mybib.bib

@Article{deSolve,
	title = {Solving Differential Equations in R: Package deSolve},
	author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
	journal = {Journal of Statistical Software},
	volume = {33},
	number = {9},
	pages = {1--25},
	year = {2010},
	coden = {JSSOBK},
	issn = {1548-7660},
	url = {http://www.jstatsoft.org/v33/i09},
	keywords = {ordinary differential equations, partial differential equations, differential algebraic equations, initial value problems, R, FORTRAN, C},
}

@Article{FME,
	title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in
		{R} Using Package {FME}},
	author = {Karline Soetaert and Thomas Petzoldt},
	journal = {Journal of Statistical Software},
	year = {2010},
	volume = {33},
	number = {3},
	pages = {1--28},
	url = {http://www.jstatsoft.org/v33/i03/},
}

@Manual{scaRabee,
	title  = {\pkg{scaRabee}: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models},
	author = {Sebastien Bihorel},
	year   = {2014},
	note   = {\proglang{R}~package version~1.1-3},
	url    = {http://CRAN.R-project.org/package=scaRabee},
}

@Manual{mkin,
	title  = {\pkg{mkin}: Kinetic Evaluation of Chemical Degradation Data},
	author = {Johannes Ranke and Katrin Lindenberger and René Lehmann},
	year   = {2016},
	note   = {\proglang{R}~package version~0.9.44},
	url    = {http://CRAN.R-project.org/package=mkin},
}

@Manual{nlmeODE,
	title  = {\pkg{nlmeODE}: Non-Linear Mixed-Effects Modelling in \pkg{nlme} Using Differential Equations},
	author = {Christoffer W. Tornoe},
	year   = {2012},
	note   = {\proglang{R}~package version~1.1},
	url    = {http://CRAN.R-project.org/package=nlmeODE},
}

@article{raue2009structural,
	title={Structural and Practical Identifiability Analysis of Partially Observed Dynamical Models by Exploiting the Profile Likelihood},
	author={Raue, Andreas and Kreutz, Clemens and Maiwald, Thomas and Bachmann, Julie and Schilling, Marcel and Klingmüller, Ursula and Timmer, Jens},
	journal={Bioinformatics},
	volume={25},
	number={15},
	pages={1923--1929},
	year={2009},
	publisher={Oxford Univ Press}
}

@article{raue2011addressing,
	title={Addressing Parameter Identifiability by Model-Based Experimentation},
	author={Raue, Andreas and Kreutz, Clemens and Maiwald, Thomas and Klingmüller, Ursula and Timmer, Jens},
	journal={IET Systems Biology},
	volume={5},
	number={2},
	pages={120--130},
	year={2011},
	publisher={IET}
}

@article{maiwald2016driving,
	title={Driving the Model to Its Limit: Profile Likelihood Based Model Reduction},
	author={Maiwald, Tim and Hass, Helge and Steiert, Bernhard and Vanlier, Joep and Engesser, Raphael and Raue, Andreas and Kipkeew, Friederike and Bock, Hans H and Kaschek, Daniel and Kreutz, Clemens and Timmer, Jens},
	journal={PloS ONE},
	volume={11},
	number={9},
	pages={e0162366},
	year={2016},
	publisher={Public Library of Science}
}

@article{raue2013lessons,
	title={Lessons Learned from Quantitative Dynamical Modeling in Systems Biology},
	author={Raue, Andreas and Schilling, Marcel and Bachmann, Julie and Matteson, Andrew and Schelker, Max and Kaschek, Daniel and Hug, Sabine and Kreutz, Clemens and Harms, Brian D and Theis, Fabian J and Klingmüller, Ursula and Timmer, Jens},
	journal={PloS ONE},
	volume={8},
	number={9},
	pages={e74335},
	year={2013},
	publisher={Public Library of Science}
}


@article{merkt2015higher,
	title={Higher-Order Lie Symmetries in Identifiability and Predictability Analysis of Dynamic Models},
	author={Merkt, Benjamin and Timmer, Jens and Kaschek, Daniel},
	journal={Physical Review E},
	volume={92},
	number={1},
	pages={012920},
	year={2015},
	publisher={APS}
}

@article{rosenblatt2016customized,
	title={Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models},
	author={Rosenblatt, Marcus and Timmer, Jens and Kaschek, Daniel},
	journal={Frontiers in Cell and Developmental Biology},
	volume={4},
	year={2016},
	publisher={Frontiers Media SA}
}

@article{squire1998using,
	title={Using Complex Variables to Estimate Derivatives of Real Functions},
	author={Squire, William and Trapp, George},
	journal={SIAM Review},
	volume={40},
	number={1},
	pages={110--112},
	year={1998},
	publisher={SIAM}
}


@article{raue2013joining,
	title={Joining Forces of Bayesian and Frequentist Methodology: A Study for Inference in the Presence of Non-Identifiability},
	author={Raue, Andreas and Kreutz, Clemens and Theis, Fabian Joachim and Timmer, Jens},
	journal={Phil. Trans. R. Soc. A},
	volume={371},
	number={1984},
	pages={20110544},
	year={2013},
	publisher={The Royal Society}
}

@article{kreutz2013profile,
	title={Profile Likelihood in Systems Biology},
	author={Kreutz, Clemens and Raue, Andreas and Kaschek, Daniel and Timmer, Jens},
	journal={FEBS Journal},
	volume={280},
	number={11},
	pages={2564--2571},
	year={2013},
	publisher={Wiley Online Library}
}

@article{kreutz2012likelihood,
	title={Likelihood Based Observability Analysis and Confidence Intervals for Predictions of Dynamic Models},
	author={Kreutz, Clemens and Raue, Andreas and Timmer, Jens},
	journal={BMC Systems Biology},
	volume={6},
	number={1},
	pages={120},
	year={2012},
	publisher={BioMed Central Ltd}
}

@article{murphy2000profile,
	title={On Profile Likelihood},
	author={Murphy, Susan A and Van der Vaart, Aad W},
	journal={Journal of the American Statistical Association},
	volume={95},
	number={450},
	pages={449--465},
	year={2000},
	publisher={Taylor \& Francis Group}
}

@book{azzalini1996statistical,
	title={Statistical Inference Based on the Likelihood},
	author={Azzalini, Adelchi},
	volume={68},
	year={1996},
	publisher={CRC Press}
}

@article{wright1999numerical,
	title={Numerical Optimization},
	author={Wright, Stephen and Nocedal, Jorge},
	journal={Springer Science},
	volume={35},
	pages={67--68},
	year={1999}
}

@article{hass2016fast,
	title={Fast Integration-Based Prediction Bands for Ordinary Differential Equation Models},
	author={Hass, Helge and Kreutz, Clemens and Timmer, Jens and Kaschek, Daniel},
	journal={Bioinformatics},
	volume={32},
	number={8},
	pages={1204--1210},
	year={2016},
	publisher={Oxford Univ Press}
}

@book{press1996numerical,
	title={Numerical Recipes in C},
	author={Press, William H and Teukolsky, Saul A and Vetterling, William T and Flannery, Brian P},
	volume={2},
	year={1996},
	publisher={Cambridge University Press Cambridge}
}