Publications

IntakeYearFirstNameLastNamePublication
2010OliverBrittonExperimentally calibrated population of models predicts and explains intersubject variability in cardiac cellular electrophysiology
2012AnnaMuszkiewiczDynamic allostery in proteins: the case of the PDZ3 domain, id2 Conference UCL
2012PaulTaylorCombining Waddington's Epigenetic Landscape With Delayed Reactions, id2 Conference UCL
2011XinZhou'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
2011LucieBowdenAn ODE model for the healing of full thickness wounds and the effects of diabetes, id2 Conference UCL
2011KatharineCoyteInvestigating Bacterial Ecology and Evolution in Complex Environments (poster), id2 Conference UCL
at UCL
2011XinZhouMicrosoft Research Project Award for 2012
2010Andrew 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)
2010Andrew JohnBissetteEli Lilly prize for excellence in organic chemistry
2010Markus 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
2010Markus 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,
2010Markus 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)
2010Markus 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.
2010Markus AlexanderGerstelQuantitative Radiation Damage Studies, 28.01.2013, Markus Gerstel, C. M. Deane, E. F. Garman; Poster presentation at the annual DTC symposium 2013
2010Markus 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
2010Markus AlexanderGerstelHi-Throughput Colorectal Crypt Monoclonality Simulation, 24.03.2011, SysBio DTC, University of Oxford.
2010GeorginaLangWilfrid Knapp Scholarship (Sciences) from St Catherine's College (2012-2014)
2010Stephen GeorgeO'KeeffeBest student presentation at the 2012 OCCAM modelling camp
2010Natalie 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.
2010Natalie 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.
2010Marta AnnaSarzynskaSarzynska, M: 'Community structure in epidemics'. Poster presented at the XXXII Dynamics Days Europe, Gothenburg (2012 _
2010Markus 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
2009KamaludinDinglePublication in preparation ‘Knudsen’s law and random billiards in irrational triangles’ with J. Lamb (Imperial) and A.Lazaro-Cami (Imperial)
2009SaraDuttaInterpreting optical mapping recordings in the ischemic heart: a combined experimental and computational investigation. FIMH (Functional Imaging and Modelling of the Heart)
2009SaraDuttaBest poster at Imperial College Cardiovascular Technology Symposium February 2012
2009JessicaMcGillenMcGillen 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)
2009JessicaMcGillenMcGillen J, Martin NK, Robey I, Gaffney EA, Maini PK. Applications of mathematical analysis to tumour acidity modelling. RIMS Kokyuroku Bessatsu, B31 . pp. 31-59
2009JessicaMcGillenMcGillen 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.
2009JessicaMcGillenOverseas Graduate Scholarship for academic achievement, St. Catherine's College, 2011-present
2009JessicaMcGillenPrize for best presentation, DTC 4th Year Conference, 2013
2009JessicaMcGillenLandahl Travel Grant, Society for Mathematical Biology, 2012
2009JessicaMcGillenNational Cancer Institute NIH grant 1U54CA143970-01 (funding for short project with Prof. Philip Maini), 2010
2009JessicaMcGillenEuropean Society for Mathematical and Theoretical Biology travel grant, 2011
2009MargaritaSchlackowMicrosoft Research Cambridge Award for a DTC summer project: Mathematical modelling and experimental verification of interactions between the RNA polymerase and cohesin complex in transcription .
2009Hong 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
2009KamaludinDingle‘Knudsen’s law and ergodicity of a polygonal billiard with noise’ at the LDSG workshop on “Random dynamical systems and applications”
2009BernadettGaalEvolution of stochastic switching, presented at the 2010 Systems Biology of Stem Cells Symposium at the University of California Irvine.
2009BernadettGaalGaal B, Pitchford JW, Wood AJ. 2010 Exact results for the evolution of stochastic switching in variable asymmetric environments. Genetics 184, 1113-9
2009KenWang‘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
2009KenWang“Local and Global sensitivity analysis Tools for Assessment and Development of Cellular and Ionic Cardiac” was presented in 2010 MEC international workshop
2009SaraDuttaInterpreting 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
2009JessicaMcGillen“Mathematical modelling of tumour acidity,” to be given at a meeting of the Centre for Mathematical Biology (upcoming in June) talk and poster.
2009SaraDuttaRecent Human Ventricular Cell Action Potential Models under Varied Ischaemic Conditions, id2 Conference UCL
2009KatherineLeonardGroup presentation to Biostruct at Heidelberg, Germany.
2009KatherineLeonardJunior Applied Mathematics Seminar, University of Oxford.
2009KatherineLeonardPresentation of talk at the University of Oxford Department of Computer Science Student Conference.
2009KatherineLeonardPresentation of poster at the Google Scholars Retreat in Zurich, Switzerland.
2009KatherineLeonardPresentation of poster at inter-DTC Systems Biology Conference, Manchester.
2009KatherineLeonardJesus College Graduate Scholarship, University of Oxford.
2009KatherineLeonardGoogle Europe Scholarship for Students with Disabilities.
2009MatthewWebberThe 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
2009MatthewWebberNeural field model of binocular rivalry waves Paul C. Bressloff · Matthew A. Webber. J Comput Neurosci (2012) 32:233–252
2009MatthewWebberFront Propagation in Stochastic Neural Fields. Paul C. Bressloff and Matthew A. Webber. SIAM J. APPLIED DYNAMICAL SYSTEMS 2012Vol. 11, No. 2, pp. 708–740
2008SuruchiBakshiPoster presentation on mathematical modelling of asymmetric stem cell division European Conference on Mathematical and Theoretical Biology – to be held in June-July, 2011
2008SuruchiBakshiPoster presentation on mathematical modelling of asymmetric stem cell division in Warwick Inter-SysBio-DTC student conference (June 2010).
2008Tiago MiguelChegancas RitoOral presentation following a proceedings publication at the 9th European Conference on Computational Biology (ECCB 2010)
2008Tiago 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.
2008Tiago MiguelChegancas RitoPoster presentation at RECOMB 2010
2008HelenCurtisRoberts T, Curtis H. Gene regulation by small RNAs. J RNAi Gene Silencing; 2010; 6(1):376-8.
2008HelenCurtisLlarena, 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.
2008HelenCurtisPoster presented at Biochemical Society Meeting, Micro RNAs and their targets: promises and pitfalls, London, UK, November 2010.
2008CarolineDahlDahl ACE and Thompson MS (2011) Biomechanics: Mechanobiology of bone. Comprehensive Biotechnology, 2nd ed Elsevier
2008CarolineDahlDahl ACE, Chavent M and Sansom MSP (2012) Bendix: intuitive helix geometry analysis and abstraction. Bioinformatics 28 (16): 2193-2194.
2008CarolineDahlDTC Systems Biology Conference 2010, Warwick
2008JenniferDe 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.
2008JenniferDe 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
2008JenniferDe 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
2008LouiseDysonPlatform session (i.e. a talk) at the Biophysical Society 54th Annual General Meeting, San Francisco. 'Mathematical modelling of cranial neural crest cell migration' 2009
2008LouiseDyson£250 award for the best Systems Biology Doctoral Training Centre short project, sponsored by Microsoft.
2008PhilipGemmellP. 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.
2008PhilipGemmellWerner, 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
2008MireilleGomesAbelson, 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,
2008MireilleGomesR. 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
2008MireilleGomesM. 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
2008SophieKayTowards In Silico Drug Discovery in the Colorectal Crypt (August 2010) CompuCell3D & Systems Biology Workbench Workshop, Indiana, USA.
2008SophieKayBiological Applicability of the Cellular Potts Model (January 2011) KAIST International Workshop on Cancer Modelling, Seoul, S.Korea.
2008SophieKayBiological Applicability of the Cellular Potts Model [PRESENTATION] (January 2011) KAIST International Workshop on Cancer Modelling, Seoul, S.Korea.
2008SophieKayJ. 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
2008SophieKayColorectal cancer: from experimental advances to computational modelling [JOURNAL PAPER] S. K. Kershaw. (Review article, in preparation)
2008SophieKayCellular Potts Modelling in the Colorectal Crypt [POSTER] (April 2011) British Applied Mathematics Colloquium, Birmingham, UK
2008SophieKaySubcellular Biochemistry of Colorectal Cancer [POSTER] (September 2011) SICC, Urbino, Italy.
2008JohnWalmsleyPoster: Phenomenological modelling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes, Warwick Systems Biology DTC conference 2010
2008JohnWalmsleyF. Liu, J. Walmsley, and K. Burrage. Parameter estimation for a phenomenological model of the cardiac action potential. ANZIAM J., 52:C482-C499, 2011.
2008JohnWalmsleyWalmsley 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.
2008JohnWalmsleyJ. 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,
2008JohnWalmsleyJ. 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.
2008JohnWalmsleyJ. 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.
2008PhilipGemmellP. 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
2008JohnWalmsleyF. 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
2008JohnWalmsleyJ. 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
2008JohnWalmsleyPhenomenological modelling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes, Warwick Systems Biology DTC conference 2010
2008TamasSzekelyA 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.
2008CarolineDahlMerit prize in IUPAC's Student Chemistry Cartoon Competition (organised by the Division of Physical and Biophysical Chemistry) 2011
2008LouiseDyson2011: Models of neural crest cell migration during development. Presented at the European Conference on Mathematical and Theoretical Biology.
2008LouiseDysonDyson, 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.
2008LouiseDysonCollins-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.
2008LouiseDysonMcLennan, 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
2008SophieKayGoogle Scholarship for Students with Disabilities, 2011-12 (only 10 such awards made across Europe, the Middle East & Africa in the 2011-2 round)
2008SophieKayFounder 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
2008TamasSzekelyHigher 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
2008TamasSzekelyUsing fast stochastic methods to simulate stem cell dynamics GRC Stochastic Physics in Biology, Jan 2013
2007SumeetAgarwalLearning Predictive Models of Gene Dynamics (given at the School of Computational and Integrative Sciences, Jawaharlal Nehru University, Delhi, 5 August 2009)
2007SumeetAgarwalEvolvability as Learnability (given to Doctoral Training Centre students, University of Oxford, 21 March 2011)
2007SumeetAgarwalDynamics 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)
2007SumeetAgarwalThe Oxford Systems Biology Doctoral Training Centre (given at the EPSRC Inter-DTC Conference, University of Warwick, 23 July 2010)
2007OrnellaCominetti"Clustering Malarial Disease Sympthoms", CABDyN Complexity Centre Network Journal Club, University of Oxford, UK
2007OrnellaCominetti"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
2007OrnellaCominetti"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
2007OrnellaCominetti"Clustering complex data using a novel fuzzy spectral method", 2010 Systems Biology InterDoctoral Training Centre Conference, University of Warwick, UK
2007OrnellaCominettiO. 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
2007OrnellaCominettiO. 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.
2007PauCreixellTalk. 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.
2007PauCreixellTalk. ReKINect: Predicting kinase (in)activation and rewiring in cancer. Protein Modules and Networks in Health and Disease in Seefeld, 2011.
2007PauCreixellTalk. Kinome-wide discovery of network-attacking mutations in cancer. PTMs in Cell Signaling in Helsingor, 2012.
2007PauCreixellCreixell, P., Schoof, E.M., Erler, J.T. & Linding, R. Navigating cancer network attractors for tumor-specific therapy. Nat. Biotechnol. 30, 842–848 (2012).
2007PauCreixellCreixell, P. & Linding, R. Cells, shared memory and breaking the PTM code. Mol. Syst. Biol. 8:598 (2012).
2007PauCreixellTan, 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).
2007PauCreixellCreixell, 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).
2007PauCreixellGonzalez-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.
2007PauCreixellPasculescu, 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.
2007PauCreixellPoster 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.
2007PauCreixellPoster presentation. Kinome-wide discovery of functional cancer mutations. Integrative Network Biology 2012: Network Medicine in Helsingor, 2012.
2007PauCreixellPoster presentation. Systems biology, cell signaling and cancer. XXX Congress of the Spanish society of biochemistry and molecular biology in Malaga, 2007.
2007PauCreixellPoster presentation. Generating protein-protein interaction networks using high-throughput yeast twohybrid. BioNets Seminar in Oxford, 2008.
2007PauCreixellPoster 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.
2007PauCreixellFEBS Travel Fellowship − 2011
2007Maria RosaDomingo SananesMaría Rosa Domingo Sananes and Béla Novák. Theoretical analysis of feedbacks at mitotic entry. FEBS 2010. Gothenburg, Sweden.
2007Maria 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.
2007Maria 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.
2007Maria 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.
2007Maria RosaDomingo SananesDomingo-Sananes MR, Novak B. Different effects of redundant feedback loops on a bistable switch. Chaos. 2010. 20(4):045120
2007MatthewGibbPlenary speaker at FIMH 2009
2007GuidoKlingbeilTalk at SIAM Parallel Processing Conference PP10 in Seattle, USA
2007GuidoKlingbeilTalk SIAM Junior Applied Mathematicians Seminar MT term 2010 in Oxford
2007GuidoKlingbeilTalk at DTC conference in Warwick, UK
2007GuidoKlingbeilTalk SIAM Junior Applied Mathematicians Seminar TT 2010 in Oxford
2007GuidoKlingbeilTalk at UK CUDA Developers conference in Oxford
2007GuidoKlingbeilGuido 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
2007GuidoKlingbeilGuido Klingbeil, Radek Erban, Mike Giles and Philip K. Maini ‘STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB’ Bioinformatics 2010
2007GuidoKlingbeilPoster presentation Inter DTC Conference, Warwick, UK
2007GuidoKlingbeilPoster presentation at BIOFORUM in Oxford
2007GuidoKlingbeilPoster Presentation SIAM student conference in Oxford
2007YaseenLadakDTC poster first year Poster at Genetics day in Department of Genetics, University of Cambridge
2007AnnaLewis“Monodisperse self-assembly in a model with protein-like interactions”, AW Wilber, JPK Doye , AA Louis, ACF Lewis, J. Chem. Phys. 131, 175102 (2009)
2007AnnaLewis“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)
2007AnnaLewis“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
2007MartonMunzDynamics-based Sequence Alignment of PDZ Domains: a Novel Approach to Quantify Dynamic Similarity of Proteins (Poster) 2009 Annual Oxford DTC conference
2007MartonMunzProtein alignments derived soley from molecular dynamics (Talk) 2010 Biophysical Society 54th Annual Meeting, San Francisco, California
2007MartonMunzM Munz and PC Biggin, JGromacs: a Java package for analysing protein simulations,
2007MartonMunzMárton 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
2007MartonMunzM 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.
2007MartonMunzDynamics-based alignment of proteins (Poster+conference) 2010 MGMS Young Modeller's Forum, London
2007MartonMunzA novel method for biclustering microarray data (Poster+conference) 2006 International Conference of Immunogenomics and Immunomics, Budpest
2007AhmedRattani"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)
2007AhmedRattaniWorkshop "Bioinformatics: Computer Methods in Molecular Biology" International Centre for Genetic Engineering and Biotechnology, Trieste ITALY
2007AhmedRattani"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
2007AhmedRattaniOral presentation "Renal Stone Proteins as Promoters of Stone Formation" 18th International Medical Sciences Students Congress 2003, Istanbul Turkey
2007AhmedRattaniOral 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"
2007AhmedRattaniShamim 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
2007AhmedRattaniNudrat Noor , Ahmed Rattani ‘Chlorproguanil-dapsone for malaria’ The Lancet, Volume 364, Issue 9447, Pages 1753 - 1754, 13 November 2004
2007AhmedRattani"Dynamic Modelling of Mitotic Exit Regulatory Network" Poster presentation at 3rd FEBS Advanced Lecture Course Systems Biology: From Molecular Biology to Biological Function 2009
2007AhmedRattaniPoster presentation "Protein in Renal Stone and Urine of Stone Formers" 7th International symposium on protein structure and function relation 2003 Karachi University
2007AlexanderRobsonThe IET Conference on Synthetic Biology, Systems Biology and Bioinformatics 2008, BioSys-Bio2008, Imperial College, London, U.K.
2007AlexanderRobsonQueensland University of Technology, Brisbane, Austrailia.
2007AlexanderRobsonRobson, 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
2007AlexanderRobsonRobson A. et. al Bayesian Applications to Single Particle Tracks: Applications to Fluo-rescence Microscopy, Biophys J. (in preparation)
2007AlexanderRobsonNenninger, A. et. al, Independent mobility of proteins and lipids in the plasma membrane of Escherichia coli, PNAS (In preparation)
2007AlexanderRobsonAmerican Biophysical Society Annual Conference 2009, Boston, U.S.A. 'Statistical Diagnostic Tools for Discriminating Diffusive Modes'
2007ChristianYates11-2009 Junior Applied Mathematics Seminar “Comparing Stochastic and Continuum Models For Cell Migration”.
2007ChristianYates10-2008 Junior Applied Mathematics Seminar “Locust Pocus: How Does Randomness Help swarms Stay Together? ”.
2007ChristianYates03-2009 Invited speaker at the 2nd Annual Oxford SIAM Student Chapter Conference: “United by noise: Randomness helps swarms stay together”.
2007ChristianYates05-2009 Mini-symposium speaker at the SIAM Snowbird Dynamical Systems conference, Snowbird, Utah: “United by noise: Randomness helps swarms stay together”.
2007ChristianYates09-2010 Invited speaker at Culham Science Centre (home of UK's fusion research programme, and JET). “United by noise: Randomness helps swarms stay together”.
2007ChristianYates10-2010 Invited Speaker at the Math-Bio-Medicine (MBM) seminar series, University of Leeds. “United by noise: Randomness helps swarms stay together”.
2007ChristianYatesInvited 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”.
2007ChristianYates05-2009 Invited speaker at Princeton University Department of Engineering: “United by noise: Randomness helps swarms stay together”.
2007ChristianYatesRefining 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
2007ChristianYatesC. 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.
2007ChristianYatesFrom 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
2007ChristianYatesT. 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).
2007ChristianYatesG. Rosser, C.A. Yates, T. Wood and D. Wilkinson (2011). “Analysing free-swimming bacterial motion”. Journal of Physical Biology (In preparation).
2007ChristianYatesD. 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).
2007ChristianYatesPatent Pending (application number 1004488.1) - Biological object tracking
2007ChristianYatesFrom microscopic to macroscopic descriptions of cell migration on growing domains. C.A. Yates, R.E. Baker and R. Erban (Poster)
2007ChristianYatesUnited 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)
2007ChristianYatesMary Somerville Prize - For obtaining a degree in the first class in mathematics finals.
2007ChristianYatesThe Nuclear Electric Prize - For attaining the highest marks in the year in the Mathematical Modelling and Scientific Computing M.Sc., Oxford.
2007SumeetAgarwalS. 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.
2007SumeetAgarwalS. Agarwal, V. Vijaya Saradhi, and H. Karnick, “Kernel-based online machine learning and support vector reduction,” Neurocomputing, vol. 71, Mar. 2008, p. 1230–1237.
2007OrnellaCominettiOrnella 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
2007SumeetAgarwalBest Poster Award, Annual Doctoral Training Centre Conference, University of Oxford, 2009
2007OrnellaCominettiO. Cominetti, "Clustering recipes: new flavours of kernel and spectral methods", Junior Applied Mathematics Seminar, Mathematical Institute, University of Oxford, UK
2007OrnellaCominettiOrnella 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 
2007OrnellaCominettiO. Cominetti, A survey on kernel and spectral methods for data clustering", Literature Seminar Series, Oxford
Centre for Collaborative Applied Mathematics, University of Oxford, UK
2007OrnellaCominettiOrnella Cominetti "Kernel and spectral methods for data clustering and image colour segmentation" Laboratory for Systems Biology and Bio-Inspired Engineering, KAIST, Oct. 2009
2007OrnellaCominettiOrnella Cominetti "DifFUZZY: A novel fuzzy clustering algorithm for complex data sets". Computational an Applied Mathematics Seminar, Department of Mathematics, Iowa State University. Sept. 2009 
2007AlexanderRobsonIM Dobbie, A Robson, N Delalez, MC Leake - Visualizing single molecular complexes in vivo using advanced fluorescence microscopy
2007SumeetAgarwalS. 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.
2007SumeetAgarwalS. 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.
2007OrnellaCominettiO. 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
2007OrnellaCominettiO. 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
2007OrnellaCominettiO. 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
2007OrnellaCominettiO. Cominetti, "Towards a multiscale computational model of WNT signaling", Seminar Laboratory of Cellular Biology, Institute of Nutrition and Food Technology, University of Chile, Chile
2007OrnellaCominettiO. Cominetti, "Clustering complex data using a novel fuzzy spectral method", 2010 Systems Biology Inter-Doctoral Training Centre Conference, University of Warwick, UK
2007OrnellaCominettiO. 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,
2007OrnellaCominettiO. Cominetti, First Prize Poster Competition 3rd Annual Oxford SIAM Student Chapter Conference. Title: "DifFUZZY: A fuzzy spectral clustering for complex data sets".
2007AnnaLewisAC Lewis, NS Jones, MA Porter, CM Deane - The function of communities in protein interaction networks at multiple scales
2007AnnaLewisAC Lewis, R Saeed, CM Deane - Predicting protein-protein interactions in the context of protein evolution
2007ChristianYatesR.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.
2007AhmedRattaniPK 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
2007ChristianYatesCA Yates, RE Baker, R Erban, PK Maini - Refining self-propelled particle models for collective behaviour
2007ChristianYatesC.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
2007AnnaLewisAC Lewis, NS Jones, MA Porter, CM Deane - What evidence is there for the homology of protein-protein interactions?
2007AhmedRattaniSA 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.
2007AlexanderRobsonA Robson, K Burrage, MC Leake - Inferring diffusion in single live cells at the single-molecule level
2007ChristianYatesModelling cell migration: from discrete to continuous
2007ChristianYatesCA Yates, RE Baker, R Erban, PK Maini - Going from microscopic to macroscopic on nonuniform growing domains
2007MatthewGibbM. 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
2007MatthewGibbM. 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
2007MatthewGibbM. 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)
2007MatthewGibbCofounder 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.
2007MartonMunzMünz et al., PLOS Computational Biology, 2012
2007ChristianYatesC.A. Yates, Invited speaker at Princeton University Department of Engineering: "United by noise: Randomness helps swarms stay together". May 2008.
2007ChristianYatesC.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.
2007ChristianYatesC.A. Yates 2009-2011 - Leathersellers' Scholarship (St Catherine's College) for academic achievement. 
2012RonjaWoloszczukLysine Acetylation Controls Local Protein Conformation by Influencing Proline Isomerization Howe, Françoise S. et al.Molecular Cell , Volume 55 , Issue 5 , 733 - 744
2011LucieBowdenBowden LG, Simpson MJ, Baker RE. Design and interpretation of cell trajectory assays. Journal of the Royal Society Interface.
2011KacperRogalaHatzopoulos, 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.
2011LucieBowdenBowden 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.
2011NicholasDavies Davies NG, Gardner A. 2014. Evolution of paternal care in diploid and haplodiploid populations. Journal of Evolutionary Biology 27: 1012-1019.
2010AndrewBissettePhysical autocatalysis driven by a bond-forming thiol-ene reaction, A. J. Bissette, B. Odell, S. P. Fletcher, Nature Communications. 2014, 5, 4607.
2010AndrewBissetteMechanisms of Autocatalysis" A. J. Bissette, S. P. Fletcher, Angew. Chem. Int. Ed. 2013, 52, 12800–12826.
2010AndrewBissetteHydrogenolysis 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.
2009BernadettGaalJohnston 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.
2009JonasSchluterSchluter J, Foster KR (2012) The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection. PLoS Biol 10(11): e1001424