Publications
Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch cultureThomas, L., Hodgson, D.A., Wentzel, A., Nieselt, K., Ellingsen, T.E., Moore. J., Morrissey, E.R., Legaie, R; The STREAM Consortium, Wohleben, W., Rodriguez-Garcia, A., Martin, J.F., Burroughs, N.J., Wellington, E.M., Smith, M.C. (2012) Mol. Cell Proteomics, 11(2): M111.013797. Extracting Fluorescent Reporter Time Courses of Cell Lineages from High-Throughput Microscopy at Low Temporal ResolutionMike J. Downey, Danuta M. Jeziorska, Sascha Ott, T. Katherine Tamai, Georgy Koentges, Keith W. Vance, Till Bretschneider, 2011, PLoS ONE 6(12): e27886. Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes2011 PLoS Computational Biology 7(10) Independently evolved virulence effectors converge onto hubs in a plant immune system networkMukhtar, M.S., Carvunis, A-R., Dreze, M., Epple, P., Steinbrenner, J., Moore, J., Tasan, M., Galli, M., Hao, T., Nishimura, M.T., Pevzner, S.J., Donovan, S.E., Ghamsari, L., Santhanam, B., Romero, V., Poulin, M.M., Gebreab, F., Gutierrez, B.J., Tam, S., Monachello, D., Boxem, M., Harbort, C.J., McDonald, N., Gai, L., Chen, H., He, Y., European Union Effectoromics Consrtium, Vandenhaute, J., Roth, F.P., Hill, D.E., Ecker, J.R., Vidal, M., Beynon, J., Braun, P., Dangl, J.L. (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science 333(6042): 596-601. Evidence for network evolution in an Arabidopsis interactome mapArabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333(6042): 601-607. High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and RegulationBreeze, E., Harrison, E., McHattie, S., Hughes, L., Hickman, R., Hill, C., Kiddle, S., Kim, Y-S., Penfold, C.A., Jenkins, D., Zhang, C., Morris, K., Jenner, C., Jackson, S., Thomas, B., Tabrett, A., Legaie, R., Moore, J.D., Wild, D.L., Ott, S., Rand, D., Beynon, J., Denby, K., Mead, A. and Buchanan-Wollaston, V. (2011) The Plant Cell 23 (3): 873-894. Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryoCéline Granier, Vasily Gurchenkov, Aitana Perea-Gomez, Anne Camus, Sascha Ott, Costis Papanayotou, Julian Iranzo, Anne Moreau, John Reid, Georgy Koentges, Délara Sabéran-Djoneidi, Jérôme Collignon (2011) Developmental Biology, 349: 350-362 Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee coloniesMoore, J., Jironkin, A., Chandler, D., Burroughs, N., Evans, D.J. and Ryabov, E.V. (2011) Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies. Journal of General Virology 92, 156-161. Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis GenomeLaura Baxter, Sucheta Tripathy, Naveed Ishaque, Nico Boot, Adriana Cabra, Eric Kemen, Marco Thines, Audrey Ah-Fong, Ryan Anderson, Wole Badejoko, Peter Bittner-Eddy, Jeffrey L. Boore, Marcus C. Chibucos, Mary Coates, Paramvir Dehal, Kim Delehaunty, Suomeng Dong, Polly Downton, Bernard Dumas, Georgina Fabro, Catrina Fronick, Susan I. Fuerstenberg, Lucinda Fulton, Elodie Gaulin, Francine Govers, Linda Hughes, Sean Humphray, Rays H. Y. Jiang, Howard Judelson, Sophien Kamoun, Kim Kyung, Harold Meijer, Patrick Minx, Paul Morris, Joanne Nelson, Vipa Phuntumart, Dinah Qutob, Anne Rehmany, Alejandra Rougon-Cardoso, Peter Ryden, Trudy Torto-Alalibo, David Studholme, Yuanchao Wang, Joe Win, Jo Wood, Sandra W. Clifton, Jane Rogers, Guido Van den Ackerveken, Jonathan D. G. Jones, John M. McDowell, Jim Beynon, and Brett M. Tyler. Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome. Science 330:6010 pp. 1549-1551 Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström methodDu, C.-J., Marcello, M., Spiller, D. G., White, M. R. H. and Bretschneider, T. , Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström method. Cytometry Part A, n/a. doi: 10.1002/cyto.a.20993, 2010 Quantitative analysis of regulatory flexibility under changing environmental conditionsEdwards, K. D., Akman, O. E., Knox, K., Lumsden, P. J., Thomson, A. W., Brown, P. E., Pokhilko, A., Kozma-Bognar, L., Nagy, F., Rand, D. A., & Millar, A. J. (2010). Molecular Systems Biology 6:424 doi:10.1038/msb.2010.81 De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory MechanismsDafyd J. Jenkins and Dov J. Stekel (2010). Journal of Molecular Evolution 71(2):128-140 Stochasticity Versus Determinism: Consequences for Realistic Gene Regulatory Network Modelling and EvolutionDafyd J. Jenkins and Dov J. Stekel (2010). Journal of Molecular Evolution 70(2):215-231 On reverse engineering of gene interaction networks using time course data with repeated measurements
E.R. Morrissey, M.A. Juárez, K. J. Denby, and N.J Burroughs (2010) . Bioinformatics 26, 2305—2312 (DOI:10.1093/bioinformatics/btq421)
Discovering transcriptional modules by Bayesian data integration
Richard S. Savage; Zoubin Ghahramani; Jim E. Griffin; Bernard J. de la Cruz; David L. Wild Bioinformatics 2010 26: i158-i167
Multiquantal release underlies the distribution of synaptic efficacies in the neocortex
Loebel A, Silberberg G, Helbig D, Markram H, Tsodyks M and Richardson MJE. Frontiers in Computational Neuroscience 3: article-no 27 (2009)
Dynamics of populations and networks of neurons with voltage-activated and calcium-activated currents
Richardson MJE. Physical Review E 80: article-no 021928 (2009)
Extracting nonlinear integrate-and-fire models from experimental data using dynamic I-V curves
Badel L, Lefort S, Berger TK, Petersen CC, Gerstner W and Richardson MJE. Biological Cybernetics 99: 361-370 (2008)
Spike-train spectra and network response functions for non-linear integrate-and-fire neurons
Richardson MJE. Biological Cybernetics 99: 381-392 (2008)
Spike-triggered averages for passive and resonant neurons receiving filtered excitatory and inhibitory synaptic drive
Badel L, Gerstner W and Richardson MJE. Physical Review E 78: article-no 011914 (2008)
Measurement and analysis of postsynaptic potentials using a novel voltage-deconvolution method
Richardson MJE and Silberberg G. Journal of Neurophysiology 99: 1020-1031 (2008)
Dynamic I-V curves are reliable predictors of naturalistic pyramidal-neuron voltage tracesBadel L, Lefort S, Brette R, Petersen CC, Gerstner W and Richardson MJE. Journal of Neurophysiology 99: 656-666 (2008) Inferring Transcriptional Networks Using Prior Biological Knowledge and Constrained State-Space Models
Angus, J. Beal, M.J., Li, J., Rangel, C., Wild, D.L. In Lawrence, N.D., Girolami, M., Rattray, M. and Sanguinetti, G. (Eds.), Learning and Inference in Computational Systems Biology, MIT Press, Cambridge, (2010), pp 117-152
R/BHC: Fast Bayesian Hierarchical Clustering for Microarray Data
Savage, R. S., Heller, K., Xu, Y., Ghahramani, Z., Truman, W.M., Grant, M.R., Denby, K.J. and Wild, D.L. BMC Bioinformatics, 10:242, (2009) (Highly Accessed Paper)
Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks
Cooke, E.J., Savage R.S. and Wild, D.L. Seminars in Cell and Developmental Biology, 20: 863–868, (2009) (Invited Review).
Reconstruction and stability of secondary structure elements in the context of protein structure prediction
Podtelezhnikov, A.A. and Wild, D.L. Biophysical Journal, 96:4399-4408, (2009).
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
Stegle, O., Denby, K.J., Wild, D.L., Ghahramani, Z. and Borgwardt, K.M. Research in Computational Molecular Biology, Lecture Notes in Bioinformatics, Ed. S. Batzoglou, Springer, Berlin, 5541, 201-216, (2009).
Modeling and Visualizing Uncertainty in Gene Expression Clusters using Dirichlet Process Mixtures
Rasmussen, C.E., de la Cruz, B.J., Ghahramani, Z., Wild, D.L. IEEE/ACM Transactions on Computational Biology & Bioinformatics, 6: 615-628, (2009).
An approach to pathway reconstruction using whole genome metabolic models and sensitive sequence searching
Saqi, M., Dobson, R.J.B., Kraben, P., Hodgson, D.A., and Wild, D.L. Journal of Integrative Bioinformatics, 6(1):107, (2009).
CRANKITE– A Fast Polypeptide Backbone Conformation Sampler
Podtelezhnikov A.A. and Wild D.L. Source Code for Biology and Medicine, 2008, 3:12.
Comment on: Efficient Monte Carlo trial moves for polypeptide simulations
Podtelezhnikov A.A. and Wild D.L. Chem. Phys. 2008 129(2):027103.
Enhancing data integration with text analysis to find proteins implicated in plant stress responseHassani-Pak, K., Legaie, R., Canevet, C., van den Berg, H.A., Moore, J.D. and Rawlings, C. (2010) Journal of Integrative Bioinformatics 7:3. Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolorMohammad T Alam, Maria E Merlo, The STREAM Consortium, David A Hodgson, Elizabeth MH Wellington, Eriko Takano, Rainer Breitling (2010). BMC Genomics 11:202. The dynamic architecture of the metabolic switch in Streptomyces coelicolorNieselt, K., Battke, F., Herbig, A., Bruheim, P., Wentzel, A., Jakobsen, O.M., Sletta, H., Alam, M.T., Merlo, M.E., Moore, J., Omara,W., Morrissey, E.R., Juarez-Hermosillo, M., Rodríguez-García, A., Nentwich, M., Thomas, L., Legaie, R., Gaze, W.H., Challis, G.L., Jansen, R.C., Dijkhuizen, L., Rand, D.A., Wild, D.L., Bonin, M., Reuther, J., Wohlleben, W., Smith, M.C.M., Burroughs, N.J., Martín, J.F., Hodgson, D.A., Takano, E., Breitling, R., Ellingsen, T.E., Elizabeth M. H. Wellington, E.M.H. (2010). BMC Genomics 11:10. (Highly Accessed Paper) Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation
Palmer, S.A., Moore, J.D., Clapham, A.J., Rose, P. and Allaby, R.G. (2009) PLoS ONE 4(7): e6301.
The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferationAlix, K., Joets, J., Ryder, C.D., Moore, J., Barker, G.C., Bailey, J.P., King, G.J. and Heslop-Harrison, J.S. (2008). The Plant Journal 56: 1030-1044. High resolution tracking of cell membrane dynamics in moving cells: An electrifying approachR.A. Tyson, D.B.A. Epstein, K.I. Anderson, T. Bretschneider, Math. Model. Nat. Phenom., 5(1):34-55, 2010. Transformation from spots to waves in a model of actin pattern formationS. Whitelam, T. Bretschneider, N.J. Burroughs, Physical Review Letters, 102:198103, 2009. Analysis of cell movement by simultaneous quantification of local membrane displacement and fluorescent intensities using Quimp2L. Bosgraaf, P.J.M. van Haastert, T. Bretschneider, Cell Motility and the Cytoskeleton, 66(3):156-165, 2009. The 3-Dimensional dynamics of actin waves, a model of cytoskeletal self-organizationT. Bretschneider, K. Anderson, M. Ecke, A. Müller-Taubenberger, B. Schroth-Diez, H.C. Ishikawa-Ankerhold, G. Gerisch, Biophys. J., 96, 2888-2900, 2009. Using single fluorescent reporter gene to infer half-life of extrinsic noise and other parameters of gene expression.
M. Komorowski, B. Finkenstadt, D. A. Rand, Biophysical Journal (to appear)
Dual positive and negative regulation of GPCR signaling by GTP Hydrolysis.B. Smith, C. Hill, L. Godfrey, D A Rand, H van den Berg, S Thornton, M Hodgkin, J Davey and G Ladds. Cellular Signalling 21 (209)1151-1160 doi:10.1016/j.cellsig.2009.03.00 Bayesian inference of biochemical kinetic parameters using the linear noise approximation.
M. Komorowski, B. Finkenstadt, C. V. Harper and D. A. Rand. BMC Bioinformatics (2009) 10 343-353
Network control analysis for time-dependent dynamical states.
D. A. Rand. To appear in Dynamics and Games in Science, in honour of Mauricio Peixoto and David Rand. Springer 2010.
Pulsatile stimulation determines timing and specificity of NF-kappa B-dependent transcription.
L. Ashall, C.A. Horton, D.E. Nelson, P. Paszek, C.V. Harper, K. Sillitoe, S. Ryan, D.G. Spiller, J.F. Unitt, D.S. Broomhead, D.B. Kell, D.A. Rand, V. Sée, and M.R.H. White. Science 324 (2009) 242-246
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
Steven J. Kiddle, Oliver P. F. Windram, Stuart McHattie, Andrew Mead, Jim Beynon, Vicky Buchanan-Wollaston, Katherine J. Denby and Sach Mukherjee (2010) Bioinformatics 26 (3):355 Prediction of photoperiodic regulators from quantitative gene circuit models.
Salazar, J. D, Saithong, T., Brown, P. E, Foreman, J., Locke, J. C. W., Halliday, K. J., Carré, I. A., Rand, D. A., Millar, A. J. Cell 139: 1170-1179, 2009
CWRML: representing crop wild relative conservation and use data in XMLMoore, J.D., Kell, S.P., Iriondo J, Ford-Lloyd, B. and Maxted, N. (2008) CWRML: representing crop wild relative conservation and use data in XML. BMC Bioinformatics 9:116. Reversal of cell polarity and actin-myosin cytoskeleton reorganization under mechanical and chemical stimulation.J. Dalous, E. Burghardt, A. Müller-Taubenberger, F. Bruckert, G. Gerisch, T. Bretschneider. Reversal of cell polarity and actin-myosin cytoskeleton reorganization under mechanical and chemical stimulation. Biophys. J., 94(3):1063-1074, 2008. TreeMos: a high-throughput phylogenomic approach to find and visualise phylogenetic mosaicism.Moore, J.D. and Allaby, R.G. (2008) TreeMos: a high-throughput phylogenomic approach to find and visualise phylogenetic mosaicism. Bioinformatics 24(5):717-718. TreeMos is a novel high-throughput graphical analysis application that allows the user to search for phylogenetic mosaicism among one or more DNA or protein sequence multiple alignments and additional unaligned sequences. Stochastic niche structure and diversity maintenance in the T cell repertoire.
E.R. Stirk, C. Molina-Paris, H.A. van den Berg. Stochastic niche structure and diversity maintenance in the T cell repertoire. Journal of Theoretical Biology 255 (2008) 237-249.
The Malthusian parameter in microbial ecology and evolution: An optimal control treatment.
H. A. van den Berg, M. V. Orlov, Yu. N. Kiselev. The Malthusian parameter in microbial ecology and evolution: An optimal control treatment. Computational Mathematics and Modeling 19 (2008) 406-428.
The development of insulin resistance in Type 2 diabetes: insights from knockout studies.R. Pattaranit, H. A. van den Berg, D. Spanswick. The development of insulin resistance in Type 2 diabetes: insights from knockout studies. Sci Prog 91 (2008) 285-316. |
|
