising from my D.Phil.
LSI2004RehanAli"Using mathematical modelling to investigate the mechanisms regulating hypoxia-mediated DNA damage response", R. Ali, Z. Bencocova, I. Pires, A. Fletcher, M. Christlieb, H. Byrne, J. M. Brady, E. Hammond, National Cancer Research Institute (NCRI), Birming
LSI2004RehanAliR. Ali ‘PET Simulation Data Development and Validation’ Focus Meeting of the MIAS-IRC on Positron Emission Tomography (PET), Manchester, Feb 2006.
LSI2004RehanAliR. Ali, D. Schottlander, M. Brady ‘PETParams: An on-line database of PET tracer studies’ American Molecular Imaging Conference’ Orlando, Florida, March, 2006
LSI2004RehanAli"Using mathematical modelling to gain new insights into how tumour cells respond to hypoxia-selective PET tracers", R. Ali, C. Kelly, S. DiSouza, A. Fletcher, J. M. Brady, M. Christlieb, National Cancer Research Institute (NCRI), Birmingham, October 2009
LSI2004RehanAliR. Ali, D. Schottlander, C. Yau, M. Brady ‘Sensitivity analysis of a three compartment model used in PET tracer kinetic modelling’ American Molecular Imaging Conference, Orlando, Florida, March, 2006
LSI2004RehanAliR. Ali, D. Schottlander, C. Yau and M. Brady, ‘Sensitivity analysis of a three compartment model used in PET tracer kinetic modelling’ American Molecular Imaging Conference, March 2006.
LSI2004RehanAli"Advanced microscope-based cytometry using brightfield image analysis", R. Ali, M. Gooding, E. Bentin, M. Christlieb, J.M. Brady, National Cancer Research Institute (NCRI), Birmingham, October 2008, supported by the Matt’s Trust Fund for Cancer
LSI2004RehanAli"Advanced Phase-Based Segmenation of Multiple Cells with Brightfield Microscopy", R. Ali, M. Gooding, M. Christlieb, J.M. Brady, IEEE Symposium on Biomedical Imaging (ISBI), Paris, France, May 2008, supported by the Linacre House Trust
LSI2004RehanAliR. Ali, S. Petroudi, C. Yau, J.M. Brady ‘Segmentation of single cancer cells for the evaluation of morphological evolution’ IEEE EMBS Student Workshop on Medical and Microscopy Image Analysis, May 2006.
LSI2004RehanAliR. Ali, M. Gooding, M. Christlieb, M. Brady ‘Phase-Based Segmentation of Cells from Brightfield Microscopy’ IEEE Symposium on Biomedical Imaging, Washington D.C., April 2007
LSI2004RehanAliR. Ali, D. Schottlander, M. Brady ‘Development and validation of a simulated human torso dynamic FHBG-PET dataset’ American Molecular Imaging Conference, Orlando, Florida, March, 2006
LSI2004RehanAliR. Ali (on behalf of C. White) ‘Hypoxia: From Modeling Molecules to Molecular Imaging’ Focus Meeting of the MIAS-IRC on Positron Emission Tomography (PET), Manchester, 2006
LSI2004RehanAliA. Candler, M. Featherstone, R. Ali, L. Maloney, A. Watts and W. B. Fischer, ‘Computational analysis of mutations in the transmembrane region of Vpu from HIV-1’ Biochimica et Biophysica Acta 1716(1) 1-10, 2005
LSI2004RehanAliV. Lemaitre, R. Ali, C. G. Kim, A. Watts and W. B. Fischer, ‘Interaction of amiloride and one of its derivatives with Vpu from HIV-1: a molecular dynamics simulation’ FEBS Letters 563 (1-3) 75-81, 2004
LSI2004KatherineAllenK. Allen, C. Yau and J. A. Noble. ‘A recursive stochastic vessel segmentation framework that robustly handles bifurcations’, Medical Image Understanding and Analysis, Dundee, Scotland, 2008.
LSI2004KatherineAllenJ. Bath, S. J. Green, K. Allen, A. J. Turberfield. ‘Mechanism for a Directional, Processive and Reversible DNA Motor’, Small, 19 March 2009. doi:10.1002/smll.200900078.
LSI2004TomBilyardT. Pilizota, T. Bilyard, F. Bai, M. Futai, H. Hosokawa and R.M. Berry ‘A programmable optical angle clamp for rotary molecular motors’ Biophys. J. 93, 264–275, 2007
LSI2004JonathanCooperJ. Cooper & S. McKeever ‘A Haskell interpreter for CellML’ Proceedings of the 12th ACM SIGPLAN International Conference on Functional Programming, Freiburg, Germany October 2007 pp 247-250
LSI2004JonathanCooperJ. Cooper, S. McKeever and A. Garny ‘On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations’ Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation, 12
LSI2004JonathanCooperJonathan Cooper and Steve McKeever. 'Experience Report: A Haskell interpreter for CellML'. Pages 247—250. New York, NY, USA. October, 2007. ACM Press.
LSI2004JonathanCooperUse of CellML in Chaste. CellML Workshop, 2009
LSI2004JonathanCooperImplementing a ToolKit for the VPH Community. International Conference on Computational Bioengineering, 2009
LSI2004JonathanCooperToward a VPH/Physiome ToolKit. Garny, A.; Cooper, J.; Hunter, P.J. WIREs Sys Bio Med, 2(2):134-147, 2009
LSI2004JonathanCooperP Pathmanathan, J Cooper, A Fletcher, G Mirams, P Murray, J Osborne, J Pitt-Francis, A Walter and S J Chapman. 'A computational study of discrete mechanical tissue models'. Physical Biology. Vol. 6. No. 3. 2009.
LSI2004JonathanCooperAlan Garny, Jonathan Cooper and Peter J. Hunter. 'Toward a VPH/Physiome ToolKit', Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009.
LSI2004JonathanCooperIMM van Leeuwen, GR Mirams, A Walter, A Fletcher, P Murray, J Osborne, S Varma, SJ Young, J Cooper, B Doyle, J Pitt-Francis, L Momtahan, P Pathmanathan, JP Whiteley, SJ Chapman, DJ Gavaghan, OE Jensen, JR King, PK Maini, SL Waters, HM Byrne, ‘An integrati
LSI2004JonathanCooperAlan Garny, David Nickerson, Jonathan Cooper, Rodrigo Weber dos Santos, Steve McKeever, Poul Nielsen and Peter Hunter. 'CellML and Associated Tools and Techniques'. Phil Trans Roy Soc A. Vol. 366. No. 1878. Pages 3017—3043. 2008.
LSI2004JonathanCooperJ. Cooper and S. McKeever ‘A model-driven approach to automatic conversion of physical units’, Software: Practice and Experience, 38(4):337-359. 2007. doi:10.1002/spe.828.
LSI2004JonathanCooperJoe Pitt-Francis, Miguel O. Bernabeu, Jonathan Cooper, Alan Garny, Lee Momtahan, James Osborne, Pras Pathmanathan, Blanca Rodriguez, Jonathan P. Whiteley, David J. Gavaghan, ‘Chaste: using agile programming techniques to develop computational biology sof
LSI2004JonathanCooperThe Virtual Physiological Human ToolKit. Cooper, J.; Cervenansky, F.; De Fabritiis, G.; Fenner, J.; Friboulet, D.; Giorgino, T.; Manos, S.; Martelli, Y.; Villà-Freixa, J.; Zasada, S. UK e-Science All Hands Meeting, 2009
LSI2004KatieFisherK.H. Fisher ‘Investigating Microtubule Associated Proteins in Drosophila using Bioinformatics’ BSCB, 29 Mar - 1 Apr 2007
LSI2004KatieFisherJ. R. Hughes, A. M. Meireles, K. H. Fisher, A. Garcia-Alonso, P. R. Antrobus, A. Wainman, N. Zitzmann, C. Deane, H. Ohkura and J. G. Wakefield, 'A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis', PLoS Biology, 6(4):e98, 2008. doi:
LSI2004KatieFisherK. H. Fisher, C. M. Deane, J. G. Wakefield, 'The functional domain grouping of microtubule associated proteins', Communicative & Integrative Biology. 1: 47-50. 2008
LSI2004KatieFisherM.R. de Planque, G.P. Mendes, M. Zagnoni, M.E. Sandison, K.H. Fisher, R.M. Berry, A. Watts, H. Morgan, ‘Controlled delivery of membrane proteins to artificial lipid bilayers by nystatin-ergosterol modulated vesicle fusion’ IEE Proc Nanobiotechnol. 153(2),
LSI2004KatieFisherA. M. Meireles, K. H. Fisher, N. Colombie, J. G. Wakefield, H. Ohkura, 'Wac: a new Augmin subunit required for chromosome alignment, but not for acentrosomal microtubule assembly in female meiosis' J. Cell Biol. 184(6), 777-784. 2009. doi: 10.1083/jcb.200
LSI2004AlexanderFletcherA. Fletcher ‘Mathematical modelling of the role of HIF-1 in tumour growth’ 7th International Conference on Systems Biology, Yokohama, Japan, 8-11 October 2006 (Poster Presentation) [One of six best abstracts: student category]
LSI2004KateHibbsK. Hibbs, J. M. Mari, E. Stride, R. J. Eckersley, A. Noble and M.-X. Tang, 'Nonlinear propagation of ultrasound through microbubble clouds: A novel numerical implementation' IEEE International Ultrasonics Symposium, New York, October 2007
LSI2004KateHibbsK. Hibbs, R. J. Eckersley, A. Noble, and M.-X. Tang, ‘Ultrasound phase velocities in SonoVue as a function of pressure and bubble concentration’ IEEE International Ultrasonics Symposium, Rome, September 2009.
LSI2004KateHibbsJ.-M. Mari, K. Hibbs, M.-X. Tang, 'A nonlinear ultrasonic scattering approach for microbubble concentration quantification' 29th Annual International Conference of the IEEE EMBS Society, Lyon, August 2007
LSI2004KateHibbsJ.-M. Mari, K. Hibbs, E. Stride, R. J. Eckersley, and M.-X. Tang, ‘An approximate nonlinear model for time gain compensation of amplitude modulated images of ultrasound contrast agent perfusion’ IEEE Transactions on Ultrasonics, Ferroelectrics, and Freque
LSI2004NicolasJeannequinN.A Jeannequin, J. Whiteley, Adaptivity for High Order Finite Element Simulations of Electrocardiological Models, Graduate student conference in numerical analysis, Oxford University Computing Laboratory, 2006
LSI2004NicolasJeannequinN.A Jeannequin, J. Whiteley, Adaptivity for High Order Finite Element Simulations of Electrocardiological Models, E.P.S.R.C. Doctoral Training Centre Student Workshop, Stratford-on-Avon, 2006
LSI2004NicolasJeannequinN.A. Jeannequin, J.P. Whiteley, Unstructured Spectral Elements and Time Adaptivity applied to the Bidomain Model, 20th Chemnitz Finite Element Method Symposium, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, J.P. Whiteley, Unstructured Spectral Elements applied to the Bidomain Model, International Conference of Numerical Analysis and Applied Mathematics, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, J. Whiteley, Adaptive Unstructured High Order Nodal Finite Elements applied to the Bidomain Equations, Conference Proceedings for Biennial Conference on Numerical Analysis, University of Dundee, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, Unstructured High Order Nodal Finite Elements to solve the Bidomain Equations, Conference Proceedings for the SANUM Conference, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, J.P. Whiteley Adaptive Unstructured High Order Nodal Finite Elements applied to the Bidomain Equations, Biennial Conference on Numerical Analysis, University of Dundee, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, J.P. Whiteley, Unstructured High Order Nodal Finite Elements to solve the Bidomain Equations, South African Society for Applied and Numerical Mathematics, University of Stellenbosch, 2007
LSI2004NicolasJeannequinN.A. Jeannequin, Time and Space Adaptivity for Parabolic Equations, Workshop on Computational and Numerical Analysis for Multiscale and Multiphysics Modelling, University of Sussex, 2005
LSI2004NicolasJeannequinN.A. Jeannequin, J.P. Whiteley, Unstructured Spectral Elements applied to the Bidomain Model, Conference Proceedings for the International Conference of Numerical Analysis and Applied Mathematics, American Institute of Physics Conference Proceedings, 2007
LSI2004PaulJenkinsP. Jenkins, R. Lyngsø and J. Hein. ‘How many transcripts does it take to reconstruct the splice graph?’ Lecture Notes in Computer Science: 6th international workshop, WABI, Zurich, Switzerland, September 2006. Proceedings, 103–114. Springer Berlin/Heidelb
LSI2004PaulJenkinsJenkins, P. A. (2012). Stopping-time resampling and population genetic inference under coalescent models. Statistical Applications in Genetics and Molecular Biology, 11(1): Art. 9
LSI2004PaulJenkinsJenkins, P. A. and Griffths, R. C. (2011). Inference from samples of DNA sequences using a two-locus model. Journal of Computational Biology, 18(1): 109-127
LSI2004PaulJenkinsJenkins, P.A. and Song, Y.S. (2009). Closed-form two-locus sampling distributions: accuracy and universality. Genetics, 183: 1087–1103.
LSI2004PaulJenkinsJenkins, P.A. and Song, Y.S. An asymptotic sampling formula for the coalescent with recombination. Annals of Applied Probability, 2010, Vol. 20, No. 3, 1005-1028
LSI2004PaulJenkinsR.C. Griffiths, P.A. Jenkins and Y. S. Song. ‘Importance sampling and the two-locus model with subdivided population structure’, Adv. Appl. Prob. 40(2):473-500, 2007. doi:10.1239/aap/1214950213.
LSI2004PaulJenkinsTessella Award for Best DTC Project in Bioinformatics (2005)
LSI2004GaryMiramsG. Mirams, H.M. Byrne, J.R. King 'A Lattice-Free Model of Early Colorectal Cancer' Society for Mathematical Biology, Annual Meeting, San Jose, USA, July 2007
LSI2004GaryMiramsJM Pitt-Francis, P Pathmanathan, MO Bernabeu, R Bordas, J Cooper, A Fletcher, GR Mirams, P Murray, J Osborne, A Walter, SJ Chapman, A Garny, IMM van Leeuwen, PK Maini, B Rodriguez, JP Whiteley, HM Byrne, DJ Gavaghan. (2009) Chaste: a test-driven approach
LSI2004GaryMiramsP Pathmanathan, J Cooper, A Fletcher, G Mirams, L Momtahan, P Murray, J Osborne, J Pitt-Francis, A Walter and SJ Chapman. (2009) A computational study of discrete mechanical tissue models. Physical Biology, 6(3), 036001.
LSI2004GaryMiramsGR Mirams, HM Byrne and JR King. (2010) A multiple timescale analysis of a mathematical model of the Wnt/beta-catenin signalling pathway. J. Mathematical Biology, 60(1), 131-160.
LSI2004PhillipMurrayMurray, P J and Edwards, C M and Tindall, M J and Maini, P K (2009) From a discrete to a continuum model of cell dynamics in one dimension. Physical Review E, 80 (3). 031912-1-031912-10.
LSI2004PhillipMurrayPitt-Francis J M, Pathmanathan P, Bernabeu, R Bordas, J Cooper, AG Fletcher, GR Mirams, P Murray, JM Osborne, A Walter, SJ Chapman, A Garny, I van Leeuwen, PK Maini, B Rodriguez, SL Waters, JP Whiteley, HM Byrne and DJ Gavaghan. Computer Physics Communica
LSI2004PhillipMurrayP Pathmanathan and J Cooper and A Fletcher and G Mirams and P Murray and J Osborne and J Pitt-Francis and A Walter and S J Chapman. A computational study of discrete mechanical
tissue models. Physical Biology, Vol. 6, No. 3, 2009
LSI2004JamesOsborneJ.M. Osborne, 'A Computational Framework for Simulating Multiphase Models of Tissue Growth.' SMB Annual Conference, Toronto Canada, August 2008
LSI2004JamesOsborneJ.M. Osborne ‘Towards a Generic Numerical Method for Simulating Avascular Tumour Growth in Three Dimensions’ SMB Annual Conference, San Jose, August 2007
LSI2004JamesOsborneJ.M. Osborne, “Multiscale modelling in systems biology.” Society for Mathematical Biology Conference, Vancouver, Canada. July 2009
LSI2004JamesOsborneJ.M. Osborne, “The effects of geometry and seeding strategies on tissues grown in a bioreactor” Society for Mathematical Biology Conference, Vancouver, Canada. July 2009
LSI2004JamesOsborne“A computational study of discrete mechanical tissue models.” Pathmanathan, P., Cooper, J., Fletcher, A., Mirams, G., Murray, P., Osborne, J. M., Pitt-Francis, J., Walter, A., and Chapman, S. J. (2009). Physical Biology, 6(3).
LSI2004JamesOsborne“Chaste: a test-driven approach to software development for biological modelling.” Pitt-Francis, J., Pathmanathan, P., Bernabeu, M. O., Bordas, R., Cooper, J., Fletcher, A. G., Mirams, G. R., Murray, P., Osborne, J. M., Walter, A., Chapman, J., Garny, A.,
LSI2004JamesOsborne“The influence of bioreactor geometry and the mechanical environment on engineered tissues.” Osborne, J, M., O'Dea, R., Whiteley, J. P., Byrne, H., and Waters, S. Journal of Biomechanical Engineering (Accepted awaiting publication)
LSI2004ZhanSuZ. Su, P. Donnelly, J. Marchini. A Bayesian multipoint allele sharing method for genome-wide studies. The American Society of Human Genetics Annual Meeting. 2007.
LSI2004ZhanSuC. Spencer*, Z. Su* and P. Donnelly and J. Marchini (2009) Designing Genome-Wide Association Studies: sample size, power, imputation and the choice of genotyping chip. PLoS Genet 5(5): e1000477. doi:10.1371/journal.pgen.1000477
LSI2004RanjitVijayanR. Vijayan, B. Iorga, and P.C. Biggin, ‘Computational approaches to ionotropic glutamate receptors’ Chapter in ‘Molecular Simulations and Biomembranes: From Biophysics to Function’ RSC Publishing (Accepted)
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Cation and anion modulatory sites in the ligand binding dimer interface of kainate receptors’, OXION Ion Channels Day, Oxford, UK, September 2007
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Selectivity and interaction of cation and anion modulatory sites in kainate receptors’ European Biophysics Congress, Genoa, Italy, July 2009. (British Biophysical Society travel award)
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘A simulation study of the ATD of ionotropic glutamate receptors’, 54th Annual Meeting of the Biophysical Society, San Francisco, USA, February 2010.
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Cation and anion modulatory sites in the ligand binding dimer interface of kainate receptors’, Bringing together biomolecular simulation and experimental studies, Manchester, UK, September 2007
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Steroids in the transmembrane region of nicotinic acetylcholine receptors - an in silico study’, 48th International Conference on the Bioscience of Lipids, Turku, Finland, September 2007.
LSI2004RanjitVijayanR.Vijayan and P.C. Biggin, ‘Ion modulatory sites in the ligand binding domain of kainate receptors’, Annual Meeting of the Biophysical Society, Long Beach, USA, January 2008.
LSI2004RanjitVijayanR. Vijayan, ‘Ion binding sites in glutamate receptors’, Young Modellers’ Forum, London, UK, November 2007 (Awarded a best talk prize)
LSI2004RanjitVijayanS. Amiri, M. Shimomura, R. Vijayan, H. Nishiwaki, M. Akamatsu, K. Matsuda, A.K. Jones, M.S.P. Sansom, P.C. Biggin, and D.B. Sattelle, ‘A role for Leu118 of loop E in agonist binding to the 7 nicotinic acetylcholine receptor’ Mol. Pharm. 73:1659-1667. 200
LSI2004RanjitVijayanM. Moroni, R. Vijayan, A. Carbone, R. Zwart, P.C. Biggin, and I. Bermudez, ‘Non-agonist binding subunit interfaces confer distinct functional signatures to the alternate stoichiometries of the 42 nicotinic receptor: an 4-4 interface is required for Zn
LSI2004RanjitVijayanR. Vijayan, A.J. R. Plested, M.L. Mayer, and P.C. Biggin, ‘Selectivity and cooperativity of modulatory ions in a neurotransmitter receptor’ Biophys. J. 96:1751-1760 2009.
LSI2004RanjitVijayanC. Chew, R. Vijayan, J. Chang, N. Zitzmann, and P.C. Biggin, ‘Determination of pore-lining residues in the Hepatitis C virus p7 protein’ Biophys. J. 96:L10-L12. 2009
LSI2004RanjitVijayanR. Vijayan, and P.C. Biggin, ‘A steroid in a lipid bilayer: localization, orientation, and energetics’ Biophys. J. 95:L45-L47. 2008
LSI2004RanjitVijayanA.J.R. Plested*, R. Vijayan*, P.C. Biggin, and M.L. Mayer, ‘Molecular basis of kainate receptor modulation by sodium’ Neuron 58:720-735. 2008 (* - Joint first author)
LSI2004RanjitVijayanR. Vijayan and P. C. Biggin. ‘Ion modulatory sites in the ligand binding domain of kainate receptors’, Department of Biochemistry DPhil poster exhibition, Oxford, June 2008. (Shared best poster prize)
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Computational studies of nicotinic acetylcholine receptors’, Engineering and Physical Sciences Research Council (EPSRC) national Doctoral Training Centre (DTC) conference, Stratford-upon-Avon, UK, September 2006 (Best poster p
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Ion modulatory sites in the ligand binding domain interface of kainate receptors’. Theory and applications of Computational Chemistry, Shanghai, China, September 2008. (Awarded a RCUK China award)
LSI2004RanjitVijayanR. Vijayan and P.C. Biggin, ‘Ion modulatory sites in the ligand binding domain interface of kainate receptors’, International Symposium on Membrane Transport and Communication, Frankfurt, Germany, November 2008. (Awarded an EMBNTrain fellowship)
LSI2004AlexanderWalterA.G. Fletcher, G.R. Mirams, P.J. Murray, A. Walter, J.-W. Kang, K.-H. Cho, P.K. Maini and H.M. Byrne Multiscale modeling of colonic crypts and early colorectal cancer, Multiscale Cancer Modeling
LSI2004AlexanderWalterA. Walter ‘Macroscale Modelling of Colorectal Cancer’ Theoretical Mechanics Seminar University of Nottingham, 2006
LSI2004AlexanderWalterPitt-Francis, J., Pathmanathan, P., Bernabeu, M. O., Bordas, R., Cooper, J., Fletcher, A. G., Mirams, G. R., Murray, P., Osborne, J. M., Walter, A., Chapman, S. J., Garny, A., van Leeuwen, I., Maini, P. K., Rodrguez, B., Waters, S. L., Whiteley, J. P., By
LSI2004AlexanderWalterP. Pathmanathan, J. Cooper, A. Fletcher, G. Mirams, L. Momtahan, P. Murray, J. Osborne, J. Pitt-Francis, A. Walter and S.J. Chapman. A computational study of discrete mechanical tissue models. Phys. Biol. 6 (2009) 036001.
LSI2004Chze LingWeeC.L. Wee, D. Bemporad, Z.A. Sands, A. Grottesi, M.S. Sansom, 'VSTx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers', Gordon Research Conferences (GRC) in Ion Channels, Tilton, NH, USA, 2006.
LSI2004Chze LingWeeBemporad D, Sands ZA, Wee CL, Grottesi A, Sansom MSP. VSTx1, a modifier of Kv channel gating, localizes to the interfacial region of lipid bilayers. Biochemistry (2006) 45:11844-55. doi:10.1021/bi061111z
LSI2004Chze LingWeeWee CL, Bemporad D, Sands Z, Gavaghan D, Sansom MSP. SGTx1, a Kv Channel Gating-Modifier Toxin, Binds to the Interfacial Region of Lipid Bilayers. Biophys. J. (2007) 92:L07-9. doi:10.1529/biophysj.106.098681
LSI2004Chze LingWeePongprayoon P, Beckstein O, Wee CL, Sansom MSP. Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate. PNAS (2009) 106:21614-8. doi: 10.1073/pnas.0907315106
LSI2004Chze LingWeeBond PJ, Wee CL, Sansom MSP. Coarse-Grained Molecular Dynamics Simulations of the Energetics of Helix Insertion into a Lipid Bilayer Biochemistry (2008) 47:11321-31. doi:10.1021/bi800642m.
LSI2004Chze LingWeeWee CL, Gavaghan D, Sansom MSP. Lipid Bilayer Deformation and the Free Energy of Interaction of a Kv Channel Gating-Modifier Toxin. Biophys J. (2008) 95:3816-26. doi:10.1529/biophysj.108.130971.
LSI2004Chze LingWeeWee CL, Balali-Mood K, Gavaghan D, Sansom MSP. The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations. Biophys. J. (2008) 95:1649-57. doi:10.1529/ biophysj.107.123190
LSI2004Chze LingWeeWee CL, Sansom MSP, Reich S, Akhmatskaya E. Improved Sampling for Simulations of Interfacial Membrane Proteins: Application of Generalized Shadow Hybrid Monte Carlo to a Peptide Toxin/Bilayer System. J. Phys. Chem. B (2008) 112:5710-5717.doi:10.1021/jp076
LSI2004Chze LingWeeD'Rozario RSG, Wee CL, Wallace EJ, Sansom MSP. The interaction of C60 and its derivatives with a lipid bilayer via molecular dynamics simulations. Nanotechnology (2009) 20:115102. doi: 10.1088/0957-4484/20/11/115102
LSI2004ChrisYauS. Colella, C. Yau, J. Taylor, G. Mirza, H. Butler, P. Clouston, A. S. Bassett, A. Seller, C. Holmes and J. Ragoussis, ‘QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data,’ Wellco
LSI2004ChrisYauC.C. Holmes and C. Yau ‘Bayesian Hidden Markov Models for Detecting Regions of Deletion and Duplication in the Human Genome using Illumina BeadChip Arrays’ Institute of Engineering and Technology Seminars on Signal Processing for Genomics, November 2006.
LSI2004ChrisYauC. Yau, S. Colella, D. Peiffer, J. Ragoussis and C. C. Holmes, Detecting Loss-of-Heterozygosity and Amplification events from Illumina SNP genotyping data in the presence of stromal contamination and intra-tumor heterogeneity. American Society Human Genet
LSI2004ChrisYauE. Giannoulatou, C. Yau, C.C. Holmes, J. Ragoussis, 'Statistical Model-based Normalisation of Illumina BeadArray SNP data' Genomics of Common Diseases, Wellcome Trust Conference Centre, Hinxton, UK, 7-10 July 2007
LSI2004ChrisYauE Giannoulatou, C Yau, S Colella, J Ragoussis, CC Holmes, "GenoSNP: a Variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.", Bioinformatics. 2008 Oct 1; 24(19):2209-14
LSI2004ChrisYauS. Colella, C. Yau, J. Taylor, G. Mirza, H. Butler, P. Clouston, A. S. Bassett, A. Seller, C. Holmes and J. Ragoussis, ‘Validation of the Infinium™ Whole Genome Genotyping assay for segmental aneuploidy profiling’ American Society of Human Genetics Annual
LSI2004ChrisYauC. Yau and J. G. Wakefield, ‘Quantitative analysis of chromosome dynamics in early Drosophila embryos’, Proceedings of the 2007 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Arlington, VA, USA, April 2007
LSI2004ChrisYauC. Yau and C. C. Holmes, 'Identifying copy number alterations and loss-of-heterozygosity in tumour samples from SNP genotyping data in the presence of stromal contamination and intra-tumour heterogeneity', International Biometric Conference, Dublin, 13 –
LSI2004ChrisYauE. Giannoulatou, C. Yau, S. Colella, J. Ragoussis and C. C. Holmes, 'GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.’ Bioinformatics. 24(19):2209-14. 2008
LSI2004ChrisYauYau, C. and Holmes, C.C. (2009) CNV discovery using SNP genotyping arraysy. Cytogenetic and Genome Research 123(1-4):307{312.
LSI2004ChrisYauC. Yau and C. C. Holmes, 'CNV discovery using SNP genotyping arrays', Cytogenetics and Genome Research. 123(1-4), 2008
LSI2004ChrisYauS. Colella, C. Yau, J. M. Taylor, G. Mirza, H. Butler, P. Clouston, A.S.Bassett, A. Seller, C. C. Holmes and J. Ragoussis, 'QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data'. Nu
LSI2003AdamAutonForce Modulation and Electrochemical Gating of Conductance in a Cytochrome, J. Phys. Cond. Mat. Vol 20 37 37412
LSI2003AdamAutonMolecularly Resolved Protein Electromechanical Properties, J. Phys. Chem. B Vol 111 30 9062-9068
LSI2003AdamAutonBoyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt M, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bus
LSI2003AdamAutonAuton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD Global distribution of genomic diversity underscores rich complex history of continental human population
LSI2003AdamAutonMolecularly Resolved Bioelectronics, Curr. Nanoscience, Vol 4 1 62-70
LSI2003AdamAutonHernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, 1000 Genomes Project, Sella G, Przeworski M ‘Classic selective sweeps were rare in recent human evolution’ Science (New York, N.Y.) 2011, 331(6019):920-4
LSI2003AdamAutonGao S, Giansanti MG, Buttrick GJ, Ramasubramanyan S, Auton A, Gatti M, Wakefield JG ‘Australian: a chromosomal passenger protein required specifically for Drosophila melanogaster male meiosis’ The Journal of Cell Biology [2008, 180(3):521-35]
LSI2003AdamAutonScanning Probe Analyses at the Bioelectronic Interface, Chapter in Engineering at the Bioelectronic Interface, RSC 2009
LSI2003MartinBishopBishop, M.J., P. Hales, G. Plank, D.J. Gavaghan, J. Scheider and V. Grau (2009) Comparison of rulebased and DTMRI-derived fibre architecture in a whole rat ventricular computational model. Poster presentation at Functional Imaging and Modelling of the Hea
LSI2003MartinBishopGibb, M. M.J. Bishop, R.A.B. Burton, P. Kohl, V. Grau, G. Plank and B. Rodriguez. The role of blood vessels in rabbit propagation dynamics and cardiac arrhythmias Presentation at Functional Imaging and Modelling of the Heart Conference, Nice, France, 2009
LSI2003MartinBishopBernabeau, M.O., M.J. Bishop, J. Pitt-Francis, D.J. Gavaghan, V. Grau, B. Rodriguez (2008) High Performance Computer Simulations for the Study of Biological Function in 3D Heart Models Incorporating Fibre Orientation and Realistic Geometry. Computers in C
LSI2003MartinBishopUnderstanding Cardiac Arrhythmias and Defibrillation Using Detailed Computational Models and Optical Imaging Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK, July 2012. Invited by Prof. Godfrey Smith.
LSI2003MartinBishopGeneration of Anatomically Detailed Computational Models from High Resolution MR Data The Multidisciplinary Cardiovascular Research Centre, University of Leeds, UK, April 2009. Invited by Dr Oliver Bernus.
LSI2003MartinBishopConstructing Ventricular Models to Investigate Cardiac Defibrillation: From Experiments to Simulations and Back Again Department of Biomedical Engineering, Division of Imaging Sciences, King’s College London, UK, November 2010. Invited by Prof. Nic Smith.
LSI2003MartinBishopPlank, G., R.A.B. Burton, P. Hales, M.J. Bishop, T. Mansoori, M.O. Bernabeu, A. Garny, A. J. Prassl, C. Bollensdorff, F. Mason, F. Mahmood, B. Rodriguez, V. Grau, J. Schneider, D.J.Gavaghan, P. Kohl (2009) Generation of histo-anatomically representative m
LSI2003MartinBishopBishop, M.J., G. Bub, D.J. Gavaghan, B. Rodriguez (2009) Application of Monte Carlo simulations to assess spatial accuracy of optical mapping signals: role of optical detection system. Physica D, Physica D: Nonlinear Phenomena, 238, 1008-1018.
LSI2003MartinBishopGernot Plank, Rebecca A.B. Burton, Patrick Hales, Martin Bishop, Tahir Mansoori,Miguel O. Bernabeu, Alan Garny, Anton J. Prassl, Christian Bollensdorff, Fleur Mason, Fahd Mahmood, Blanca Rodriguez, Vicente Grau, Jürgen E. Schneider, David Gavaghan and Pet
LSI2003MartinBishopBishop, M.J., G. Plank, R.A.B. Burton, J. Schneider, D.J. Gavaghan, V. Grau and P. Kohl (2010) Development of an anatomically-detailed MRI-derived rabbit ventricular model and assessment of its impact on simulations of electrophysiological function, Am J
LSI2003MartinBishopMartin J. Bishop, Gernot Plank, Rebecca A. B. Burton, Jürgen E. Schneider, David J. Gavaghan, Vicente Grau and Peter Kohl ‘Development of an anatomically detailed MRI-derived rabbit ventricular model and assessment of its impact on simulations of electrop
LSI2003MartinBishopArevalo, H., M.J. Bishop, B. Rodriguez, N. Trayanova. Photon scattering during optical mapping distorts the spatiotemporal organization in VF. Poster presentation at Heart Rhythm Society, San Francisco, USA, 2008.
LSI2003MartinBishopHales, P.W., R.A.B. Burton, F. Mason, C. Bollensdorf, M. J. Bishop, G. Plank, P. Kohl and J.E. Schneider. Cardiac diffusion tensor magnetic resonance imaging for high resolution reconstruction of individual whole hearts. Poster presentation at ISMRM, Hawa
LSI2003MartinBishopBernabeau, M.O., M.J. Bishop, J. Pitt-Francis, D.J. Gavaghan, V. Grau and B. Rodriguez. High performance computer simulations for the study of biological function in 3D heart models incorporating fibre orientation and realistic geometry. Poster presentati
LSI2003MartinBishopLloyd S, Gavaghan D, Boyd D, Noble D, Rodriguez B, Maharaj T, Bishop M.J., Clayton R, Handley J, Brodlie K and Plank G. Integrative Biology: Real science through e-Science. All Hands Meeting, Nottingham, 2006.
LSI2003MartinBishopBishop, M.J., Rodriguez, B., Eason, J.C., Whiteley, J.P., Noble, J.A., Trayanova, N. and Gavaghan, D.J. Direct optical mapping signal synthesis over a geometrically accurate ventricular model. Poster presentation at Heart Rhythms Society, New Orleans, LA,
LSI2003MartinBishopWinner: Tessella Industries Prize for Best Short 8-Week Project in Medical Imaging, as part of the LSI DTC
LSI2003MartinBishopRuner-Up: Presentation Competition, Early Career Prize Symposium (Sciences), University of Oxford
LSI2003MartinBishop3rd place: Poster Presentation Competition at the GRC on Cardiac Arrhythmia Mechanisms, Il Ciocco, Italy
LSI2003MartinBishopWinner: Best Poster Presentation Competition at the GRC on Cardiac Arrhythmia Mechanisms, California, USA
LSI2003MartinBishopWinner: Student Paper & Presentation Competition at the XXVIII IEEE EMBS, New York, USA
LSI2003XavierDidelotXavier Didelot, Jesse E. Taylor, and Joseph C. Watkins ‘A Duality Identity between a Model of Bacterial Recombination and the Wright–Fisher Diffusion’ Markov Processes and Related Topics: A Festschrift for Thomas G. Kurtz Vol. 4 (2008) 315–324
LSI2003XavierDidelotStefan Kulick, Claudia Moccia, Xavier Didelot, Daniel Falush, Christian Kraft, Sebastian Suerbaum ‘Mosaic DNA Imports with Interspersions of Recipient Sequence after Natural Transformation of Helicobacter pylori’ PLoS ONE 3(11): e3797
LSI2003XavierDidelotDaniel Falush, Mia Torpdahl, Xavier Didelot, Donald F Conrad, Daniel J Wilson and Mark Achtman ‘Mismatch induced speciation in Salmonella: model and data’ Phil. Trans. R. Soc. B 29 November 2006 vol. 361 no. 1475 2045-2053
LSI2003XavierDidelotXavier Didelot, Aaron Darling and Daniel Falush ‘Inferring genomic flux in bacteria’Genome Res. 2009. 19: 306-317
LSI2003XavierDidelotJunlong Zhang, Fang Zhang, Xavier Didelot, Kimberley D Bruce, Felino R Cagampang, Manu Vatish, Mark Hanson, Hendrik Lehnert, Antonio Ceriello and Christopher D Byrne ‘Maternal high fat diet during pregnancy and lactation alters hepatic expression of insul
LSI2003XavierDidelotXavier Didelot, Rachel Urwin, Martin C. J. Maiden and Daniel Falush ‘Genealogical typing of Neisseria meningitidis’Microbiology 155 (2009), 3176-3186
LSI2003XavierDidelotXavier Didelot, Daniel Lawson and Daniel Falush ‘SimMLST: simulation of multi-locus sequence typing data under a neutral model’ Bioinformatics (2009) 25 (11): 1442-1444.
LSI2003XavierDidelotGiovanna Morelli, Xavier Didelot, Barica Kusecek, Sandra Schwarz, Christelle Bahlawane, Daniel Falush, Sebastian Suerbaum, Mark Achtman ‘Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families’ PLoS Genet 6(7):
LSI2003XavierDidelotXavier Didelot, Daniel Lawson, Aaron Darling and Daniel Falush ‘Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences’ Genetics December 2010 vol. 186 no. 4 1435-1449
LSI2003XavierDidelotLynn Kennemann, Xavier Didelot, Toni Aebischer, Stefanie Kuhn, Bernd Drescher, Marcus Droege, Richard Reinhardt, Pelayo Correa, Thomas F. Meyer, Christine Josenhans, Daniel Falush, and Sebastian Suerbaum ‘Helicobacter pylori genome evolution during human
LSI2003XavierDidelotXavier Didelot, and Martin C.J. Maiden ‘Impact of recombination on bacterial evolution’ Trends in Microbiology Volume 18, Issue 7, July 2010, Pages 315-322
LSI2003XavierDidelotden Bakker Henk ; Didelot Xavier ; Fortes Esther ; Nightingale Kendra ; Wiedmann Martin ‘Lineage specific recombination rates and microevolution in Listeria monocytogenes’ Journal: BMC Evolutionary Biology Year: 2008 Vol: 8 Issue: 1 Pages/record No.: 277
LSI2003XavierDidelotXavier Didelot, Margaret Barker, Daniel Falush and Fergus G. Priest ‘Evolution of pathogenicity in the Bacillus cereus group’ Systematic and Applied Microbiology Volume 32, Issue 2, April 2009, Pages 81-90
LSI2003XavierDidelotXavier Didelot, Mark Achtman, Julian Parkhill, Nicholas R. Thomson, and Daniel Falush ‘A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?’ Genome Res. 2007. 17: 61
LSI2003XavierDidelotVartul Sangal, Heather Harbottle, Camila J. Mazzoni, Reiner Helmuth, Beatriz Guerra,Xavier Didelot,Bianca Paglietti,Wolfgang Rabsch, Sylvain Brisse, François-Xavier Weill,Philippe Roumagnac, and Mark Achtman ‘Evolution and Population Structure of Salmonel
LSI2003XavierDidelotHenk C den Bakker, Xavier Didelot, Esther D Fortes, Kendra K Nightingale and Martin Wiedmann ‘Lineage specific recombination rates and microevolution in Listeria monocytogenes’ BMC Evolutionary Biology 2008, 8:277
LSI2003XavierDidelotMichiel Vos and Xavier Didelot ‘A comparison of homologous recombination rates in bacteria and archaea’ The ISME Journal (2009) 3, 199–208
LSI2003XavierDidelotXavier Didelot and Daniel Falush ‘Inference of Bacterial Microevolution Using Multilocus Sequence Data’ Genetics March 2007 vol. 175 no. 3 1251-1266
LSI2003ChristophErbenTakayuki Kato, Russell P. Goodman, Christoph M. Erben, Andrew J. Turberfield and Keiichi Namba ‘High-Resolution Structural Analysis of a DNA Nanostructure by cryoEM’ Nano Lett., 2009, 9 (7), pp 2747–2750
LSI2003ChristophErbenRussell P. Goodman, Mike Heilemann, Sören Doose, Christoph M. Erben, Achillefs N. Kapanidis & Andrew J. Turberfield ‘Reconfigurable, braced, three-dimensional DNA nanostructures’ Nature Nanotechnology 3, 93 - 96 (2008)
LSI2003ChristophErbenRussell P. Goodman Dr, Christoph M. Erben Dr, Jonathan Malo Dr, Wei M. Ho, Mireya L. McKee Dr1, Achillefs N. Kapanidis Dr1, Andrew J. Turberfield Prof. ‘A Facile Method for Reversibly Linking a Recombinant Protein to DNA’ ChemBioChem, Volume 10, Issue 9,
LSI2003CatKellyKelly C J, Kelly M, Bejot R, Bayly S, Guo Q and Brady J M. 2008. Relating Redox Potential and Partition Coefficient of Hypoxia-Selective 64Cu-ATSM Analogues to PET Tracer Characteristics: A Theoretical Approach. Society of Nuclear Medicine Annual Meeting.
LSI2003CatKellyNew College Research Bursary
LSI2003CatKelly2007 Finalist, Science, Engineering & Technology for Europe.
LSI2003NailaMimouniGerton Lunter, Andrea Rocco, Naila Mimouni, Andreas Heger, Alexandre Caldeira, and Jotun Hein ‘Uncertainty in homology inferences: Assessing and improving genomic sequence alignment’ Genome Res. 2008. 18: 298-309
LSI2003PaulMundayRichard G. Humphreys, Stephen M. Taylor, Paul A. Manning, Paul D. Munday and Jeff Powell, "Performance of 94GHz receivers for passive imaging", Proc. SPIE 6548, 65480H (2007)
LSI2003AlexRowleyTingying Peng; Rowley, A.B.; Ainslie, P.N.; Poulin, M.J.; Payne, S.J.; ‘Wavelet Phase Synchronization Analysis of Cerebral Blood Flow Autoregulation’ Volume: 57 Issue: 4 960 – 968 2010
LSI2003AlexRowleyTingying Peng, Philip N Ainslie, James D Cotter, Carissa Murrell, Kate Thomas, Michael J A Williams, Keith George, Rob Shave, Alex B Rowley and Stephen J Payne ‘The effects of age on the spontaneous low-frequency oscillations in cerebral and systemic car
LSI2003RamazanSaeedRamazan Saeed and Charlotte Deane ‘An assessment of the uses of homologous interactions’ Bioinformatics (2008) 24 (5): 689-695.
LSI2003RamazanSaeedAnna C. F. Lewis, Ramazan Saeed and Charlotte M. Deane ‘Predicting protein–protein interactions in the context of protein evolution’ Mol. BioSyst., 2010, 6, 55-64
LSI2003RamazanSaeedRamazan Saeed and Charlotte M Deane ‘Using the protein interaction network to predict protein folds without homology’ BMC Systems Biology 2007, 1 p69 (from BioSysBio 2007: Systems Biology, Bioinformatics and Synthetic Biology Manchester, UK. 11–13 January
LSI2003DanStokeley1966-Pos Multi Level Insights Into The Ligand Binding Mode Of Membrane Bound Fatty Acid Amide Hydrolase
Kia Balali-mood1, Christo Christov2, Adrian Mulholland2, Alessio Loddio2, Dan Stokeley1, Mark Sansom1 Biophysical Journal Volume 94, Issue 2, Suppleme
LSI2003DanStokeleyCo-founder & Director at Sharpen Ltd (http://www.sharpenapp.com/)
LSI2003XavierDidelotD. Ashley Robinson, Daniel Falush, Edward J. Feil, Xavier Didelot ‘Sequence-Based Analysis of Bacterial Population Structures’ Bacterial Population Genetics in Infectious Disease, 37–60, 2010 Print ISBN: 9780470424742
LSI2003AdamAutonS. Myers, C.C. Spencer, A. Auton, L. Bottolo, C. Freeman et al., ‘The distribution and causes of meiotic recombination in the human genome’ Biochem Soc Trans 34: 526-530. 2006
LSI2003AdamAutonK. Bryc, A. Auton, M.R. Nelson, J.R. Oksenberg, S.L. Hauser, S. Williams, A. Froment, J. Bodo, C. Wambebe, S.A. Tishkoff and C.D. Bustamante, "Genome-wide patterns of population structure and admixture in West Africans and African Americans", PNAS, Decemb
LSI2003AdamAutonA. Auton and G. McVean, Recombination rate estimation in the presence of hotspots, Genome Res. 17:1219-1227, 2007
LSI2003AdamAutonA. Auton, K. Bryc, A. Boyko, K. Lohmueller, J. Novembre, A. Reynolds, A. Indap, M.H. Wright, J. Degenhardt, R. Gutenkunst, K.S. King, M.R. Nelson and C.D. Bustamante, "Global distribution of genomic diversity underscores rich complex history of continenta
LSI2003AdamAutonG. Hellenthal, A. Auton and D. Falush, "Inferring Human Colonization History Using a Copying Model", PLOS Genetics, vol 4(5), May 2008.
LSI2003AdamAutonS. Myers, C. Freeman, A. Auton, P. Donnelly, and G. McVean, "A common sequence motif associated with recombination hot spots and genome instability in humans", Nature Genetics, vol 40, pp. 1124 - 1129, August 2008.
LSI2003AdamAutonA.R. Boyko, R.H. Boyko, C.M. Boyko, H.G. Parker, M. Castelhano, L. Corey, J.D. Degenhardt, A. Auton, M. Hedimbi, R. Kityo, E.A. Ostrander, J. Schoenebeck, R.J. Todhunter, P. Jones and C.D. Bustamante, "Complex population structure in African village dogs
LSI2003MartinBishopM.J. Bishop, B. Rodriguez, N. Trayanova, D.J. Gavaghan ‘Modulation of Virtual-Electrode Polarization Images due to 3D Fluorescent Photon Scattering’ Presented at the XXVIII Conference of the IEEE Engineering in Medicine and Biology Society, New York 2006
LSI2003MartinBishopM.J. Bishop, B. Rodríguez, J.C. Eason, J.P. Whiteley, N. Trayanova, D.J. Gavaghan ‘Panoramic Optical Mapping Signal Synthesis.’ Presented at the Second Physiological Flow Meeting: Cardiovascular Fluid Dynamics and Models, 25-27th Sept. 2005 Edinburgh, UK.
LSI2003MartinBishopS. Lloyd, D.J. Gavaghan, D. Boyd, D. Noble, B. Rodriguez, T, Maharaj, M.J. Bishop, R, Clayton, J, Handley, K, Brodlie, G, Plank ‘Integrative Biology: Real science through e-Science’ All Hands Meeting, 2006.
LSI2003MartinBishopM.J. Bishop, B. Rodriguez, F. Qu, I.R. Efimov, D.J. Gavaghan, N. Trayanova ‘A combined experimental and theoretical investigation into the role of photon scattering in fluorescent signal distortion during optical recordings of arrhythmia and defibrillatio
LSI2003MartinBishopM.J. Bishop, B. Rodríguez, J.C. Eason, J.P. Whiteley, J.A. Noble, N. Trayanova, D.J. Gavaghan ‘Direct optical mapping signal synthesis over a geometrically accurate ventricular model.’ Heart Rhythm, 2(5):S220, 2005. Presented at Heart Rhythms Society 2005
LSI2003MartinBishopJ.P. Whiteley, M.J. Bishop, D.J. Gavaghan. 'Soft Tissue Modelling of Cardiac Fibres for Use in Coupled Mechano-Electric Simulations', Bulletin of Mathematical Biol. 69(7):2199-2225, 2007.
LSI2003MartinBishopM.J. Bishop, B. Rodriguez, J. Eason, J.P. Whiteley, N. Trayanova, D.J. Gavaghan, ‘Synthesis of voltage-sensitive optical signals: Application to panoramic optical mapping.’ Biophys. J., 90, 2938-2945, 2006. doi:10.1529/biophysj.105.076505.
LSI2003MartinBishopM.J. Bishop, D.J. Gavaghan, N. Trayanova, B.Rodriguez 'Photon Scattering Effects in Optical Mapping of Propagation and Arrhythmogenesis in the Heart' J Cardiovasc Electrophysiol. 40(6 S):S75-80, 2007.
LSI2003MartinBishopM.J. Bishop, B. Rodriguez, N. Trayanova, and D.J. Gavaghan ‘Inference of Intramural Wavefront Orientation from Optical Recordings in Realistic Whole-Heart Models’ Biophys. J., 91, 3957-3958, 2006. doi:10.1529/biophysj.106.092544.
LSI2003MartinBishopM.J. Bishop, B. Rodríguez, F. Qu, I.R. Efimov, D.J. Gavaghan, N. Trayanova. 'The role of photom scattering in optical signal distortion during arrhythmia and defibrillation' Biophys J. 93(10): 3714-3726, 2007.
LSI2003HelenCarstairsH.M. Carstairs, J. Yajima, J. Bath, R.A. Cross, A.J. Turberfield, 'A Kinesin-based Molecular Shuttle' The Biophysical Society 52nd Annual Meeting 2nd-6th February 2008, Long Beach, California.
LSI2003HelenCarstairsH.M. Carstairs, J. Yajima, J. Bath, R.A. Cross & A.J. Turberfield, 'A Kinesin-based Molecular Shuttle' IoP Physics meets Biology 13–16th July 2008, St. Catherine’s College, Oxford, UK.
LSI2003HelenCarstairsH.M.J. Carstairs, J. Yajima, J. Bath, R.A. Cross & A.J. Turberfield ‘A Kinesin-based Molecular Shuttle’ Foundations of Nanoscience 2007, Snowbird, Utah.
LSI2003HelenCarstairsH.M. Carstairs, J. Yajima, J. Bath, R.A. Cross, A.J. Turberfield, 'A Kinesin-based Molecular Shuttle' The Dynamic Cell Meeting 2009 (Biochemical Journal Young Investigator’s Award)
LSI2003HelenCarstairsCarstairs H. M., Lymperopoulos K., Kapanidis A. N., Bath J., Turberfield A. J, 2009. DNA Monofunctionalization of Quantum Dots. Chembiochem. 10(11), pp.1781-3
LSI2003ChristophErbenC.M. Erben, R.P. Goodman, A.J. Turberfield, 'DNA Cages', Biophysical Society 52nd Annual Meeting, Long Beach (USA), 2-6 February 2008.
LSI2003ChristophErbenC.M. Erben ‘A Self-Assembled DNA Bipyramid’ 4th International Conference on Foundations of Nanoscience, Snowbird, Utah, April 2007.
LSI2003ChristophErbenC. Erben, Selected to take part in the Presentation by Britain’s Early-Stage Physicists at the House of Commons, London, November 2006. [Won the £500 Unilever Commendation Award at this event]
LSI2003ChristophErbenC.M. Erben, R.P. Goodman, A.J. Turberfield ‘A Protein Cage Made from DNA’, 3rd Annual Conference Foundations of Nanoscience, Snowbird, Utah, April 2006.
LSI2003ChristophErbenR.P. Goodman, M. Heilemann, S. Doose, C.M. Erben, A.N. Kapanidis, A.J. Turberfield, 'Reconfigurable, braced, three-dimensional DNA nanostructures' Nature Nanotech., 3: 93-96. 2008
LSI2003ChristophErbenT.Kato, R.P. Goodman, C.M. Erben, A.J. Turberfield, K. Namba, ‘High-Resolution Structural Analysis of a DNA Nanostructure by CryoEM’ Nano Lett., 9, 2747, 2009
LSI2003ChristophErbenC. M. Erben, R. P. Goodman and A. J. Turberfield, 'A Self-Assembled DNA Bipyramid' J. Am. Chem. Soc. 129(22) 6992-6993, 2007
LSI2003ChristophErbenC. M. Erben, R. P. Goodman, A. J. Turberfield, ‘Single-Molecule Protein Encapsulation in a Rigid DNA Cage’ Angew. Chem. Int. Ed. 45(44), 7414-7417, 2006
LSI2003ChristophErbenR.P. Goodman, I.A.T Schaap, C.F. Tardin, C.M. Erben, R.M. Berry, C.F. Schmidt, A.J. Turberfield, ‘Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication’ Science, 310, 1661, 2005, doi: 10.1126/science.1120367
LSI2003ChristophErbenR.P. Goodman, C.M. Erben, J. Malo, W.M. Ho, M.L. McKee, A.N. Kapanidis, A.J. Turberfield, ‘A Facile Method for Reversibly Linking a Recombinant Protein to DNA’ ChemBioChem, 10, 1551, 2009
LSI2003ChristophErbenChristoph Erben: Patent Pending
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean ‘Estimating meiotic gene conversion rates from population genetic data’, Genetics. 177:881-894, 2007. doi:10.1534/genetics.107.078907.
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean, S. Myers and G.A.T. McVean ‘Investigating the evidence for gene conversion using an approximation to the coalescent’ Séminaire Européen de Statistique (SemStat)/European Mathematical Society (EMS); Warwick, Sept. 2005
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean, S. Myers and G.A.T. McVean ‘Investigating the evidence for gene conversion using an approximation to the coalescent’ Joint Biochemical Society/Genetics Society meeting - Meiosis and the causes and consequences of recomb
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean, S. Myers and G.A.T. McVean ‘Investigating the evidence for gene conversion using an approximation to the coalescent’ Second Summer School Mathematics in Biology and Medicine - Mathematics in Biology and Medicine; Estori
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean, S. Myers and G.A.T. McVean 'Investigating the evidence for gene conversion using an approximation to the coalescent'. European Society for Evolutionary Biology conference, (ESEB), Krakow, August 2005.
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean ‘A statistical model to estimate the rate of gene conversion from population genetic data’ European Molecular Biology Organisation (EMBO), Hyderabad, Dec 2006
LSI2003JoannaGayJ. Gay, S. Myers and G.A.T. McVean, S. Myers and G.A.T. McVean ‘Investigating the evidence for gene conversion using an approximation to the coalescent’ EPSRC student conference, Birmingham, Aug 2005 [shared poster prize]
LSI2003CatKellyC.J. Kelly, K. Smallbone, T. Roose and J.M. Brady ‘A Systems Biology approach to assessing the feasibility of hypoxia imaging candidates’. International Symposium for Biomedical Imaging, 13 April 2007.
LSI2003CatKellyC.J. White and J.M. Brady ‘A semi-automatic approach to the delineation of tumour boundaries from PET data using level sets’ Abstract 314: Society of Nuclear Medicine Annual Meeting, 2005.
LSI2003CatKellyC.J. White and J.M. Brady ‘Hypoxia: From Modelling Molecules to Molecular Imaging’ Abstract 574: Society of Nuclear Medicine Annual Meeting, 2006.
LSI2003CatKellyC.J. Kelly and J.M. Brady, ‘A model to simulate tumour oxygenation and dynamic [18F]-Fmiso PET data’ Phys. Med. Biol. 51, 5859-5873. 2006
LSI2003KarenLeesK. Lees ‘Identifying Gene Clusters and Regulatory Themes using Time course Expression Data, Hidden Markov models and Transcription Factor Information’ Bioinformatics Student Symposium, Oxford, August 2004
LSI2003KarenLeesK. Lees ‘Gene Microarray analysis using Angular Distribution Decomposition’ MPBB06: Molecular Biology of Plant Pathogens, Birnam, Scotland, 2006
LSI2003KarenLeesK. Lees ‘Gene Microarray analysis using Angular Distribution Decomposition’ Bioinformatics/Statistical Genetics Student Symposium, Oxford, July 2006
LSI2003KarenLeesK. Lees, S. Roberts, P. Skamnioti and S. Gurr, ‘Gene Microarray Analysis using Angular Distribution Decomposition’ Journal of Computational Biology, 14(1) 68-83, 2007
LSI2003StephenMayhewS.D. Mayhew, G.D. Iannetti, M.W. Woolrich, R.G. Wise ‘Automated measurement of single trial amplitude and latency of laser-evoked potentials (LEPs) by multiple linear regression’ 12th Annual Meeting of the Organization for Human Brain Mapping(HBM), Floren
LSI2003StephenMayhewS.D. Mayhew, S.G. Dirckx, R.K.N. Niazy, G.D. Iannetti, R.G. Wise ‘Simultaneous recording of auditory-evoked brain potentials and continuous, high-field functional MRI in humans’ 13th Annual Meeting of the Organization for Human Brain Mapping, Chicago, Jun
LSI2003StephenMayhewS.D. Mayhew, S.G. Dirckx, R.K.N. Niazy, G.D. Iannetti, R.G. Wise ‘Habituation of the visual evoked potential (VEP) amplitude is not reflected in simultaneously acquired fMRI BOLD signal’ 13th Annual Meeting of the Organization for Human Brain Mapping, Chi
LSI2003StephenMayhewS.D. Mayhew, S.G. Dirckx, R.K.N. Niazy, G.D. Iannetti, R.G. Wise ‘Simultaneous recording of auditory-evoked brain potentials and continuous, high-field functional MRI in humans’ 16th Meeting of the International Society for Magnetic Resonance in Medicine,
LSI2003StephenMayhewS.D. Mayhew, G.D. Iannetti, R. Rogers, K.P. Pattinson, R.G. Wise ‘Wavelet time-frequency analysis of laser-evoked potential (LEP) power modulated by opioid induced analgesia’ 13th Annual Meeting of the Organization for Human Brain Mapping, Chicago, June 1
LSI2003StephenMayhewS.D. Mayhew, G.D. Iannetti, M.W. Woolrich and R.G. Wise, ‘Automated single-trial measurement of amplitude and latency of laser-evoked potentials (LEPs) using multiple linear regression’ Clinical Neurophysiology, 117(6) 1331-1344, 2006
LSI2003StephenMayhewMayhew SD, McIntosh BM, Dirckx SG, Iannetti GD, Wise RG. 2010. Coupling of simultaneously acquired electrophysiological and haemodynamic responses during visual stimulation. Magn. Reson. Imag. 28(8):1066-77.
LSI2003StephenMayhewK.T. Pattinson, R. Rogers, S.D. Mayhew, I. Tracey, R.G. Wise ‘Pharmacological fMRI: measuring opioid effects on the BOLD response to hypercapnia’ Journal of Cerebral Blood Flow Metabolism, 27, 414-423, 2007
LSI2003StephenMayhewPattinson KT, Rogers R, Mayhew SD, MacIntosh BJ, Lee MC, Wise RG. 2008. Remifentanil-induced cerebral blood flow effects in normal humans: dose and ApoE genotype. Anesth Analg. 105(1):167-75.
LSI2003StephenMayhewR.G. Wise, K.T. Pattinson, D. Bulte, P. Chiarelli, S.D. Mayhew, G. Balanos, D. O’Connor, T. Pragnell, P. Robbins, I. Tracey, P. Jezzard ‘Dynamic forcing of end-tidal carbon dioxide and oxygen applied to functional magnetic resonance imaging’ Journal of Ce
LSI2003StephenMayhewA.K. Harvey, K.T.S. Pattinson, J.C.W. Brooks, S.D. Mayhew, M. Jenkinson, R.G. Wise, 'Brainstem functional magnetic resonance imaging: Disentangling signal from physiological noise' J. MRI. 28:6, 1337-1344. 2008.
LSI2003StephenMayhewPattinson KT, Mitsis GD, Harvey AK, Jbabdi S, Dirckx S, Mayhew SD, Rogers R, Tracey I, Wise RG. 2009. Determination of the human brainstem respiratory control network and its cortical connections in vivo using functional and structural imaging. Neuroimage. 15;44(2):295-305.
LSI2003StephenMayhewS.D. Mayhew, R. Rogers, P. Dunckley, I. Tracey and R.G. Wise ‘Does Hypoxia modulate the stimulus evoked BOLD response?’ Poster at International Society for Magnetic Resonance in Medicine (ISMRM). Seattle, May 2006.
LSI2003StephenMayhew2006-07 - Meeting of the International Society for Magnetic Resonance in Medicine, Student Stipend.
LSI2003NailaMimouniSelection constraints on non-coding RNAs ISMB/ECCB 2007, July 21-25, 2007, Vienna, Austria
LSI2003NailaMimouniN.K. Mimouni, R. Lyngsoe and J. Hein, An Analysis of Structural Influences on Selection in RNA Genes, The International Conference on Intelligent Systems for Molecular Biology (ISMB) and The European Conference on Computational Biology (ECCB) (ISMB/ECCB-2
LSI2003NailaMimouniN.K. Mimouni, G. Lunter and J. Hein ‘Aligning non-coding functional DNA’ The Young Bioinformatics Forum, The Oxford Said Business School, 20 October, 2004
LSI2003NailaMimouniN.K. Mimouni, G. Lunter and J. Hein ‘The hunt for genomic dark matter: Aligning non-coding functional DNA’ Mathematical and Statistical Aspects of Molecular Biology (MASAMB-2005), Hertfordshire, 21-22 March, 2005.
LSI2003NailaMimouniN.K. Mimouni, R. Lyngsoe and J. Hein ‘Measuring Selection in RNA molecules’ European Conference on Computational Biology (ECCB-2005), Madrid, 28 Sept.-01 Oct., 2005.
LSI2003NailaMimouniN.K. Mimouni, G. Lunter and J. Hein ‘Gap Attraction: An objective quality measure for whole-genome alignments’ Intelligent Systems in Molecular Biology (ISMB-2005), Detroit, 22-29 June, 2005.
LSI2003NailaMimouniN.K. Mimouni. Evolution of non-coding RNAs. The Medical Research Centre Functional Genetics Unit (MRC FGU), Poole, June 2006.
LSI2003NailaMimouniN.K. Mimouni. Modelling evolution and selection in Bioinformatics. The John Radcliffe Hospital, Oxford, January 2007.
LSI2003NailaMimouniN.K. Mimouni. Selection in RNA and Statistical Alignment. The National Institute for Medical Research (NIMR), London, May 2006.
LSI2003NailaMimouniN.K. Mimouni. The new RNA hypothesis and non-coding RNAs, Mansfield College Senior Common Room (SCR), February 2007.
LSI2003NailaMimouniAn analysis of structural influences on selection in RNA genes by Mimouni, Naila K, Griffiths-Jones, Sam, Lyngsø, Rune B, Hein, Jotun Published in Molecular biology and evolution (01/2009)
LSI2003NailaMimouniG. Lunter, A. Rocco, N.K. Mimouni, A. Heger, A. Caldeira, and J. Hein ‘Uncertainty in Homology Inferences: Assessing and Improving Genomic Sequence Alignment’, Genome Res.,18(2):298-309. 2008.
LSI2003AlexRowleyH. Abatay, A.B. Rowley and S.J. Payne ‘Instabilities in Nitric Oxide behaviour due to a flow feedback mechanism’ Proceedings of IEE International Control Conference, Glasgow, August 2006. [Winner of Best Student Paper Prize]
LSI2003AlexRowleyA.B. Rowley, T. Peng, and S.J. Payne ‘Time varying multivariate system identification of cerebral autoregulation’ 23rd International Symposium on Cerebral Blood Flow, Metabolism and Function, May 2007.
LSI2003AlexRowleyA.B. Rowley and S.J. Payne ‘Quantifying nonlinear coupling in cerebral haemodynamics using information transfer’ 23rd International Symposium on Cerebral Blood Flow, Metabolism and Function, 2007
LSI2003AlexRowleyA.B. Rowley, C.J. Stephens and S.J. Payne ‘A compact physiological model of the autoregulation of cerebral blood vessels’ 22nd International Symposium on Cerebral Blood Flow, Metabolism and Function, June 2005. Journal of Cerebral Blood Flow & Metabolism,
LSI2003AlexRowleyA.B. Rowley, M. Banaji, C.J. Stephens and S.J. Payne ‘The role of stretch-sensitive channels in the vasomotion of cerebral vessels’. Physiological Flow Meeting, Edinburgh, September 2005.
LSI2003AlexRowleyO.D. Price, A.B. Rowley and S.J. Payne, ‘The measurement of cerebral metabolic rate of oxygen with cytochrome oxidase’ 23rd International Symposium on Cerebral Blood Flow, Metabolism and Function, May 2007
LSI2003AlexRowleyS.J. Payne, C.J. Stephens and A.B. Rowley ‘A compact physiological model of blood flow autoregulation’ Physiological Flow Meeting, Nottingham, April 2005.
LSI2003AlexRowleyT. Peng, A.B. Rowley and S.J. Payne ‘Multivariate system identification of cerebral autoregulation’ 23rd International Symposium on Cerebral Blood Flow, Metabolism and Function, May 2007.
LSI2003AlexRowleyM.G.F. Catherall, A.B. Rowley, and S.J. Payne ‘The response of the cerebral microvasculature to regional changes in cerebral blood flow’ 23rd International Symposium on Cerebral Blood Flow, Metabolism and Function, May 2007.
LSI2003AlexRowleyM.A. Chappell, A.B. Rowley and S.J. Payne ‘Automatic Doppler bubble detection: The utility of wavelets’ Proceedings of 31st EUBS conference, Norway, August 2006.
LSI2003AlexRowleyS.J. Payne, H.J. Morris, and A.B. Rowley ‘A combined haemodynamic and biochemical model of cerebral autoregulation’ Proceedings of 27th IEEE EMBS conference, 2295-2298, Shanghai, China, September 2005.
LSI2003AlexRowleyA.B. Rowley, C.J. Stephens and S.J. Payne ‘A compact physiological model of the role of vascular smooth muscle cells in autoregulation of blood flow’. Computational Cell Biology conference, Lenox, MA, USA, March 2005.
LSI2003AlexRowleyThe Role of Photon Scattering in Voltage−Calcium Fluorescent Recordings of Ventricular Fibrillation DJ Gavaghan MJ Bishop A Rowley B Rodriguez G Plank and G Bub 2011.
LSI2003AlexRowleyA.B. Rowley, S.J. Payne, I. Tachtsidis, M.J. Ebden, J.P. Whiteley, D.J. Gavaghan, L. Tarassenko, M. Smith, C.E. Elwell and D.T. Delpy, ‘Synchronization between arterial blood pressure and cerebral oxyhaemoglobin concentration investigated by wavelet cross
LSI2003AlexRowleyCornhill Prize for my D.Phil. This was awarded by the department of Engineering science, University of Oxford.
LSI2003RamazanSaeedR. Saeed, ‘Is there a relationship between protein connectivity and evolutionary rate?’, ECCB 2005.
LSI2003RamazanSaeedR. Saeed ‘Is there a relationship between protein connectivity and evolutionary rate?’ Student Symposium: ECCB 2005, [Won honorary mention for best talk].
LSI2003RamazanSaeedR. Saeed, ‘Protein protein interactions, evolutionary rate, abundance and age’, BMC Bioinformatics, 7(128), 2007. doi: 10.1186/1471-2105-7-128.
LSI2003DanStokeleyD. Stokeley ‘Towards a multi-scale model of Long QT Syndrome’ National Biomedical Computational Resource Summer Institute, San Diego, 2006 and OXION day, Oxford, 2006
LSI2003DanStokeleyKia Balali-mood, Christo Christov, Adrian Mulholland, Alessio Loddio, Dan Stokeley, Mark Sansom (2008) 'Poster 1966-Pos Multi Level Insights Into The Ligand Binding Mode Of Membrane Bound Fatty Acid Amide Hydrolase', Biophysical Journal. 94(2):660-665.
LSI2003DanStokeleySouthern J, Pitt-Francis J, Whiteley J, Stokeley D, Kobashi H, Nobes R, Kadooka Y, Gavaghan D. Review: Multi-scale computational modelling in biology and physiology. Prog Biophys Mol Biol. 2008 Jan-Apr;96(1-3):60-89. Epub 2007 Aug 11. Review.PMID: 1788850
LSI2003DanStokeleyStokeley D, Bemporad D, Gavaghan D, Sansom MS. 'Conformational dynamics of a lipid-interacting protein: MD simulations of saposin B', Biochemistry. 2007 Nov 27;46(47):13573-80. Epub 2007 Nov 6.
LSI2003NashToledoN.C. Toledo, M.R.R. de Planque, S.A. Contera, J.F. Ryan ‘Lipid Bilayer Coating of Multiwalled Carbon Nanotubes’ Seventh International Conference on the Science and Application of Nanotubes, 2006
LSI2003NashToledoN.C. Toledo, H. Burch, S. Contera, K. Voitchovsky, N. Grobert, and J.F. Ryan ‘Wrapping of raw and modified multiwalled carbon nanotubes with the 2D ordered purple membrane’ NanoteC, University of Sussex, Brighton, 2005
LSI2003NashToledoN.C. Toledo, M. R. R. de Planque, S. Antoranz Contera, N. Grobert, J. F. Ryan ‘Lipid-modulated assembly of magnetized iron-filled carbon nanotubes in millimeter-scale structures’ Japanese Journal of Applied Physics, 46(4B):2799-2805, 2007.
LSI2003HenryWinstanleyH. F. Winstanley, S. Abeln, and C. M. Deane ‘How old is your fold?’ Bioinformatics, 21, 449-458, 2005.
LSI2003HenryWinstanleyM. Hieda, H.F. Winstanley, P.K. Maini, F.J. Iborra and P.R. Cook, ‘Different populations of RNA polymerase II in living mammalian cells’ Chromosome Research, 13, 135–144, 2005
LSI2002DanielGallichanDaniel Gallichan, Jesper L. R. Andersson, Mark Jenkinson, Matthew D. Robson, Karla L. Miller ‘Reducing distortions in diffusion-weighted echo planar imaging with a dual-echo blip-reversed sequence’ Magnetic Resonance in Medicine, Volume 64, Issue 2, pages
LSI2002DanielGallichanB.J. MacIntosh, K.T. Pattinson, D. Gallichan, I. Ahmad, K.L. Miller, D.A. Feinberg, R.G. Wise, P. Jezzard. Measuring the effects of remifentanil on cerebral blood flow and arterial arrival time using 3D GRASE MRI with pulsed arterial spin labelling. J. Ce
LSI2002DanielGallichanS. Nagel, M. Papadakis, R. Chen, L.C. Hoyte, K.J. Brooks, D. Gallichan, N.R. Sibson, C. Pugh, A.M. Buchanan. Neuroprotection by dimethyloxalylglycine following permanent and transient focal cerebral ischemia in rats. J. Cereb. Blood Flow Metab. 2011, 31 (
LSI2002DanielGallichanJingyi Xie, Stuart Clare, Daniel Gallichan, Roger N. Gunn, Peter Jezzard ‘Real-time adaptive sequential design for optimal acquisition of arterial spin labeling MRI data’ Magnetic Resonance in Medicine, Volume 64, Issue 1, pages 203–210, July 2010
LSI2002DanielGallichanDaniel Gallichan, Chris. A. Cocosco, Andrew Dewdney, Gerrit Schultz, Anna Welz, Jürgen Hennig, Maxim Zaitsev ‘Simultaneously driven linear and nonlinear spatial encoding fields in MRI’ Magnetic Resonance in Medicine, Volume 65, Issue 3, pages 702–714, Mar
LSI2002DanielGallichanSimon Nagel, Michalis Papadakis, Ruoli Chen, Lisa C Hoyte, Keith J Brooks, Daniel Gallichan, Nicola R Sibson, Chris Pugh and Alastair M Buchan ‘Neuroprotection by dimethyloxalylglycine following permanent and transient focal cerebral ischemia in rats’ Jou
LSI2002TaniaSaxlTania Saxl, Faaizah Khan, Matteo Ferla, David Birch and John Pickup ‘A fluorescence lifetime-based fibre-optic glucose sensor using glucose/galactose-binding protein’Analyst, 2011, 136, 968-972
LSI2002DannyAxfordDavis, J. J. et al. Molecular bioelectronics. Journal of Materials Chemistry 15, 2160-2174
LSI2002RobinFreemanT Naumowicz, R Freeman, A Heil, M Calsyn, E Hellmich, A Brändle, T Guilford, and J Schiller. Autonomous monitoring of vulnerable habitats using a wireless sensor network. Proceedings of the workshop on Real-world wireless sensor networks, pp51-55, 2008
LSI2002RobinFreemanR. Freeman ‘Analysing Avian Navigation’, 8th Bioinformatics Day, Oxford, 2006 (on behalf of S. Roberts who could not attend)
LSI2002RobinFreemanR. Freeman ‘Applications of Process Algebra in Systems Biology’ , 8th Bioinformatics Day, Oxford, 2006
LSI2002RobinFreemanT. Guilford, J. Meade, D. Biro, C. Perrins, R. Freeman, S. Roberts, F. Bonadonna, D. Boyle and L. Maurice ‘Precision tracking of the Manx Shearwater, Puffinus puffinus’, 2nd International Workshop on the Manx Shearwater and other Procellariiforms, Belfast
LSI2002RobinFreemanK.K. Lau, S. Roberts, D. Biro, R. Freeman, J. Meade, T. Guilford, ‘An edge-detection approach to investigating pigeon navigation’ J Theor Biol. 239(1) 71-8, 2006
LSI2002RobinFreemanD. Biro, R. Freeman, J. Meade, S. Roberts, T. Guilford ‘Pigeons combine compass and landmark guidance in familiar route navigation’, Proceedings of the National Academy of Sciences, 104(18):7471-7476, 2007.
LSI2002RobinFreemanT Guilford, J Meade, R Freeman, T Evans, F Bonadonna, D Boyle, C M Perrins, ‘GPS tracking of the foraging movements of Manx Shearwaters Puffinus puffinus breeding on Skomer Island, Wales’, 150(3):462-473, 2008. doi: 10.1111/j.1474-919X.2008.00805.x.
LSI2002DanielGallichanD. Gallichan and P. Jezzard 'Fitting kinetic models to ASL data: is one TI sufficient for all brain regions?' NMR Symposium, March 22nd 2006, Cambridge.
LSI2002DanielGallichanM.A. Chappell, A.R. Groves, D. Gallichan, and M.W. Woolrich ‘Bayesian inference of Kinetic Curve models for ASL perfusion measurements’ 16th Meeting of the International Society for Magnetic Resonance in Medicine, ISMRM, Berlin, May 19-24th, 2007.
LSI2002DanielGallichanD. Gallichan and P. Jezzard 'Comparison of ASL Kinetic Curves between subjects and between brain areas', ISMRM, May 6-12 2006, Seattle
LSI2002DanielGallichanD. Gallichan and P. Jezzard 'Choosing a presaturation method in Arterial Spin Labelling: A simulation-based approach' BCISMRM, September 1-2 2005, Oxford.
LSI2002DanielGallichanD. Gallichan and P. Jezzard ‘Simulating the tagging process in Velocity-Selective ASL’ ISMRM, May 2007, Berlin
LSI2002DanielGallichanD. Gallichan and P. Jezzard ‘Fitting kinetic models to ASL data: is one TI sufficient for all brain regions?’ NMR Symposium, March 2006, Cambridge 
LSI2002DanielGallichanMirams GR, Arthurs CJ, Bernabeu MO, Bordas R, Cooper J, et al. (2013) Chaste: An Open Source C++ Library for Computational Physiology and Biology.PLoS Comput Biol 9(3): e1002970
LSI2002DanielGallichanM.W. Woolrich, P. Chiarelli, D. Gallichan, J. Perthen and T.T. Liu ‘Bayesian inference of hemodynamic changes in functional arterial spin labeling data’ Magnetic Resonance in Medicine 56:4 901-906, 2006
LSI2002DanielGallichanP.A. Chiarelli, D.P. Bulte, D. Gallichan, S.K. Piechnik, R.W. Wise, P. Jezzard ‘Flow-Metabolism Coupling in Human Visual, Motor, and Supplementary Motor Areas Assessed by Magnetic Resonance Imaging’ Magnetic Resonance in Medicine, 57:3 538-547, 2007
LSI2002DanielGallichanD. Gallichan, J. Scholz, A. Bartsch, T.E.Behrens, M.D.Robson, K.L.Miller. Addressing a Systematic Vibration Artifact in Diffusion-Weighted MRI', Human Brain Mapipng 2010 Feb;31(2):193-202. doi: 10.1002/hbm.20856.
LSI2002DanielGallichanP.A.Chiarelli, D.P.Bulte, R. Wise, D. Gallichan, P. Jezzard. 'A calibration method for quantitative BOLD fMRI based on hyperoxia', Neuroimage 2007;37:808-820.
LSI2002DanielGallichanJ. Xie, D. Gallichan, R.N.Gunn, P. Jezzard. 'Optimal design of pulsed arterial spin labeling MRI experiments', Magn. Reson. Med. 2008;59:826-834.
LSI2002DanielGallichanD.Gallichan, P. Jezzard. 'Modeling the effects of dispersion and pulsatility of blood flow in pulsed arterial spin labeling', Magn. Reson. Med. 2008;60:53-63.
LSI2002DanielGallichanB.J.MacIntosh, K.T.S.Pattinson, D. Gallichan, I. Ahmad, K.L.Miller, D.A.Feinberg, R.G.Wise, P. Jezzard. 'Measuring the effects of remifentanil on cerebral blood flow and arterial arrival time using 3D GRASE MRI with pulsed arterial spin labelling', J. Cer
LSI2002DanielGallichanD. Gallichan, P. Jezzard. 'Variation in the shape of pulsed arterial spin labeling kinetic curves across the healthy human brain and its implications for CBF quantification', Magn. Reson. Med. 2009;61:686-695.
LSI2002DanielGallichanJ.A.McNab, D. Gallichan, K.L.Miller. '3D Steady-State Diffusion-Weighted Imaging With Trajectory Using Radially Batched Internal Navigator Echoes (TURBINE)', Magn. Reson. Med. 2010;63:235-242.
LSI2002DanielGallichanD. Gallichan, M.D.Robson, A. Bartsch, K.L.Miller. 'TREMR: Table Resonance Elastography with MR', Magn. Reson. Med. 2009;62:815-821.
LSI2002StephenMcCauleyS. McCauley and J. Hein, ‘Using hidden Markov models and observed evolution to annotate viral genomes’ Bioinformatics, 22(11) 1308-1316, 2006
LSI2002StuartReidS.W. Reid, M.C. Leake, J.H. Chandler, C.J. Lo, J.P. Armitage, R.M. Berry ‘The maximum number of torque-generating units in the flagellar motor of Escherichia coli is at least 11’ Proc Natl Acad Sci U S A. 2006 May 23;103(21):8066-71. Epub 2006 May 12. PMI
LSI2002TaniaSaxlSaxl T, Leake MC, Sandison M, Morgan H & Berry RM. Electrorotation of the bacterial flagellar motor. 2005. Bacterial Locomotion and Signal Transduction Symposium.
LSI2002TaniaSaxlSaxl T. Measuring local concentration of metabolites. 2009. Quantitative Imaging in Systems Biology, Oxford.
LSI2002TaniaSaxlSaxl T. Shining Light on Diabetes: Using fluorescence to monitor glucose. 2009 Science, Engineering and Technology (SET) for Britain, Houses of Parliament (Selected finalist).
LSI2002TaniaSaxlSaxl T, Zhi Z-L, Khan F, Matthews D, Ameer-Beg S, Pickup JC. Nano-engineered microcapsules for in vivo glucose monitoring. 2008. CLINAM: 1st European conference for Clinical Nanomedicine.
LSI2002TaniaSaxlSaxl T, Zhi Z-L, Khan F, Matthews D, Ameer-Beg S, Pickup JC. A ‘smart tattoo’ for in vivo glucose monitoring in diabetes. 2008. European Science Foundation Conference in Biomedicine: Nanomedicine.
LSI2002TaniaSaxlKhan F, Saxl TE, Pickup JC. Fluorescence intensity- and lifetime-based glucose sensing using an engineered high-K(d) mutant of glucose/galactose-binding protein. Anal Biochem. 2010 Apr 1;399(1):39-43. Epub 2009 Dec 2. PubMed PMID:19961827.
LSI2002TaniaSaxlSaxl T, Khan F, Matthews DR, Zhi ZL, Rolinski O, Ameer-Beg S, Pickup J. Fluorescence lifetime spectroscopy and imaging of nano-engineered glucose sensor microcapsules based on glucose/galactose-binding protein. Biosens Bioelectron. 2009 Jul 15;24(11):3229
LSI2002TaniaSaxlPickup JC, Zhi ZL, Khan F, Saxl T, Birch DJ. Nanomedicine and its potential in diabetes research and practice. Diabetes Metab Res Rev. 2008 Nov-Dec;24(8):604-10. Review. PubMed PMID: 18802934.
LSI2002TaniaSaxlPickup JC, Khan F, Zhi Z-L, Saxl T. Fluorescence in Clinical Nanometrology: its Potential Role in Diabetes Research and Management. European journal of nanomedicine, 2009 (2) 16-21.
LSI2002TaniaSaxlSaxl T. Smart Tattoos and Implanted Islets: Dealing with Diabetes. Nano Magazine, 2009 (11) 30-32.
LSI2002KieranSmallboneK. Smallbone, R.A. Gatenby, R.J. Gillies, P.K. Maini, D.J. Gavaghan, ‘Metabolic changes during carcinogenesis: potential impact on invasiveness’ The Seventh International Conference on Systems Biology, Yokohama Japan, October 2006
LSI2002KieranSmallboneC.J. Kelly, K. Smallbone, T. Roose and J.M. Brady ‘A Systems Biology approach to assessing the feasibility of hypoxia imaging candidates’. To be presented at International Symposium for Biomedical Imaging, 13th April 2007. Presentation
LSI2002KieranSmallboneK Smallbone, E Simeonidis, N Swainston, P Mendes (2010). Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 4: 6.
LSI2002KieranSmallboneK Smallbone, PK Maini, RA Gatenby (2010). Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity. Biol Direct.
LSI2002KieranSmallboneK. Smallbone, D.J. Gavaghan, R.A. Gatenby, and P.K. Maini, ‘The role of acidity in solid tumour growth and invasion’, J. Theor. Biol. 235:476-484, 2005
LSI2002KieranSmallboneK. Smallbone, R.A. Gatenby, R.J. Gillies, P.K. Maini, D.J. Gavaghan, ‘Metabolic changes during carcinogenesis: potential impact on invasiveness’ J. Theor. Biol. 244: 703-713. 2007
LSI2002KieranSmallboneE Murabito, E Simeonidis, K Smallbone, J Swinton (2009). Capturing the essence of a metabolic network: A flux balance analysis approach. J Theor Biol 260: 445-452.
LSI2002KieranSmallboneR.A. Gatenby, K. Smallbone, P.K. Maini, F. Rose, J. Averill, R. Nagle, L. Worrall, R.J. Gillies, 'Cellular adaptations to hypoxia and acidosis during somatic evolution of breast cancer', British Journal of Cancer 97, 646–653, 2007. doi:10.1038/sj.bjc.6603
LSI2002KieranSmallboneK Smallbone, E Simeonidis (2009). Flux balance analysis: A geometric perspective. J Theor Biol 258: 311-315.
LSI2002KieranSmallboneK Smallbone, E Simeonidis, DS Broomhead, DB Kell (2007). Something from nothing - Bridging the gap between constraint-based and kinetic modelling. FEBS J 274: 5576-5585.
LSI2002KieranSmallboneCJ Kelly, K Smallbone, JM Brady (2008). Tumour glycolysis: The many faces of HIF. J Theor Biol 254: 508-513.
LSI2002KieranSmallboneMJ Herrgård, N Swainston, P Dobson, WB Dunn, KY Arga, M Arvas, N Blüthgen, S Borger, R Costenoble, M Heinemann, M Hucka, N Le Novère, P Li, W Liebermeister, ML Mo, AP Oliveira, D Petranovic, S Pettifer, E Simeonidis, K Smallbone, I Spasić, D Weichart, R B
LSI2002KieranSmallboneK Smallbone, RA Gatenby, PK Maini (2008). Mathematical modelling of tumour acidity. J Theor Biol 255: 106-112
LSI2002KieranSmallboneM Bilalić, K Smallbone, P McLeod, F Gobet (2009). Why are (the best) women so good at chess? Participation rates and gender differences in intellectual domains. Proc R Soc B 276: 1161-1165.
LSI2002KieranSmallboneK. Smallbone, D.J. Gavaghan, P.K. Maini, J.M. Brady. ‘Quiescence as a mechanism for cyclical hypoxia and acidosis’, J. Math. Biol. 55(5-6):767-79, 2007. doi:10.1007/s00285-007-0105-7.
LSI2002KieranSmallboneK. Smallbone  ‘The Role of Acidity in Tumour Development’ EPSRC Student Conference, 2005 [shared poster prize]
LSI2002JamesSouthernJ. Southern, G. Plank, E.J. Vigmond and J. Whiteley, 'Solving the coupled system improves computational efficiency of the Bidomain equations', IEEE Trans. Biomed. Eng., 2009. doi:10.1109/TBME.2009.2022548.
LSI2002JamesSouthernRafel Bordas, Bruno Carpentieri, Giorgio Fotia, Fabio Maggio, Ross Nobes, Joe Pitt-Francis, and James Southern Simulation of cardiac electrophysiology on next-generation high-performance computers Phil. Trans. R. Soc. A May 28, 2009 367:1951-1969, doi:10.
LSI2002JamesSouthernMiguel O. Bernabeu, Rafel Bordas, Pras Pathmanathan, Joe Pitt-Francis, Jonathan Cooper, Alan Garny, David J. Gavaghan, Blanca Rodriguez, James A. Southern, and Jonathan P. Whiteley. Chaste: incorporating a novel multi-scale spatial and temporal algorithm
LSI2002JamesSouthernJ. Southern, J. Pitt-Francis, J. Whiteley, D. Stokeley, H. Kobashi, R. Nobes, Y. Kadooka and D.J. Gavaghan, 'Multi-scale computational modelling in biology and physiology', Prog. Biophys. Mol. Biol., 2007. doi:10.1016/j.pbiomolbio.2007.07.019.
LSI2011JackMillerHyperpolarised Spectral Spatial EPI at 7 T, Miller, JJ, Lau, AZ, Tyler, DJ, Proceedings of the 4th International DNP Symposium
LSI2011JackMillerMiller, J J “The Speed of Light: Constancy and Cosmos (Grandy): A Review" Kaleidoscope 6.1 (2014)
LSI2010RichardMasonR.P. Mason and A. Papachristodoulou. 'Dynamic Edge Adaptation in Delayed Oscillator Networks. Proc of the 51st IEEE Conference on Decision and Control, Maui, HI, 2012.
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Guaranteed error bounds for structured complexity reduction of biochemical networks.” Journal of Theoretical Biology, 304:172-182
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Layering in networks: The case of biochemical systems.” In Proceedings of the American Control Conference (ACC), Washington D.C., pp.4544-4549
LSI2010FirdausAbd WahabPrafulla Aryal, Firdaus Abd-Wahab, Giovanna Bucci, Mark S P Sansom, and Stephen J Tucker. A hydrophobic barrier deep within the inner pore of the TWIK-1 K2P potassium channel. Nature Communications, 5, July 2014.
LSI2010RichardMasonR.P. Mason and A. Papachristodoulou. 'Chordal Sparsity, Decomposing SDPs and the Lyapunov Equation. Proceedings of the American Control Conference (ACC), Portland, OR, 2014.
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Layered decomposition for the model order reduction of timescale separated biochemical reaction networks.” Journal of Theoretical Biology, 356:113-122
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Signal propagation across layered biochemical networks.” In Proceedings of the American Control Conference (ACC), Portland OR, pp.3399-3404
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Synthetic Biology: A Control Engineering Perspective.” In Proceedings of the European Control Conference (ECC), Strasbourg, France, pp.1182-1186
LSI2010TomPrescottT. P. Prescott & A. Papachristodoulou. “Structured storage functions for cascaded systems” In Proceedings of the IEEE Conference on Decision and Control (CDC), Los Angeles CA, in press
LSI2002RobinFreemanFreeman & D Biro. Modelling Group Navigation: Dominance and Democracy in Homing Pigeons. Journal of Navigation, 62. 2009.
LSI2002DannyAxfordXiaoyun J, Geoff Sutton, Gwyndaf Evans, Danny Axford, Robin Owen and David I Stuart ‘How baculovirus polyhedra fit square pegs into round holes to robustly package viruses’ The EMBO Journal (2010) 29, 505 - 514
LSI2002DannyAxfordJ. Aishima, R. L. Owen, D. Axford, E. Shepherd, G. Winter, K. Levik, P. Gibbons, A. Ashton and G. Evans ‘High-speed crystal detection and characterization using a fast-readout detector’ Acta Cryst. (2010). D66, 1032-1035
LSI2002DannyAxfordJ. Hausmann, E. Christodoulou, M. Kasiem, V. De Marco, L. A. van Meeteren, W. H. Moolenaar, D. Axford, R. L. Owen, G. Evans and A. Perrakis ‘Mammalian cell expression, purification, crystallization and microcrystal data collection of autotaxin/ENPP2, a se
LSI2002DannyAxfordG. Evans, D. Axford and R. L. Owen ‘The design of macromolecular crystallography diffraction experiments’ Acta Cryst. (2011). D67, 261-270
LSI2002DannyAxfordJ. J. Davis, D. A. Morgan, C. L. Wrathmell, D. N. Axford, J. Zhao and N. Wang ‘Molecular Bioelectronics’ Journal of Materials Chemistry, 15(22), pp 2160-2174, 2005
LSI2002DannyAxfordD. Axford, J.J. Davis, N. Wang, D. Wang, T. Zhang, J. Zhao, B. Peters. ‘Molecularly resolved protein electromechanical properties’. J. Phys. Chem. B, 2007, 111 (30):9062–9068. doi: 10.1021/jp070262o.
LSI2002DannyAxfordD. Axford ‘Interfacing Biomolecules with Nanoscale circuitry’ Veeco users meeting, Oxford, November 2005.
LSI2002DannyAxfordDavis, J. J., Peters, B., Xi, W. & Axford, D. Molecularly-resolved bioelectronics. Current Nanoscience 4
LSI2002DannyAxfordD. N Axford and J. J Davis ‘Electron flux through apo-and holoferritin’ Nanotechnology 18, 2007
LSI2002EllaChaseE.K. Chase, G. McVean, K.P. Day, AE Barry ‘Diversity of DBL Domains of the Major Surface Antigen of Plasmodium falciparum’ Int. Meeting on Molecular Epidemiology & Evolutionary Genetics of Infectious Diseases, Valencia, July 2004.
LSI2002EllaChaseE.K. Chase, A.E. Barry, K.P. Day, G. McVean ‘A new method for quantifying recombination in the var genes encoding the major surface antigens of P. falciparum’ Gordon Research Conference, Malaria, August 2005.
LSI2002RobinFreemanT. Guilford, J. Meade, J. Willis, R.A. Phillips, D. Boyle, S. Roberts, M. Collett, R. Freeman, and C.M. Perrins. Migration and stopover in a small pelagic seabird, the Manx shearwater 'Puffinus puffinus': insights from machine learning. Proc. Roy. Soc. B
LSI2002RobinFreemanR Freeman, T. Dennis, T Landers, D Thompson, E Bell, et al. 2010 Black Petrels (Procellaria parkinsoni) Patrol the Ocean Shelf-Break: GPS Tracking of a Vulnerable Procellariiform Seabird. PLoS ONE 5(2), 2010.
SABS-IDC2009GregoryRossRoss GA, Morris GM, Biggin PC (2012) Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites. PLoS ONE 7(3): e32036
SABS-IDC2009LeilaAlexanderLori C, Lantella A, Pasquo A, Alexander LT, Knapp S, Chiaraluce R, & Consalvi V (2013) Effect of single amino acid substitution observed in cancer on Pim-1 kinase thermodynamic stability and structure. PLOS ONE (in press, accepted)
SABS-IDC2010JamesDunbarJ. Dunbar, A. Fuchs, J. Shi, CM. Deane, ABangle: Characterising the VH-VL orientation in antibodies, Protein Eng. Des. & Sel., 2013, 26(10), 611-620
SABS-IDC2011DavidBowkettPresented a poster (Phylogenetic Analysis of Plant Homeodomain Fingers) at 3rd Oxford Symposium on Epigenetics Mechanisms in Health and Disease.
SABS-IDC2011DavidBowkettWon SABS-IDC short project prize 2012
SABS-IDC2011RadoslawNowak"Chemical tools for human 2-oxoglutarate dependent oxygenases NO66 and MINA53", Radoslaw Nowak, Catrine Johansson, Anthony Tumber, Dafydd Owen, David Pryde, Udo Oppermann, 3rd Oxford Symposium on Epigenetics Mechanisms in Health and Disease: Neuropsychiatry and inflamation: epigenetic target discovery beyond oncology. Oxford, March 14-15, 2013, SBS.
SABS-IDC2010Anthony JamesConnorAnthony Connor, Jonathan Cooper, Helen Byrne, Philip Maini, Steve McKeever, 'Object-Oriented Paradigms for Modelling Vascular Tumour Growth: a Case Study'. Proceedings of SIMUL 2012, The Fourth International Conference on Advances in System Simulation, 18
SABS-IDC2010Anthony JamesConnorMcKeever, S., Gill, M., Connor, A. J., & Johnson, D. (2013). Abstraction in Physiological Modelling Languages (pp. 1–8). Accepted (to be presented at the 3rd International Workshop on Model-driven Approaches for Simulation Engineering).
SABS-IDC2010Anthony JamesConnorDavid Johnson, Anthony Connor, Steve McKeever, 'Modular Markup for Simulating Vascular Tumour Growth'. Proceedings of the 5th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation (5th IARWISOCI) - The TUMOR Workshop, 22-
SABS-IDC2010AndrewElliottElliott, A: 'A systematic study of Parkinson’s disease network construction through sub-sampling and seed lists'. EMBL Networks in the Life Sciences Workshop (October 2012)
SABS-IDC2010JeanHelieINTERACTIONS OF TWO AMPHIPATHIC CELL-PENETRATING PEPTIDES WITH COMPLEX MODEL MEMBRANES: INSIGHTS FROM MOLECULAR DYNAMICS SIMULATIONS
Author Block: Jean Helie1, Francesca Milletti2, Charlotte M. Deane1, Mark S.P. Sansom1.
1Oxford University, Oxford, United Kingdom, 2Hoffmann-La Roche, Nutley, NJ, USA, it was presented in 2013 at the 57th Biophysical Society Annual Meeting
SABS-IDC2010JamesDunbarEMTRAIN workshop at AstraZeneca where I presented my research to other industrially sponsored PhD students from across Europe
SABS-IDC2010Nicholas CharlesDunkleyPatient-specific Predictions in the Intensive Care Unit using a Bayesian Ensemble Alistair Johnson, Nic Dunkley, Louis Mayaud, Athanasios Tsanas, Andrew Kramer and Gari Clifford
SABS-IDC2010Nicholas CharlesDunkleyComputing in Cardiology Challenge (2012).
SABS-IDC2010LauraJenningsReview: Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. J. Med. Chem. 55:9393 (2012) Jennings, L and Rooney, T
SABS-IDC2010Henry RobertWilman3Dsig, 13th July 2012, Long Beach California. Oral presentation: Kinks in Transmembrane Helices. Henry R. Wilman, Jiye Shi, Charlotte M. Deane.
SABS-IDC2010Henry RobertWilmanPoster Prize at UCB PhD Day, October 2012
SABS-IDC2009Kok PhinChooiNov 2011: Commendation for performance at PRS transfer viva (Department of Organic Chemistry, Oxford)
Nov 2011: Commendation for performance at PRS transfer viva (Department of Organic Chemistry, Oxford)
SABS-IDC2009JieqingJiaoJiao, J., Salinas, C.A., Searle, G.E., Gunn, R.N., Schnabel, J.A.: Joint estimation of subject motion and tracer kinetic parameters of dynamic PET data in an EM framework. Proc. SPIE 83140A (2012).
SABS-IDC2009JieqingJiaoJiao, J., Searle, G.E., Schnabel, J.A., G.E., Gunn, R.N.: Pharmacokinetic model based groupwise image registration of 4D brain PET data and its impact on clinical occupancy studies with [11C]-(+)-PHNO. International Symposium on Cerebral Blood Flow, Metab
SABS-IDC2009JieqingJiaoJiao, J., Searle, G.E., Tziortzi, A.C., Salinas, C.A., Gunn, R.N., Schnabel, J.A.: Spatio-temporal pharmacokinetic model based registration of 4D brain PET data. Proc. MICCAI Workshop on Spatiotemporal Image Analysis for Longitudinal and Time-Series Image
SABS-IDC2009JieqingJiaoJiao, J., Schnabel, J.A., Gunn, R.N.: A Generalised Spatio-Temporal Registration Framework for Dynamic PET Data: Application to Neuroreceptor Imaging. (under review
SABS-IDC2009JieqingJiaoJiao, J., Searle, G.E., Tziortzi, A.C., Salinas, C.A., Gunn, R.N., Schnabel, J.A.: Spatio-temporal pharmacokinetic model based registration of 4D PET neuroimaging data. (under review)
SABS-IDC2009JieqingJiao2011: CSSAUK High-Level Entrepreneurship Challenge Honourable Mention
SABS-IDC2009JieqingJiao2013: ISCBFM Young Investigator Travel Bursary by International Symposium on Cerebral Blood Flow, Metabolism and Function and International Conference on Quantification of Brain Function with PET
SABS-IDC2009JieqingJiao2012: Guarantors of Brain Student Award
SABS-IDC2009MatthiasSchmidtSimulation-Based Prediction of Phosphatidylinositol 4,5-Bisphosphate Binding to an Ion Channel. Matthias R. Schmidt, Phillip J. Stansfeld, Stephen J. Tucker, Mark S.P. Sansom (Biochemistry, 2012).
SABS-IDC2009MatthiasSchmidtFeatured in PSI Nature "Research Advances section" for March 2012
SABS-IDC2009MatthiasSchmidtState-Independent Intracellular Access of Quaternary Ammonium Blockers to the Pore of TREK-1. Markus Rapedius (*), Matthias R. Schmidt (*), Chetan Sharma, Phillip J. Stansfeld, Markus Rapedius, Mark S.P. Sansom, Thomas Baukrowitz, Stephen J. Tucker (Chann
SABS-IDC2009MatthiasSchmidtStructure of a KirBac Potassium Channel with an Open Bundle-Crossing Indicates a Mechanism of Channel Gating. Vassily N. Bavro, Rita de Zorzi, Matthias R. Schmidt, Joao R.C. Muniz, Lejla Zubcevic, Mark S.P. Sansom, Catherine Venien-Bryan, Stephen J. Tucke
SABS-IDC2009MatthiasSchmidtStructure of a KirBac Potassium Chann el with an Open Bundle-Crossing Indicates a Mechanism of Channel Gating. Vassily N. Bavro (*), Rita de Zorzi (*), Matthias R. Schmidt, Joao R.C. Muniz, Lejla Zubcevic, Mark S.P. Sansom, Catherine Venien-Bryan, Stephen
SABS-IDC2009MatthiasSchmidtState-Independent Intracellular Access of Quaternary Ammonium Blockers to the Pore of TREK-1. Markus Rapedius (*), Matthias R. Schmidt (*), Chetan Sharma, Phillip J. Stansfeld, Markus Rapedius, Mark S.P. Sansom, Thomas Baukrowitz, Stephen J. Tucker (Chann
SABS-IDC2009MatthiasSchmidtR.deBoer, D.Klunder, R.Penterman, C.deWitz, R.Schroeders, J.Lub,M.R.Schmidt, Advances in Microarray Technologies,Stockholm,Sweden,2009 (Poster)
SABS-IDC2009MatthiasSchmidtM.R.Schmidt, Philips Technical Note PR-­‐TN 2006/01132: Optical spectroscopy on joints for rheumatoid arthritis
SABS-IDC2009MatthiasSchmidtM.R. Schmidt, Philips Technical Note PR-­‐TN 2009/00302: The wire grid biosensor for nucleic acid testing
SABS-IDC2009KonradKrawczyki-Patch web service: inter-protein contact prediction using local network information, Krawczyk, K., Hamer R., Luo, Q., Armitage, J., Reinert, G., Deane, C.M.; poster presented at ECCB 2010.
SABS-IDC2009LydiaLe PageBritish Chapter of ISMRM, Manchester, MT 2011/12, Oral presentation: Assessment of PDK inhibition in the isolated perfused rat heart using hyperpolarized pyruvate
SABS-IDC2009LydiaLe PageAlternative Muscle Club, Oxford, TT 2011, Flash Talk: Development and Application of Magnetic Resonance techniques for studying drug effects in the healthy and diseased heart.
SABS-IDC2009MatthiasSchmidtM.R.Schmidt, P.J.Stansfeld, M.Rapedius T.Baukrowitz, S.J.Tucker, M.S.P.Sansom, Biophysical Journal,vol.100,issue 3, pp 431a, Baltimore
SABS-IDC2009LydiaLe PageThe International Society for Magnetic Resonance in Medicine, Melbourne, HT 2012, e-Poster: Investigating pharmacological modification of cardiac pyruvate metabolism using hyperpolarized magnetic resonance
SABS-IDC2009LydiaLe PageImaging Festival, Oxford, MT 2012/13, Poster: Assessment of real-time cardiac and hepatic glucose metabolism in the diabetic rat
SABS-IDC2009LydiaLe PageEMTRAIN workshop, Manchester, HT2012, Oral presentation: Development and Application of Magnetic Resonance Techniques for the Study of Drug Effects on Metabolism in the Healthy and Diseased Heart
SABS-IDC2009LydiaLe PageSociety for Heart and Vascular Metabolism, Oxford, TT 2012, Poster: Real-time assessment of pharmacologically altered metabolism in the rat heart using hyperpolarised [1-13C] pyruvate
SABS-IDC2009LydiaLe PageMitOx Meeting, Oxford, MT 2012/13, Oral Presentation: Assessment of real-time, in vivo cardiac and hepatic glucose metabolism in the diabetic rat using hyperpolarized 13C pyruvate, Won best PhD presentation, sponsored by Merck
SABS-IDC2009LydiaLe PageDiabetes UK, Manchester, HT 2013, Poster: Assessment of real-time, in vivo cardiac and hepatic glucose metabolism in the diabetic rat, using hyperpolarized 13C pyruvate
SABS-IDC2009TimothyRooneyREVIEW: Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. Hewings, D. S.; Rooney, T. P. C.; Jennings, L. E.; Hay, D.; Schofield, C. J.; Brennan, P. E.; Knapp, S.; Conway, S. J.,J. Med. Chem., 2012, 55, 9393.
SABS-IDC2009TimothyRooneyMarch 2013: Bronze award for chemistry research presented at SET for BRITAIN, house of commons.
SABS-IDC2009TimothyRooneyDecember 2011: Prize for poster presented at Biological and Medicinal Chemistry Symposium.
SABS-IDC2009TimothyRooneyApril 2012: David Kelly prize for best poster at Bio-Organic Postgraduate Symposium.
SABS-IDC2009MatthiasSchmidtStructural and Mechanistic Insights into Gating of K2P Channels. M. Rapedius, P.L. Piechotta, P.J. Stansfeld, M.R. Schmidt, M.K. Bollepalli, G. Ehrlich, I. Andres-Enguix, H. Fritzenschaft, N. Decher, M.S.P. Sansom, S.J. Tucker, T. Baukrowitz (Poster at the Biophysical Society Meeting, San Diego, March 2012).
SABS-IDC2009MatthiasSchmidtX-Ray Crystal Structure of a Prokaryotic Kir channel in an Open Conformation: Insights into the Mechanism of Opening at the Bundle-Crossing Gate. Vassily N. Bavro (*), Rita de Zorzi (*), Matthias R. Schmidt, Joao R.C. Muniz, Lejla Zubcevic, Mark S.P. Sansom, Catherine Venien-Bryan, and Stephen J. Tucker. (Poster presented at the meeting of the Physiological Society in Oxford, July 2011)
SABS-IDC2012JinwooLeemDunbar, J., Krawczyk, K., Leem J., Baker T., Fuchs A., Georges G., Shi J., and Deane C.M. (2014). Nucleic Acids Res. 42. D1140-D1146
SABS-IDC2011StefanVerhoogMizuta, S.; Galicia-López, O.; Engle, K. M.; Verhoog, S.; Wheelhouse, K.; Rassias, G.; Gouverneur, V. Chemistry – A European Journal 2012, 18, 8583-8587.
SABS-IDC2011StefanVerhoogGao, Z.; Lim, Y. H.; Tredwell, M.; Li, L.; Verhoog, S.; Hopkinson, M.; Kaluza, W.; Collier, T. L.; Passchier, J.; Huiban, M.; Gouverneur, V. Angew. Chem. Int. Ed. 2012, 51, 6733-6737.
SABS-IDC2011SamuelGrayerCH-01 is a Hypoxia-Activated Prodrug That Sensitizes Cells to Hypoxia/Reoxygenation Through Inhibition of Chk1 and Aurora A Cindy Cazares-Körner, Isabel M. Pires, I. Diane Swallow, Samuel C. Grayer, Liam J. O’Connor, Monica M. Olcina, Martin Christlieb, Stuart J. Conway, and Ester M. Hammond Articles ASAP (As Soon As Publishable) Publication Date (Web): April 18, 2013 (Articles); ACS Chemical Biology
SABS-IDC2011StefanVerhoogMizuta, S.; Engle, K. M.; Verhoog, S.; Galicia-López, O.; O’Duill, M.; Médebielle, M.; Wheelhouse, K.; Rassias, G.; Thompson, A. L.; Gouverneur, V. Organic Letters 2013, 15, 1250-1253.
SABS-IDC2011StefanVerhoogMizuta, S.; Verhoog, S.; Engle, K. M.; Khotavivattana, T.; O’Duill, M.; Wheelhouse, K.; Rassias, G.; Médebielle, M.; Gouverneur, V. Journal of the American Chemical Society 2013, 135, 2505-2508.
SABS-IDC2011RachelShamo SchillerSchiller, R.; Scozzafava, G.; Tumber, A.; Wickens, J. R.; Bush, J. T.; Rai, G.; Lejeune, C.; Choi, H.; Yeh, T.-L.; Chan, M. C.; Mott, B. T.; McCullagh, J. S. O.; Maloney, D. J.; Schofield, C. J.; Kawamura, A. A cell-permeable ester derivative of the JmjC histone demethylase inhibitor IOX1. ChemMedChem 2014, 9, 566–71.
SABS-IDC2011AngelinaMeasuresJennings, L. E.; Measures, A. R.; Wilson, B. G.; Conway, S. J. Phenotypic Screening and Fragment-Based Approaches to the Discovery of Small-Molecule Bromodomain Ligands. Future Medicinal Chemistry 2014, 6, 179–204.
SABS-IDC2010Kylie AnnBeattieK.A. Beattie, C. Luscombe, G. Williams, J. Munoz-Muriedas, D.J Gavaghan, Y. Cui, G.R. Mirams, Evaluation of an in silico cardiac safety assay: Using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge, Journal of Pharmacological and Toxicological Methods (2013), http://dx.doi.org/10.1016/j.vascn.2013.04.004
SABS-IDC2010JamesDunbarABangle: Characterising the VH-VL orientation in antibodies. J.Dunbar, A.Fuchs, J.Shi and C.M.Deane. Protein Engineering Design and Selection. 2013. doi:10.1093/protein/gzt020.
SABS-IDC2010KylieBeattieBeattie, K. A., Luscombe, C., Williams, G., Munoz-Muriedas, J., Gavaghan, D. J., Cui, Y., & Mirams, G. R. (2013). Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge. Journal of pharmacological and toxicological methods, 68(1), 88-96
SABS-IDC2010JamesDunbarJ. Dunbar, B. Knapp, A. Fuchs, J. Shi and CM. Deane. Examining variable domain orientations in antigen receptors gives insight into TCR-like antibody design, PLOS Comp. Bio., 2014, 10(9), e1003852
SABS-IDC2010JamesDunbarB. Knapp, J. Dunbar and CM. Deane. Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study, PLOS Comp. Bio., 2014, 10(8), e1003748
SABS-IDC2010JamesDunbarJ. Dunbar, K. Krawczyk, J. Leem, T. Baker, A. Fuchs, G. Georges, J. Shi and CM. Deane, SAbDab: the Structural Antibody Database, Nucleic Acids Res., 2014, 42, D1140-D1146
SABS-IDC2010HenryWilmanWilman, H. R., Shi, J. and Deane, C. M. (2014), Helix kinks are equally prevalent in soluble and membrane proteins. Proteins: Structure, Function, and Bioinformatics 82: 1960–1970. doi: 10.1002/prot.24550
SABS-IDC2010HenryWilmanHenry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, and Bernhard Knapp (2014), Crowdsourcing Yields a New Standard for Kinks in Protein Helices. Journal of Chemical Information and Modeling 54 (9): 2585-2593
SABS-IDC2009LydiaLe PageM.S. Dodd, D.R. Ball, M.A. Schroeder, L. M. Le Page, H. J. Atherton, L.C. Heather, A-M. Seymour, H. Ashrafian, H. Watkins, K. Clarke and D.J. Tyler, “In vivo alterations in cardiac metabolism and function in the spontaneously hypertensive rat heart”, Cardiovascular Research, 2012
SysBio2010OliverBrittonExperimentally calibrated population of models predicts and explains intersubject variability in cardiac cellular electrophysiology
SysBio2012AnnaMuszkiewiczDynamic allostery in proteins: the case of the PDZ3 domain, id2 Conference UCL
SysBio2012PaulTaylorCombining Waddington's Epigenetic Landscape With Delayed Reactions, id2 Conference UCL
SysBio2011XinZhou'Post-myocardial Infarction Ionic Remodelling and HERG Block Prolong the Action Potential and Facilitate Alternans in a Human Ventricular Model of the Epicardial Border Zone'. Presented at the 36th meeting of the European Working Group on Cardiac Cellular
SysBio2011LucieBowdenAn ODE model for the healing of full thickness wounds and the effects of diabetes, id2 Conference UCL
SysBio2011KatharineCoyteInvestigating Bacterial Ecology and Evolution in Complex Environments (poster), id2 Conference UCL
at UCL
SysBio2011XinZhouMicrosoft Research Project Award for 2012
SysBio2010Andrew JohnBissetteBisette, A and Fletcher, S: 'A click chemistry model for self-reproducing systems'. Poster presented at Gordon Research Conference on the Origin of Life, Galveston, Texas (January 2012)
SysBio2010Andrew JohnBissetteEli Lilly prize for excellence in organic chemistry
SysBio2010Markus AlexanderGerstelSiemate – A Social Travel Guide, Manuela Schauer, Markus Gerstel, Adriano Pastore, 2007, published in: Effective Collaboration in Dynamic Communities with Service-Oriented Architectures, Ana Balevic, Bruno Bozionek, Bernhard Kirchmair, Nikolaus Konrad, Ph
SysBio2010Markus AlexanderGerstelIntroductory Tutorial in Parallel Programming, with talks on OpenMP and Profiling, 25.–29.09.2009, together with Marcel Meyer and Stefan Wallentowitz, part of the doctoral seminar on Advanced Computing (course 20) of the 2009 Ferienakademie summer school,
SysBio2010Markus AlexanderGerstelOptimizing the spatial distribution of dose in X-ray macromolecular crystallography, O. B. Zeldin, Markus Gerstel, E. F. Garman, 2013, J. Synchrotron Rad. 20, 49–57. electronic preprint (PDF)
SysBio2010Markus AlexanderGerstelMethod and arrangement for supporting a user and a user group, 20.08.2007, US Patent Application 20090055753, together with co-inventors Manuela Schauer, Adriano Pastore, Bruno Bozionek, Ana Balevic.
SysBio2010Markus AlexanderGerstelQuantitative Radiation Damage Studies, 28.01.2013, Markus Gerstel, C. M. Deane, E. F. Garman; Poster presentation at the annual DTC symposium 2013
SysBio2010Markus AlexanderGerstelUnderstanding Specific Radiation Damage, 14.-16.03.2012, Markus Gerstel, Isaac Turner, C. M. Deane, E. F. Garman; Poster presentation at Seventh International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
SysBio2010Markus AlexanderGerstelHi-Throughput Colorectal Crypt Monoclonality Simulation, 24.03.2011, SysBio DTC, University of Oxford.
SysBio2010GeorginaLangWilfrid Knapp Scholarship (Sciences) from St Catherine's College (2012-2014)
SysBio2010Stephen GeorgeO'KeeffeBest student presentation at the 2012 OCCAM modelling camp
SysBio2010Natalie ClarePearsonPearson N, Shipley R J, Waters S L, Oliver J M. Multiphase modelling of the influence of fluid fl ow and chemical concentration on tissue growth in hollow fibre membrane bioreactors. Submitted (2013) to special edition of Mathematical Medicine & Biology.
SysBio2010Natalie ClarePearsonKelly C J, Hussien K, Shipley R J, Stratford M, Pearson N, Muschel R J. Modulation of oxidative metabolism through the PI3K-Akt-mTOR pathway reduces hypoxia in cancer cells: a novel indication for established drugs. Submitted (2012) to Cancer Research.
SysBio2010Marta AnnaSarzynskaSarzynska, M: 'Community structure in epidemics'. Poster presented at the XXXII Dynamics Days Europe, Gothenburg (2012 _
SysBio2010Markus AlexanderGerstelBeam Profiling on an in-house X-ray generator for radiation damage studies, 23-27.09.2012, E. F. Garman, Markus Gerstel; Talk at the 20th Bruker AXS Users' Meeting, Bad Herrenalb
SysBio2009KamaludinDinglePublication in preparation ‘Knudsen’s law and random billiards in irrational triangles’ with J. Lamb (Imperial) and A.Lazaro-Cami (Imperial)
SysBio2009SaraDuttaInterpreting optical mapping recordings in the ischemic heart: a combined experimental and computational investigation. FIMH (Functional Imaging and Modelling of the Heart)
SysBio2009SaraDuttaBest poster at Imperial College Cardiovascular Technology Symposium February 2012
SysBio2009JessicaMcGillenMcGillen J, Martin MK, Robertson D, Altman N, Carley KM. “300 Cities Virtual Experiment,” Institute for Software Research, Dept. of Computer Science, Carnegie Mellon University (Technical Report)
SysBio2009JessicaMcGillenMcGillen J, Martin NK, Robey I, Gaffney EA, Maini PK. Applications of mathematical analysis to tumour acidity modelling. RIMS Kokyuroku Bessatsu, B31 . pp. 31-59
SysBio2009JessicaMcGillenMcGillen JB, Martin NK, Robey IF, Gaffney EA, Maini PK (2012). Applications of mathematical analysis to tumour acidity modelling. U. Kyoto RIMS Kokyuroku Bessatsu, B31:31-59.
SysBio2009JessicaMcGillenOverseas Graduate Scholarship for academic achievement, St. Catherine's College, 2011-present
SysBio2009JessicaMcGillenPrize for best presentation, DTC 4th Year Conference, 2013
SysBio2009JessicaMcGillenLandahl Travel Grant, Society for Mathematical Biology, 2012
SysBio2009JessicaMcGillenNational Cancer Institute NIH grant 1U54CA143970-01 (funding for short project with Prof. Philip Maini), 2010
SysBio2009JessicaMcGillenEuropean Society for Mathematical and Theoretical Biology travel grant, 2011
SysBio2009MargaritaSchlackowMicrosoft Research Cambridge Award for a DTC summer project: Mathematical modelling and experimental verification of interactions between the RNA polymerase and cohesin complex in transcription .
SysBio2009Hong YoungNohP. J. Bream, H. Y. Noh, A. Kohn, M. A. Smith, E. Phoka, M. Barahona and S. R. Schultz, "Analysis of Functional and Causal Neural Networks in the Visual Cortex." First Imperial College London Institute of Biomedical Engineering ‘Symposium of the Neuroscien
SysBio2009KamaludinDingle‘Knudsen’s law and ergodicity of a polygonal billiard with noise’ at the LDSG workshop on “Random dynamical systems and applications”
SysBio2009BernadettGaalEvolution of stochastic switching, presented at the 2010 Systems Biology of Stem Cells Symposium at the University of California Irvine.
SysBio2009BernadettGaalGaal B, Pitchford JW, Wood AJ. 2010 Exact results for the evolution of stochastic switching in variable asymmetric environments. Genetics 184, 1113-9
SysBio2009KenWang‘A Local Sensitivity Analysis Method for Developing Cardiac Models with Identifiable Parameters: Application to L-type Calcium Channels Regulation’ was accepted in IEEE eScience 2010 conference
SysBio2009KenWang“Local and Global sensitivity analysis Tools for Assessment and Development of Cellular and Ionic Cardiac” was presented in 2010 MEC international workshop
SysBio2009SaraDuttaInterpreting Optical Mapping Recordings in the Ischemic Heart: A Combined Experimental and Computational Investigation, T. Alexander Quinn Sara Dutta Martin J. Bishop Pras Pathmanathan Peter Lee Peter Kohl and Blanca Rodriguez. Lecture Notes in Computer S
SysBio2009JessicaMcGillen“Mathematical modelling of tumour acidity,” to be given at a meeting of the Centre for Mathematical Biology (upcoming in June) talk and poster.
SysBio2009SaraDuttaRecent Human Ventricular Cell Action Potential Models under Varied Ischaemic Conditions, id2 Conference UCL
SysBio2009KatherineLeonardGroup presentation to Biostruct at Heidelberg, Germany.
SysBio2009KatherineLeonardJunior Applied Mathematics Seminar, University of Oxford.
SysBio2009KatherineLeonardPresentation of talk at the University of Oxford Department of Computer Science Student Conference.
SysBio2009KatherineLeonardPresentation of poster at the Google Scholars Retreat in Zurich, Switzerland.
SysBio2009KatherineLeonardPresentation of poster at inter-DTC Systems Biology Conference, Manchester.
SysBio2009KatherineLeonardJesus College Graduate Scholarship, University of Oxford.
SysBio2009KatherineLeonardGoogle Europe Scholarship for Students with Disabilities.
SysBio2009MatthewWebberThe e_x000B_ects of noise on binocular rivalry
waves: a stochastic neural field model Matthew A Webber and Paul C Bresslof. Journal of Statistical Mechanics: Theory and Experiment
SysBio2009MatthewWebberNeural field model of binocular rivalry waves Paul C. Bressloff · Matthew A. Webber. J Comput Neurosci (2012) 32:233–252
SysBio2009MatthewWebberFront Propagation in Stochastic Neural Fields. Paul C. Bressloff and Matthew A. Webber. SIAM J. APPLIED DYNAMICAL SYSTEMS 2012Vol. 11, No. 2, pp. 708–740
SysBio2008SuruchiBakshiPoster presentation on mathematical modelling of asymmetric stem cell division European Conference on Mathematical and Theoretical Biology – to be held in June-July, 2011
SysBio2008SuruchiBakshiPoster presentation on mathematical modelling of asymmetric stem cell division in Warwick Inter-SysBio-DTC student conference (June 2010).
SysBio2008Tiago MiguelChegancas RitoOral presentation following a proceedings publication at the 9th European Conference on Computational Biology (ECCB 2010)
SysBio2008Tiago MiguelChegancas RitoTiago Rito, Zi Wang, Charlotte M. Deane and Gesine Reinert (2010), “How threshold behaviour affects the use of subgraphs for network comparison”, Bioinformatics 26 (18): i611-i61.
SysBio2008Tiago MiguelChegancas RitoPoster presentation at RECOMB 2010
SysBio2008HelenCurtisRoberts T, Curtis H. Gene regulation by small RNAs. J RNAi Gene Silencing; 2010; 6(1):376-8.
SysBio2008HelenCurtisLlarena, M., Bailey, D., Curtis, H. and O’Hare, P. Different Mechanisms of Recognition and ER Retention by Transmembrane Transcription Factors CREB-H and ATF6. Traffic; 2010; 11(1):48-69.
SysBio2008HelenCurtisPoster presented at Biochemical Society Meeting, Micro RNAs and their targets: promises and pitfalls, London, UK, November 2010.
SysBio2008CarolineDahlDahl ACE and Thompson MS (2011) Biomechanics: Mechanobiology of bone. Comprehensive Biotechnology, 2nd ed Elsevier
SysBio2008CarolineDahlDahl ACE, Chavent M and Sansom MSP (2012) Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 28 (16): 2193-2194.
SysBio2008CarolineDahlDTC Systems Biology Conference 2010, Warwick
SysBio2008JenniferDe BeyerJennifer A. de Beyer and Jan-Hendrik S. Hofmeyr (2008). Homeostasis in branched metabolic networks: a study of regulatory design. Talk abstract in proceedings: International Study Group for Systems Biology – August 17-20 2008, Elsinore, Denmark.
SysBio2008JenniferDe BeyerJennifer A. de Beyer, Mark A. J. Roberts, Kathryn A. Scott, David Staunton and Judith P. Armitage (2011). Methylation based adaptation in Rhodobacter sphaeroides chemotaxis. Poster abstract in proceedings: Bacterial Locomotion and Signal Transduction (BLA
SysBio2008JenniferDe BeyerAlice C. Ind, Steven L. Porter, Mostyn T. Brown, Elaine D. Byles, Jennifer A. de Beyer, Scott A. Godfrey, and Judith P. Armitage (2009). Inducible-Expression Plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Applied and Environmental Micro
SysBio2008LouiseDysonPlatform session (i.e. a talk) at the Biophysical Society 54th Annual General Meeting, San Francisco. 'Mathematical modelling of cranial neural crest cell migration' 2009
SysBio2008LouiseDyson£250 award for the best Systems Biology Doctoral Training Centre short project, sponsored by Microsoft.
SysBio2008PhilipGemmellP. Gemmell, K. Burrage, B. Rodriguez, and T.A. Quinn, "The Effects of Parameter Variation on a Rabbit Ventricular Cell Model". Conf Proc IEEE Eng Med Biol Soc; 2010:2662-5. doi: 10.1109/IEMBS.2010.5626617.
SysBio2008PhilipGemmellWerner, G. D., Gemmell, P., Grosser, S., Hamer, R., & Shimeld, S. M. (2012). Analysis of a deep transcriptome from the mantle tissue of Patella vulgata Linnaeus (Mollusca: Gastropoda: Patellidae) reveals candidate biomineralising genes. Marine Biotechnolo
SysBio2008MireilleGomesAbelson, J. Davies, R. Fraser, M. Gomes, T. Kuo, S. Sedfawi, S. Taylor, E. Zuviria, & J. Glasgow. Protein Structure from Contact Maps: A Hierarchical Approach. In 2006 German Conference on Bioinformatics (GCB 2006) Abstracts, pp. 62, Tübingen, Germany,
SysBio2008MireilleGomesR. Fraser, M. Gomes, & J. Glasgow. The packing attribute of alpha helices as an advisor to evaluate proposed protein structures. In 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Com
SysBio2008MireilleGomesM. Gomes, R. Hamer, C. Deane, & G. Reinert. Investigating the Specificity of the Histidine Kinase Response Regulator Complexes using Mutual Information. In 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) Onlin
SysBio2008SophieKayTowards In Silico Drug Discovery in the Colorectal Crypt (August 2010) CompuCell3D & Systems Biology Workbench Workshop, Indiana, USA.
SysBio2008SophieKayBiological Applicability of the Cellular Potts Model (January 2011) KAIST International Workshop on Cancer Modelling, Seoul, S.Korea.
SysBio2008SophieKayBiological Applicability of the Cellular Potts Model [PRESENTATION] (January 2011) KAIST International Workshop on Cancer Modelling, Seoul, S.Korea.
SysBio2008SophieKayJ. M. Osborne, A. Walter, S. K. Kershaw, G. R. Mirams, A. G. Fletcher, P. Pathmanathan, D. Gavaghan, O. E. Jensen, P. K. Maini, H. M. Byrne ‘A hybrid approach to multiscale modelling of cancer’. Phil. Trans. R. Soc. A (2010) 368, 5013 – 5028
SysBio2008SophieKayColorectal cancer: from experimental advances to computational modelling [JOURNAL PAPER] S. K. Kershaw. (Review article, in preparation)
SysBio2008SophieKayCellular Potts Modelling in the Colorectal Crypt [POSTER] (April 2011) British Applied Mathematics Colloquium, Birmingham, UK
SysBio2008SophieKaySubcellular Biochemistry of Colorectal Cancer [POSTER] (September 2011) SICC, Urbino, Italy.
SysBio2008JohnWalmsleyPoster: Phenomenological modelling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes, Warwick Systems Biology DTC conference 2010
SysBio2008JohnWalmsleyF. Liu, J. Walmsley, and K. Burrage. Parameter estimation for a phenomenological model of the cardiac action potential. ANZIAM J., 52:C482-C499, 2011.
SysBio2008JohnWalmsleyWalmsley et al, Phenomenological modelling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes, Conf Proc IEEE Eng Med Biol Soc. 2010. Pages 1457-60. 2010.
SysBio2008JohnWalmsleyJ. Walmsley, J.F. Rodriguez, G.R. Mirams, K. Burrage, I.R. E?mov, and B. Rodriguez. Messenger RNA expression levels predict cellular electrophysiologic remodeling in failing human hearts using a population-based simulation study. Heart Rhythm, 9(11):1913,
SysBio2008JohnWalmsleyJ. Walmsley, K. Burrage, J.M. Pitt-Francis, G. R. Mirams, and B. Rodriguez. Stochasticity in action potential duration enhances dispersion of repolarisation at fast pacing rates. Biophys. J., 102(3):592a-593a, 2012.
SysBio2008JohnWalmsleyJ. Walmsley, J.F. Rodriguez, G.R. Mirams, K. Burrage, I.R. Efimov, and B. Rodriguez. mRNA expression levels predict cellular electrophysiological remodeling in failing human hearts: A population-based simulation study. PLOS ONE, accepted, 2012.
SysBio2008PhilipGemmellP. Gemmell, K. Burrage, B. Rodriguez, and T.A. Quinn, “Exploring the parameter space of a rabbit ventricular action potential model to investigate the effect of variation on action potential and calcium transients,” Proceedings of the 32nd Annual Internat
SysBio2008JohnWalmsleyF. Liu J. Walmsley and K. Burrage, "Parameter estimation for a phenomenological model of the cardiac action potential". 15th Biennial Computational Techniques and Applications Conference, 2010
SysBio2008JohnWalmsleyJ. Walmsley, G. Mirams, M. Bahoshy, C. Bollensdorff, B. Rodriguez, and K. Burrage, “Phenomenological modeling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes.” In Proceedings of the 32nd Annual International Confer
SysBio2008JohnWalmsleyPhenomenological modelling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes, Warwick Systems Biology DTC conference 2010
SysBio2008TamasSzekelyA higher−order numerical framework for stochastic simulation of chemical reaction systems' Tamas Szekely Jr.‚ Kevin Burrage‚ Radek Erban and Konstantinos Zygalakis BMC Systems Biology. Vol. 6. No. 1. Pages 85. 2012.
SysBio2008CarolineDahlMerit prize in IUPAC's Student Chemistry Cartoon Competition (organised by the Division of Physical and Biophysical Chemistry) 2011
SysBio2008LouiseDyson2011: Models of neural crest cell migration during development. Presented at the European Conference on Mathematical and Theoretical Biology.
SysBio2008LouiseDysonDyson, L., Maini, P.K. and Baker, R.E. “Macroscopic limits of individual-based models for motile cell populations with volume exclusion”. In review in Phys. Rev. E.
SysBio2008LouiseDysonCollins-Hooper, H., Woolley, T.E., Dyson, L., Patel, A., Potter, P., Baker, R.E., Gaffney,E.A., Maini, P.K., Dash, P.R. and Patel, K. “Age related changes in speed and mechanism of adult skeletal muscle stem cell migration”. Stem Cells. 30, 1182-1195, 2012.
SysBio2008LouiseDysonMcLennan, R., Dyson, L., Prather, K.W., Morrison, J.A., Baker, R.E., Maini, P.K. and Kulesa, P.M. “Multiscale Mechanisms of Cell Migration During Development: Theory and Experiment”. Development. 139, 2935-2944, 2012
SysBio2008SophieKayGoogle Scholarship for Students with Disabilities, 2011-12 (only 10 such awards made across Europe, the Middle East & Africa in the 2011-2 round)
SysBio2008SophieKayFounder of the Open Science Training Initiative (OSTI), developed throughout my Panton Fellowship with the OKFN. A description of the initiative can be found below; further information is available on the initiative's website
SysBio2008TamasSzekelyHigher order numerical simulation of stochastic chemical reaction systems Szekely, Tamas, Jr.; Zygalakis, Konstantinos C.; Burrage, Kevin; Erban, Radek Conference: 8th EBSA European Biophysics Congress EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 40 Supplement: 1 Pages: 118-118 Published: AUG 2011
SysBio2008TamasSzekelyUsing fast stochastic methods to simulate stem cell dynamics GRC Stochastic Physics in Biology, Jan 2013
SysBio2007SumeetAgarwalLearning Predictive Models of Gene Dynamics (given at the School of Computational and Integrative Sciences, Jawaharlal Nehru University, Delhi, 5 August 2009)
SysBio2007SumeetAgarwalEvolvability as Learnability (given to Doctoral Training Centre students, University of Oxford, 21 March 2011)
SysBio2007SumeetAgarwalDynamics and Inference on Biological Networks (given to M.Sc. in Biology (Integrative Bioscience) students, Department of Zoology, University of Oxford, 28 October 2009 and 26 October 2010)
SysBio2007SumeetAgarwalThe Oxford Systems Biology Doctoral Training Centre (given at the EPSRC Inter-DTC Conference, University of Warwick, 23 July 2010)
SysBio2007OrnellaCominetti"Clustering Malarial Disease Sympthoms", CABDyN Complexity Centre Network Journal Club, University of Oxford, UK
SysBio2007OrnellaCominetti"Kernel and spectral methods for data clustering and image segmentation", Seminar at the Laboratory for Systems Biology and Bio-Inspired Engineering, KAIST, Republic of Korea
SysBio2007OrnellaCominetti"An overview of Clustering and Clustering Methods", Talk at the post-doctoral researchers weekly meeting, Oxford Centre for Integrative Systems Biology, University of Oxford, UK
SysBio2007OrnellaCominetti"Clustering complex data using a novel fuzzy spectral method", 2010 Systems Biology InterDoctoral Training Centre Conference, University of Warwick, UK
SysBio2007OrnellaCominettiO. Cominetti, P. Maini, R. Erban and D. Kulasiri (2008)"Multiscale Modelling of Carcino-genesis: From a cellular automaton model to a system of PDEs". Centenary Symposium on Mathematical and Statistical Modelling in Medicine and Health Science, Book of Ab
SysBio2007OrnellaCominettiO. Cominetti (2007)"Theoretical comparison of the metabolic capabilities of Saccha-romyces erevisiae and Pichia pastoris for the production of SOD". Engineering dissertation, Faculty of Physical and Mathematical Sciences, University of Chile.
SysBio2007PauCreixellTalk. Predicting network rewiring and kinase (in)activation in cancer. ICREA conference on the network medicine approaches to human disease: from computers to the clinics at the Institute of Catalan Studies in Barcelona, 2011.
SysBio2007PauCreixellTalk. ReKINect: Predicting kinase (in)activation and rewiring in cancer. Protein Modules and Networks in Health and Disease in Seefeld, 2011.
SysBio2007PauCreixellTalk. Kinome-wide discovery of network-attacking mutations in cancer. PTMs in Cell Signaling in Helsingor, 2012.
SysBio2007PauCreixellCreixell, P., Schoof, E.M., Erler, J.T. & Linding, R. Navigating cancer network attractors for tumor-specific therapy. Nat. Biotechnol. 30, 842–848 (2012).
SysBio2007PauCreixellCreixell, P. & Linding, R. Cells, shared memory and breaking the PTM code. Mol. Syst. Biol. 8:598 (2012).
SysBio2007PauCreixellTan, C.S.H., Schoof, E.M.*, Creixell, P.*, Pasculescu, A., Lim, W.A., Pawson, T., Bader, G.D. & Linding, R.Response to Comment on “Positive selection of tyrosine loss in metazoan evolution”. Science 332, 917 (2011).
SysBio2007PauCreixellCreixell, P., Schoof, E.M., Tan, C.S.H. & Linding, R. Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues. Phil. Trans. R. Soc. B. 367, 2584–2593 (2012).
SysBio2007PauCreixellGonzalez-Perez, A.*, Mustonen, V.*, Reva, B.*, Ritchie, G.*, Creixell, P., Karchin, R. et al. Identifying functional and driver variants in cancer genomes. Submitted to Nature Methods.
SysBio2007PauCreixellPasculescu, A., Creixell, P.*, Schoof, E.M.*, Olhovsky, M., Tian, R., Vanderlaan, R., Pawson, T., Linding, R. & Colwill, K. CoreFlow: A flexible playground for integration, analysis and modelling of complex biological data. Submitted to Nature Methods.
SysBio2007PauCreixellPoster presentation. Identifying residues determining kinase specificity by uncovering kinase-substrate coevolution patterns. 16th Meeting on protein phosphorylation and cell signaling at the Salk Institute in San Diego, 2010.
SysBio2007PauCreixellPoster presentation. Kinome-wide discovery of functional cancer mutations. Integrative Network Biology 2012: Network Medicine in Helsingor, 2012.
SysBio2007PauCreixellPoster presentation. Systems biology, cell signaling and cancer. XXX Congress of the Spanish society of biochemistry and molecular biology in Malaga, 2007.
SysBio2007PauCreixellPoster presentation. Generating protein-protein interaction networks using high-throughput yeast twohybrid. BioNets Seminar in Oxford, 2008.
SysBio2007PauCreixellPoster presentation. Finding determinants of kinase specicity and kinase-substrate network rewiring in cancer. AACR-NCI Systems Biology Conference at Hyatt Regency in San Diego, 2011.
SysBio2007PauCreixellFEBS Travel Fellowship − 2011
SysBio2007Maria RosaDomingo SananesMaría Rosa Domingo Sananes and Béla Novák. Theoretical analysis of feedbacks at mitotic entry. FEBS 2010. Gothenburg, Sweden.
SysBio2007Maria RosaDomingo SananesMaria Rosa Domingo Sananes, Orsolya Kapuy and Bela Novak. The role of regulation of CDK-counteracting phosphatases in mitotic entry. International Conference on Systems Biology 2010. Edinburgh, UK.
SysBio2007Maria RosaDomingo SananesNovak B, Kapuy O, Domingo-Sananes MR, Tyson JJ. Regulated protein kinases and phosphatases in cell cycle decisions. Curr Opin Cell Biol. 2010. 22:801-808.
SysBio2007Maria RosaDomingo SananesKapuy O, Barik D, Domingo Sananes MR, Tyson JJ, Novák B. Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol. 2009. 100(1-3): 47-56.
SysBio2007Maria RosaDomingo SananesDomingo-Sananes MR, Novak B. Different effects of redundant feedback loops on a bistable switch. Chaos. 2010. 20(4):045120
SysBio2007MatthewGibbPlenary speaker at FIMH 2009
SysBio2007GuidoKlingbeilTalk at SIAM Parallel Processing Conference PP10 in Seattle, USA
SysBio2007GuidoKlingbeilTalk SIAM Junior Applied Mathematicians Seminar MT term 2010 in Oxford
SysBio2007GuidoKlingbeilTalk at DTC conference in Warwick, UK
SysBio2007GuidoKlingbeilTalk SIAM Junior Applied Mathematicians Seminar TT 2010 in Oxford
SysBio2007GuidoKlingbeilTalk at UK CUDA Developers conference in Oxford
SysBio2007GuidoKlingbeilGuido Klingbeil, Radek Erban, Mike Giles, and Philip K. Maini ‘Fat vs. thin threading approach on GPUs: application to stochastic simulation of chemical reactions’ IEEE TRANSACTIONS ON PARALLEL & DISTRIBUTED SYSTEMS May 2010
SysBio2007GuidoKlingbeilGuido Klingbeil, Radek Erban, Mike Giles and Philip K. Maini ‘STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB’ Bioinformatics 2010
SysBio2007GuidoKlingbeilPoster presentation Inter DTC Conference, Warwick, UK
SysBio2007GuidoKlingbeilPoster presentation at BIOFORUM in Oxford
SysBio2007GuidoKlingbeilPoster Presentation SIAM student conference in Oxford
SysBio2007YaseenLadakDTC poster first year Poster at Genetics day in Department of Genetics, University of Cambridge
SysBio2007AnnaLewis“Monodisperse self-assembly in a model with protein-like interactions”, AW Wilber, JPK Doye , AA Louis, ACF Lewis, J. Chem. Phys. 131, 175102 (2009)
SysBio2007AnnaLewis“Self-Assembly and Evolution of Homomeric Protein Complexes”, G Villar, AW Wilber, AJ Williamson, P Thiara, JPK Doye, AA.Louis, MN Jochum, ACF Lewis, and ED Levy, Physical Review Letters 102, 118106 (2009)
SysBio2007AnnaLewis“Processing and properties of porous piezoelectric materials with high hydrostatic figures of merit”, CR Bowen, , A Perry, ACF Lewis and H Kara, Journal of the European Ceramic Society, Volume 24, Issue 2, 2004, Pages 541-545
SysBio2007MartonMunzDynamics-based Sequence Alignment of PDZ Domains: a Novel Approach to Quantify Dynamic Similarity of Proteins (Poster) 2009 Annual Oxford DTC conference
SysBio2007MartonMunzProtein alignments derived soley from molecular dynamics (Talk) 2010 Biophysical Society 54th Annual Meeting, San Francisco, California
SysBio2007MartonMunzM Munz and PC Biggin, JGromacs: a Java package for analysing protein simulations,
SysBio2007MartonMunzMárton Münz, Rune Lyngsø, Jotun Hein and Philip C Biggin ‘Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity’ BMC Bioinformatics 2010, 11:188
SysBio2007MartonMunzM Munz, R Lyngso, J Hein and PC Biggin, Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity, BMC Bioinformatics 2010, 11:188.
SysBio2007MartonMunzDynamics-based alignment of proteins (Poster+conference) 2010 MGMS Young Modeller's Forum, London
SysBio2007MartonMunzA novel method for biclustering microarray data (Poster+conference) 2006 International Conference of Immunogenomics and Immunomics, Budpest
SysBio2007AhmedRattani"Identification of Meloperoxidase in the nidus of Calcium Oxalate Stone" 3rd Human Proteomic Organization Annual World Congress Oct 25-27 2004, China; Molecular And Cellular Proteomics ISSN No: 1535-9784 Oct 2004 Vol 3 No 10 (Supplement)
SysBio2007AhmedRattaniWorkshop "Bioinformatics: Computer Methods in Molecular Biology" International Centre for Genetic Engineering and Biotechnology, Trieste ITALY
SysBio2007AhmedRattani"Identification of Antimicrobial Peptides in the Matrix of Calcium Oxate (CaOx) Renal stones" 8th Symposium on Protein Structure Function Relationship Jan 7-10 2005 Karachi Pakistan
SysBio2007AhmedRattaniOral presentation "Renal Stone Proteins as Promoters of Stone Formation" 18th International Medical Sciences Students Congress 2003, Istanbul Turkey
SysBio2007AhmedRattaniOral presentation at Faculty Seminar Department of Biological and Biomedical Science, Aga Khan University Medical College titled "A Multidisciplinary Approach for Assessing the Treatment of Methicillin-Resistant Staphylococcus Aureus Micrcobe"
SysBio2007AhmedRattaniShamim Mushtaq, Anwar Ali Siddiqui, Zulfiqar Ali Naqvi, Ahmed Rattani, Jamsheer Talati, Carina Palmberg and Jawed Shafqat ‘Identification of myeloperoxidase, α-defensin and calgranulin in calcium oxalate renal stones’ Clinica Chimica Acta Volume 384, Issu
SysBio2007AhmedRattaniNudrat Noor , Ahmed Rattani ‘Chlorproguanil-dapsone for malaria’ The Lancet, Volume 364, Issue 9447, Pages 1753 - 1754, 13 November 2004
SysBio2007AhmedRattani"Dynamic Modelling of Mitotic Exit Regulatory Network" Poster presentation at 3rd FEBS Advanced Lecture Course Systems Biology: From Molecular Biology to Biological Function 2009
SysBio2007AhmedRattaniPoster presentation "Protein in Renal Stone and Urine of Stone Formers" 7th International symposium on protein structure and function relation 2003 Karachi University
SysBio2007AlexanderRobsonThe IET Conference on Synthetic Biology, Systems Biology and Bioinformatics 2008, BioSys-Bio2008, Imperial College, London, U.K.
SysBio2007AlexanderRobsonQueensland University of Technology, Brisbane, Austrailia.
SysBio2007AlexanderRobsonRobson, A. et al., Developing Statistical Diagnostic Tools For Discriminating Between Different Dffusive Modes Of Fluorescently Tagged Protein Complexes In Living Cells For Short Duration Trajectories, 2009 Biophysical Society Meeting Abstracts, Biophysic
SysBio2007AlexanderRobsonRobson A. et. al Bayesian Applications to Single Particle Tracks: Applications to Fluo-rescence Microscopy, Biophys J. (in preparation)
SysBio2007AlexanderRobsonNenninger, A. et. al, Independent mobility of proteins and lipids in the plasma membrane of Escherichia coli, PNAS (In preparation)
SysBio2007AlexanderRobsonAmerican Biophysical Society Annual Conference 2009, Boston, U.S.A. 'Statistical Diagnostic Tools for Discriminating Diffusive Modes'
SysBio2007ChristianYates11-2009 Junior Applied Mathematics Seminar “Comparing Stochastic and Continuum Models For Cell Migration”.
SysBio2007ChristianYates10-2008 Junior Applied Mathematics Seminar “Locust Pocus: How Does Randomness Help swarms Stay Together? ”.
SysBio2007ChristianYates03-2009 Invited speaker at the 2nd Annual Oxford SIAM Student Chapter Conference: “United by noise: Randomness helps swarms stay together”.
SysBio2007ChristianYates05-2009 Mini-symposium speaker at the SIAM Snowbird Dynamical Systems conference, Snowbird, Utah: “United by noise: Randomness helps swarms stay together”.
SysBio2007ChristianYates09-2010 Invited speaker at Culham Science Centre (home of UK's fusion research programme, and JET). “United by noise: Randomness helps swarms stay together”.
SysBio2007ChristianYates10-2010 Invited Speaker at the Math-Bio-Medicine (MBM) seminar series, University of Leeds. “United by noise: Randomness helps swarms stay together”.
SysBio2007ChristianYatesInvited speaker at the third annual Systems Biology Inter-DTC Conference (University of Warwick Systems Biology Centre, 2010) “A comparison of stochastic and analytical models for cell migration”.
SysBio2007ChristianYates05-2009 Invited speaker at Princeton University Department of Engineering: “United by noise: Randomness helps swarms stay together”.
SysBio2007ChristianYatesRefining self-propelled particle models for collective behaviour. Yates, Christian A. and Baker, Ruth E. and Erban, Radek and Maini, Philip K. (2009) Refining self-propelled particle models for collective behaviour. Refining self-propelled particle models
SysBio2007ChristianYatesC. Escudero, C.A. Yates, R. Erban, I.D. Couzin, J. Buhl, I.G. Kevrekidis and P.K. Maini, (2010). “Ergodic directional switching in mobile insect groups”. Physical Review E 82(1) 11926.
SysBio2007ChristianYatesFrom Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains. Baker, Ruth E. and Yates, C. A. and Erban, R. (2010) From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains. Bulletin of Mathematical Biology . I
SysBio2007ChristianYatesT. Wood, C.A. Yates, D. Wilkinson and G. Rosser (2011). “Visual tracking of bacteria using the Gaussian Mixture Probability Hypothesis Density Filter”. IEEE Transactions on Circuits and Systems for Video Technology (Submitted).
SysBio2007ChristianYatesG. Rosser, C.A. Yates, T. Wood and D. Wilkinson (2011). “Analysing free-swimming bacterial motion”. Journal of Physical Biology (In preparation).
SysBio2007ChristianYatesD. Wilkinson, T. Wood, G. Rosser, C.A. Yates and J.P. Armitage (2011). “Extracting characteristic data on free-swimming bacteria using innovative tracking techniques.” Proceedings of the National Academy of Sciences (In preparation).
SysBio2007ChristianYatesPatent Pending (application number 1004488.1) - Biological object tracking
SysBio2007ChristianYatesFrom microscopic to macroscopic descriptions of cell migration on growing domains. C.A. Yates, R.E. Baker and R. Erban (Poster)
SysBio2007ChristianYatesUnited by noise: randomness helps swarms stay together. C.A. Yates, R. Erban, C. Escudero, I. Couzin, J. Buhl, I. Kevrekidis, P. Maini and D. Sumpter.(Poster)
SysBio2007ChristianYatesMary Somerville Prize - For obtaining a degree in the first class in mathematics finals.
SysBio2007ChristianYatesThe Nuclear Electric Prize - For attaining the highest marks in the year in the Mathematical Modelling and Scientific Computing M.Sc., Oxford.
SysBio2007SumeetAgarwalS. Agarwal, S. Godbole, and D. Punjani, Shourya Roy, “How Much Noise Is Too Much: A Study in Automatic Text Classification,” In Proceedings of the Seventh IEEE International Conference on Data Mining (ICDM), 2007, pp. 3-12.
SysBio2007SumeetAgarwalS. Agarwal, V. Vijaya Saradhi, and H. Karnick, “Kernel-based online machine learning and support vector reduction,” Neurocomputing, vol. 71, Mar. 2008, p. 1230–1237.
SysBio2007OrnellaCominettiOrnella Cominetti, Philip K. Maini, Radek Erban and Don Kulasiri. "Multiscale Modelling of Carcinogenesis: From a cellular automaton model to a system of PDEs" Centenary Symposium on Mathematical and Statistical Modelling in Medicine and Health Science, Q
SysBio2007SumeetAgarwalBest Poster Award, Annual Doctoral Training Centre Conference, University of Oxford, 2009
SysBio2007OrnellaCominettiO. Cominetti, "Clustering recipes: new flavours of kernel and spectral methods", Junior Applied Mathematics Seminar, Mathematical Institute, University of Oxford, UK
SysBio2007OrnellaCominettiOrnella Cominetti  "A novel fuzzy clustering algorithm for systems biology". Seminar at the Department of Wine, Food and Molecular Biosciences, Lincoln University, New Zealand. Sept. 2009 
SysBio2007OrnellaCominettiO. Cominetti, A survey on kernel and spectral methods for data clustering", Literature Seminar Series, Oxford
Centre for Collaborative Applied Mathematics, University of Oxford, UK
SysBio2007OrnellaCominettiOrnella Cominetti "Kernel and spectral methods for data clustering and image colour segmentation" Laboratory for Systems Biology and Bio-Inspired Engineering, KAIST, Oct. 2009
SysBio2007OrnellaCominettiOrnella Cominetti "DifFUZZY: A novel fuzzy clustering algorithm for complex data sets". Computational an Applied Mathematics Seminar, Department of Mathematics, Iowa State University. Sept. 2009 
SysBio2007AlexanderRobsonIM Dobbie, A Robson, N Delalez, MC Leake - Visualizing single molecular complexes in vivo using advanced fluorescence microscopy
SysBio2007SumeetAgarwalS. Agarwal, C.M. Deane, M.A. Porter, and N.S. Jones, “Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks,” PLoS Computational Biology, vol. 6, Jun. 2010, p. e1000817.
SysBio2007SumeetAgarwalS. Agarwal, C. Vaz, A. Bhattacharya, and A. Srinivasan, “Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM),” BMC Bioinformatics, vol. 11 Suppl 1, 2010, p. S29.
SysBio2007OrnellaCominettiO. Cominetti, "Cancer Systems Biology: An Overview", Talk at the Laboratory of Bioinformatics and Mathematics of the Genome, Centre for Mathematical Modeling, University of Chile, Chile
SysBio2007OrnellaCominettiO. Cominetti, "DifFUZZY: A fuzzy clustering method for complex data sets", Contributed talk, Computational Biology Session, 2010 Annual meeting of the Society for Mathematical Biology, Rio de Janeiro, Brazil
SysBio2007OrnellaCominettiO. Cominetti, "Data Clustering in Cancer Systems Biology", Talk at the Laboratory of Bioinformatics and Mathematics of the Genome, Centre for Mathematical Modeling, University of Chile, Chile
SysBio2007OrnellaCominettiO. Cominetti, "Towards a multiscale computational model of WNT signaling", Seminar Laboratory of Cellular Biology, Institute of Nutrition and Food Technology, University of Chile, Chile
SysBio2007OrnellaCominettiO. Cominetti, "Clustering complex data using a novel fuzzy spectral method", 2010 Systems Biology Inter-Doctoral Training Centre Conference, University of Warwick, UK
SysBio2007OrnellaCominettiO. Cominetti, A. Matzavinos, S. Samarasinghe, D. Kulasiri, S. Liu, P.K. Maini, and R. Erban, “DifFUZZY: a fuzzy clustering algorithm for complex datasets,” International Journal of Computational Intelligence in Bioinformatics and Systems Biology, vol. 1,
SysBio2007OrnellaCominettiO. Cominetti, First Prize Poster Competition 3rd Annual Oxford SIAM Student Chapter Conference. Title: "DifFUZZY: A fuzzy spectral clustering for complex data sets".
SysBio2007AnnaLewisAC Lewis, NS Jones, MA Porter, CM Deane - The function of communities in protein interaction networks at multiple scales
SysBio2007AnnaLewisAC Lewis, R Saeed, CM Deane - Predicting protein-protein interactions in the context of protein evolution
SysBio2007ChristianYatesR.E. Baker, C.A. Yates and R. Erban (2009). “Connecting microscopic models for directional sensing and domain growth with macroscopic models for cell motility”. Bulletin of Mathematical Biology 72(3), 719-762.
SysBio2007AhmedRattaniPK Vinod, P Freire, A Rattani, A Ciliberto, F Uhlmann, B Novak - Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles
SysBio2007ChristianYatesCA Yates, RE Baker, R Erban, PK Maini - Refining self-propelled particle models for collective behaviour
SysBio2007ChristianYatesC.A. Yates and K. Burrage, (2011). “Look before you leap: A confidence based method for selecting species criticality and leap size whilst avoiding negative populations in tauleaping”. Journal of Chemical Physics Vol 134
SysBio2007AnnaLewisAC Lewis, NS Jones, MA Porter, CM Deane - What evidence is there for the homology of protein-protein interactions?
SysBio2007AhmedRattaniSA Touati, D Cladière, LM Lister, I Leontiou, JP Chambon, A Rattani, F Böttger, O Stemmann, K Nasmyth, M Herbert, K Wassmann - Cyclin A2 is required for sister chromatid segregation, but not separase control, in mouse oocyte meiosis.
SysBio2007AlexanderRobsonA Robson, K Burrage, MC Leake - Inferring diffusion in single live cells at the single-molecule level
SysBio2007ChristianYatesModelling cell migration: from discrete to continuous
SysBio2007ChristianYatesCA Yates, RE Baker, R Erban, PK Maini - Going from microscopic to macroscopic on nonuniform growing domains
SysBio2007MatthewGibbM. Gibb, M. Bishop, R. Burton, P. Kohl, V. Grau, G. Plank, B. Rodríguez, (2009). “The Role of Blood Vessels in Rabbit Propagation Dynamics and Cardiac Arrhythmias”. Functional Imaging and Modeling of the Heart, 268-276
SysBio2007MatthewGibbM. Gibb, R. Burton, C. Bollendsdorff, C. Alfonso, T. Mansoori, U. Schotten, D. Gavaghan, R. Rodríguez, J. Schneider, P. Kohl, V. Grau, (2012). “Resolving the Three-Dimensional Histology of the Heart”. Computational Methods in Systems Biology, 2-16
SysBio2007MatthewGibbM. Gibb, M. Bishop, R. Rodríguez, P. Kohl, R. Burton, V. Grau, (2012). “Transformational Diffusion Smoothing: 3D Reconstruction of High Resolution Cardiac Histology”. IEEE Transactions on Medical Imaging (in preparation)
SysBio2007MatthewGibbCofounder of 80000hours.org; charity that provides evidence-based advice about ethical careers; we now have 6 full-time staff and 20 part-time volunteers, with a 2013 budget of over $150,000.
SysBio2007MartonMunzMünz et al., PLOS Computational Biology, 2012
SysBio2007ChristianYatesC.A. Yates, Invited speaker at Princeton University Department of Engineering: "United by noise: Randomness helps swarms stay together". May 2008.
SysBio2007ChristianYatesC.A. Yates, R. Erban, C. Escudero, I.D Couzin, J. Buhl, I.G. Kevrekidis, P.K. Maini. ‘Inherent noise can facilitate coherence in collective swarm motion’ Proc Natl Acad Sci USA. 106(14):5464-5469, 2009. doi: 10.1073/pnas.0811195106.
SysBio2007ChristianYatesC.A. Yates 2009-2011 - Leathersellers' Scholarship (St Catherine's College) for academic achievement. 
SysBio2012RonjaWoloszczukLysine Acetylation Controls Local Protein Conformation by Influencing Proline Isomerization Howe, Françoise S. et al.Molecular Cell , Volume 55 , Issue 5 , 733 - 744
SysBio2011LucieBowdenBowden LG, Simpson MJ, Baker RE. Design and interpretation of cell trajectory assays. Journal of the Royal Society Interface.
SysBio2011KacperRogalaHatzopoulos, G. N., Erat, M. C., Cutts, E., Rogala, K. B., Slater, L. M., Stansfeld, P. J., & Vakonakis, I. (2013). Structural analysis of the G-box domain of the microcephaly protein CPAP suggests a role in centriole architecture. Structure, 21(11), 2069-2077.
SysBio2011LucieBowdenBowden LG, Maini PK, Moulton DE, Tang JB, Wang XT, Liu PY, Byrne HM. An ordinary differential equation model for full thickness wounds and the effects of diabetes. Journal of Theoretical Biology.
SysBio2011NicholasDavies Davies NG, Gardner A. 2014. Evolution of paternal care in diploid and haplodiploid populations. Journal of Evolutionary Biology 27: 1012-1019.
SysBio2010AndrewBissettePhysical autocatalysis driven by a bond-forming thiol-ene reaction, A. J. Bissette, B. Odell, S. P. Fletcher, Nature Communications. 2014, 5, 4607.
SysBio2010AndrewBissetteMechanisms of Autocatalysis" A. J. Bissette, S. P. Fletcher, Angew. Chem. Int. Ed. 2013, 52, 12800–12826.
SysBio2010AndrewBissetteHydrogenolysis of allyl and benzyl halides and related compounds. A. J. Bissette and S. P. Fletcher. In: Gary A. Molander and Paul Knochel (eds.), Comprehensive Organic Synthesis, 2nd edition, Vol 8, Oxford; Elsevier; 2014. pp. 1164-1184.
SysBio2009BernadettGaalJohnston IG, Gaal B, Neves RPd, Enver T, Iborra FJ, Jones NS. (2012) Mitochondrial Variability as a Source of Extrinsic Cellular Noise. PLoS Comput Biol 8(3): e1002416.
SysBio2009JonasSchluterSchluter J, Foster KR (2012) The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection. PLoS Biol 10(11): e1001424