TY - JOUR AU - Toni, T. AU - Stumpf, M. P. H. PY - 2010 DA - 2010// TI - Simulation-based model selection for dynamical systems in systems and population biology JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp619 DO - 10.1093/bioinformatics/btp619 ID - Toni2010 ER - TY - BOOK AU - Sivia, D. AU - Skilling, J. PY - 2006 DA - 2006// TI - Data Analysis: A Bayesian Tutorial PB - OUP CY - Oxford ID - Sivia2006 ER - TY - JOUR AU - Skilling, J. PY - 2006 DA - 2006// TI - Nested sampling for general Bayesian computations JO - Bayesian Anal VL - 1 UR - https://doi.org/10.1214/06-BA127 DO - 10.1214/06-BA127 ID - Skilling2006 ER - TY - JOUR AU - Leloup, J. C. AU - Gonze, D. AU - Goldbeter, A. PY - 1999 DA - 1999// TI - Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora JO - J Biol Rhythms VL - 14 UR - https://doi.org/10.1177/074873099129000948 DO - 10.1177/074873099129000948 ID - Leloup1999 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Computational systems biology JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01254 DO - 10.1038/nature01254 ID - Kitano2002 ER - TY - JOUR AU - Pokhilko, A. AU - Hodge, S. K. AU - Stratford, K. AU - Knox, K. D. AU - Edwards, K. AU - Thomson, A. W. AU - Mizuno, T. AU - Millar, A. J. PY - 2010 DA - 2010// TI - Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model JO - Mol Syst Biol VL - 6 UR - https://doi.org/10.1038/msb.2010.69 DO - 10.1038/msb.2010.69 ID - Pokhilko2010 ER - TY - JOUR AU - Aitken, S. AU - Alexander, D. A. AU - Beggs, J. D. PY - 2011 DA - 2011// TI - Modelling reveals kinetic advantages of co-transcriptional splicing JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1002215 DO - 10.1371/journal.pcbi.1002215 ID - Aitken2011 ER - TY - JOUR AU - Mendes, P. AU - Kell, D. PY - 1998 DA - 1998// TI - Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.10.869 DO - 10.1093/bioinformatics/14.10.869 ID - Mendes1998 ER - TY - JOUR AU - Feroz, F. AU - Gair, J. R. AU - Hobson, M. P. AU - Porter, E. K. PY - 2009 DA - 2009// TI - Use of the MULTINEST algorithm for gravitational wave data analysis JO - Classical Quantum Gravity VL - 26 UR - https://doi.org/10.1088/0264-9381/26/21/215003 DO - 10.1088/0264-9381/26/21/215003 ID - Feroz2009 ER - TY - JOUR AU - Feroz, F. AU - Hobson, M. P. AU - Bridges, M. PY - 2009 DA - 2009// TI - MULTINEST: an efficient and robust Bayesian inference tool for cosmology and particle physics JO - Mon Not Roy Astron Soc VL - 398 UR - https://doi.org/10.1111/j.1365-2966.2009.14548.x DO - 10.1111/j.1365-2966.2009.14548.x ID - Feroz2009 ER - TY - JOUR AU - Mukherjee, P. AU - Parkinson, D. AU - Liddle, A. PY - 2006 DA - 2006// TI - A nested sampling algorithm for cosmological model selection JO - Astrophysical J VL - 638 UR - https://doi.org/10.1086/501068 DO - 10.1086/501068 ID - Mukherjee2006 ER - TY - JOUR AU - Feroz, F. AU - Hobson, M. P. PY - 2008 DA - 2008// TI - Multimodal nested sampling: an efficient and robust alternative to Markov Chain Monte Carlo methods for astronomical data analyses JO - Mon Not R Astron Soc VL - 384 UR - https://doi.org/10.1111/j.1365-2966.2007.12353.x DO - 10.1111/j.1365-2966.2007.12353.x ID - Feroz2008 ER - TY - JOUR AU - Feroz, F. AU - Balan, M. P. AU - Hobson, S. T. PY - 2011 DA - 2011// TI - Detecting extrasolar planets from stellar radial velocities using Bayesian evidence JO - Mon Not Roy Astron Soc VL - 415 UR - https://doi.org/10.1111/j.1365-2966.2011.18962.x DO - 10.1111/j.1365-2966.2011.18962.x ID - Feroz2011 ER - TY - BOOK AU - Murray, I. PY - 2007 DA - 2007// TI - Advances in Markov chain Monte Carlo methods PB - PhD Thesis UCL CY - University College London, London ID - Murray2007 ER - TY - CHAP AU - Robert, C. P. AU - Wraith, D. ED - Goggans, P. M. ED - Chan, C. Y. PY - 2009 DA - 2009// TI - Computational methods for Bayesian model choice BT - American Institute of Physics Conference Series, Volume 1193 of American Institute of Physics Conference Series PB - American Institute of Physics CY - Melville ID - Robert2009 ER - TY - JOUR AU - Chopin, N. AU - Robert, C. PY - 2010 DA - 2010// TI - Properties of nested sampling JO - Biometrika VL - 97 UR - https://doi.org/10.1093/biomet/asq021 DO - 10.1093/biomet/asq021 ID - Chopin2010 ER - TY - CHAP AU - Skilling, J. ED - Goggans, P. M. ED - Chan, C. Y. PY - 2009 DA - 2009// TI - Nested sampling’s convergence BT - American Institute of Physics Conference Series, Volume 1193 of American Institute of Physics Conference Series PB - American Institute of Physics CY - Melville ID - Skilling2009 ER - TY - JOUR AU - Keeton, C. R. PY - 2011 DA - 2011// TI - On statistical uncertainty in nested sampling JO - Mon Notices R Astronomical Soc VL - 414 UR - https://doi.org/10.1111/j.1365-2966.2011.18474.x DO - 10.1111/j.1365-2966.2011.18474.x ID - Keeton2011 ER - TY - JOUR AU - Chatpatanasiri, R. PY - 2009 DA - 2009// TI - How to sample from a truncated distribution if you must JO - Artif Intell Rev VL - 31 UR - https://doi.org/10.1007/s10462-009-9121-x DO - 10.1007/s10462-009-9121-x ID - Chatpatanasiri2009 ER - TY - JOUR AU - Vyshemirsky, V. AU - Girolami, M. A. PY - 2008 DA - 2008// TI - Bayesian ranking of biochemical system models JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm607 DO - 10.1093/bioinformatics/btm607 ID - Vyshemirsky2008 ER - TY - BOOK AU - Calderhead, B. PY - 2007 DA - 2007// TI - A Study of Population MCMC for estimating Bayes Factors over Nonlinear ODE Models PB - PhD Thesis CY - University of Glasgow, Glasgow ID - Calderhead2007 ER - TY - JOUR AU - Calderhead, B. AU - Girolami, M. PY - 2009 DA - 2009// TI - Estimating Bayes factors via thermodynamic integration and population MCMC JO - Comput Stat Data Anal VL - 53 UR - https://doi.org/10.1016/j.csda.2009.07.025 DO - 10.1016/j.csda.2009.07.025 ID - Calderhead2009 ER - TY - JOUR AU - Girolami, M. PY - 2008 DA - 2008// TI - BioBayes: A software package for Bayesian inference in systems biology JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn338 DO - 10.1093/bioinformatics/btn338 ID - Girolami2008 ER - TY - JOUR AU - Down, T. A. AU - Bergmann, C. M. AU - Su, J. AU - Hubbard, T. J. P. PY - 2007 DA - 2007// TI - Large-scale discovery of promoter motifs in Drosophila melanogaster JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030007 DO - 10.1371/journal.pcbi.0030007 ID - Down2007 ER - TY - JOUR AU - Kirk, P. AU - Thorne, T. AU - Stumpf, M. P. PY - 2013 DA - 2013// TI - Model selection in systems and synthetic biology JO - Curr Opin Biotechnol VL - 24 UR - https://doi.org/10.1016/j.copbio.2013.03.012 DO - 10.1016/j.copbio.2013.03.012 ID - Kirk2013 ER - TY - JOUR AU - Kass, R. AU - Raferty, A. PY - 1995 DA - 1995// TI - Bayes factors JO - J Am Stat Assoc VL - 90 UR - https://doi.org/10.1080/01621459.1995.10476572 DO - 10.1080/01621459.1995.10476572 ID - Kass1995 ER - TY - CHAP AU - Dondelinger, F. AU - Rogers, S. AU - Filippone, M. AU - Cretella, R. AU - Palmer, T. AU - Smith, R. AU - Millar, A. AU - Husmeier, D. PY - 2012 DA - 2012// TI - Parameter inference in mechanistic models of cellular regulation and signalling pathways using gradient matching BT - Proc. 9th International Workshop on Computational Systems Biology, Ulm. Tampere: Tampere International Center for Signal Processing ID - Dondelinger2012 ER - TY - JOUR AU - Neal, R. M. PY - 2003 DA - 2003// TI - Slice sampling JO - Ann Stat VL - 31 UR - https://doi.org/10.1214/aos/1056562461 DO - 10.1214/aos/1056562461 ID - Neal2003 ER - TY - JOUR AU - Heron, E. A. AU - Finkenstadt, B. AU - Rand, D. A. PY - 2007 DA - 2007// TI - Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm367 DO - 10.1093/bioinformatics/btm367 ID - Heron2007 ER - TY - BOOK AU - Dunlap, J. C. AU - Loros, J. J. AU - DeCoursey, P. J. PY - 2003 DA - 2003// TI - Chronobiology: Biological Timekeeping PB - Sinauer CY - Sunderland ID - Dunlap2003 ER - TY - JOUR AU - Dodd, A. N. AU - Salathia, N. AU - Hall, A. AU - Kévei, E. AU - Tóth, R. AU - Nagy, F. AU - Hibberd, J. M. AU - Millar, A. J. AU - Webb, A. A. PY - 2005 DA - 2005// TI - Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage JO - Science VL - 309 UR - https://doi.org/10.1126/science.1115581 DO - 10.1126/science.1115581 ID - Dodd2005 ER - TY - JOUR AU - Resco, V. AU - Hartwell, J. AU - Hall, A. PY - 2009 DA - 2009// TI - Ecological implications of plants ability to tell the time JO - Ecol Lett VL - 12 UR - https://doi.org/10.1111/j.1461-0248.2009.01295.x DO - 10.1111/j.1461-0248.2009.01295.x ID - Resco2009 ER - TY - JOUR AU - Zhang, E. E. AU - Kay, S. A. PY - 2010 DA - 2010// TI - Clocks not winding down: unravelling circadian networks JO - Nat Rev Mol Cell Biol VL - 11 UR - https://doi.org/10.1038/nrm2995 DO - 10.1038/nrm2995 ID - Zhang2010 ER - TY - JOUR AU - Akman, O. E. AU - Locke, J. C. AU - Tang, S. AU - Carré, I. AU - Millar, A. J. AU - Rand, D. A. PY - 2008 DA - 2008// TI - Isoform switching facilitates period control in the Neurospora crassa circadian clock JO - Mol Syst Biol VL - 4 UR - https://doi.org/10.1038/msb.2008.28 DO - 10.1038/msb.2008.28 ID - Akman2008 ER - TY - JOUR AU - Ramsey, S. AU - Orrell, D. AU - Bolouri, H. PY - 2005 DA - 2005// TI - Dizzy: Stochastic simulation of large-scale genetic regulatory networks JO - J Bioinformatics Comput Biol VL - 03 UR - https://doi.org/10.1142/S0219720005001132 DO - 10.1142/S0219720005001132 ID - Ramsey2005 ER - TY - BOOK AU - Wilkinson, D. PY - 2006 DA - 2006// TI - Stochastic Modelling for Systems Biology PB - Chapman and Hall/CRC CY - London ID - Wilkinson2006 ER - TY - JOUR AU - Wilkinson, D. PY - 2009 DA - 2009// TI - Stochastic modelling for quantitative description of heterogeneous biological systems JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2509 DO - 10.1038/nrg2509 ID - Wilkinson2009 ER - TY - JOUR AU - Gonze, D. AU - Halloy, J. AU - Goldbeter, A. PY - 2002 DA - 2002// TI - Biochemical clocks and molecular noise: theoretical study of robustness factors JO - J Chem Phys VL - 116 UR - https://doi.org/10.1063/1.1475765 DO - 10.1063/1.1475765 ID - Gonze2002 ER - TY - JOUR AU - Geyer, C. PY - 1992 DA - 1992// TI - Practical Markov Chain Monte Carlo JO - Stat Sci VL - 7 UR - https://doi.org/10.1214/ss/1177011137 DO - 10.1214/ss/1177011137 ID - Geyer1992 ER -