mybib.bib

@Article{kaschek2017dynamic,
  title = {A Dynamic Mathematical Model of Bile Acid Clearance in HepaRG Cells},
  author = {Daniel Kaschek and Ahmad Sharanek and Andr{\'e} Guillouzo and Jens Timmer and Richard J Weaver},
  journal = {Toxicological Sciences},
  year = {2017},
  publisher = {Oxford University Presss},
}

@Article{brun2001practical,
  title = {Practical Identifiability Analysis of Large Environmental Simulation Models},
  author = {Roland Brun and Peter Reichert and Hans R K{\"u}nsch},
  journal = {Water Resources Research},
  volume = {37},
  number = {4},
  pages = {1015--1030},
  year = {2001},
  publisher = {John Wiley \& Sons},
  doi = {10.1029/2000wr900350},
}

@Manual{inline,
  title = {\pkg{inline}: Functions to Inline \proglang{C}, \proglang{C++}, \proglang{Fortran} Function Calls from \proglang{R}},
  author = {Oleg Sklyar and Duncan Murdoch and Mike Smith and Dirk Eddelbuettel and Romain Fran\c{c}ois and Karline Soetaert},
  year = {2018},
  note = {\proglang{R}~package version~0.3.15},
  url = {https://CRAN.R-project.org/package=inline},
}

@Article{CollocInfer,
    title = {\pkg{CollocInfer}: Collocation Inference in Differential Equation Models},
    author = {Giles Hooker and James O. Ramsay and Luo Xiao},
    journal = {Journal of Statistical Software},
    year = {2016},
    volume = {75},
    number = {2},
    pages = {1--52},
    doi = {10.18637/jss.v075.i02},
}
  
@Manual{pomp,
  title = {\pkg{pomp}: Statistical Inference for Partially Observed Markov Processes},
  author = {Aaron A. King and Edward L. Ionides and Carles Breto and Stephen P. Ellner and Matthew J. Ferrari and Bruce E. Kendall and Michael Lavine and Dao Nguyen and Daniel C. Reuman and Helen Wearing and Simon N. Wood and Sebastian Funk and Steven G. Johnson},
  year = {2017},
  note = {\proglang{R}~package version~1.14},
  url = {https://CRAN.R-project.org/package=pomp},
}

@Article{deSolve,
  title = {Solving Differential Equations in \proglang{R}: Package \pkg{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},
  issn = {1548-7660},
  doi = {10.18637/jss.v033.i09},
}

@Article{FME,
  title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in  \proglang{R} Using Package \pkg{FME}},
  author = {Karline Soetaert and Thomas Petzoldt},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {33},
  number = {3},
  pages = {1--28},
  doi = {10.18637/jss.v033.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 = {https://CRAN.R-project.org/package=scaRabee},
}

@Manual{mkin,
  title = {\pkg{mkin}: Kinetic Evaluation of Chemical Degradation Data},
  author = {Johannes Ranke and Katrin Lindenberger and Ren{\'e} Lehmann},
  year = {2019},
  note = {\proglang{R}~package version~0.9.48.1},
  url = {https://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 = {https://CRAN.R-project.org/package=nlmeODE},
}

@Manual{cOde,
  title = {\pkg{cOde}: Automated \proglang{C} Code Generation for \pkg{deSolve}, \pkg{bvpSolve} and `Sundials'},
  author = {Daniel Kaschek},
  year = {2018},
  note = {\proglang{R}~package version~0.4.1},
  url = {https://CRAN.R-project.org/package=cOde},
}

@Manual{trust,
  title = {\pkg{trust}: Trust Region Optimization},
  author = {Charles J. Geyer},
  year = {2015},
  note = {\proglang{R}~package version~0.1-7},
  url = {https://CRAN.R-project.org/package=trust},
}

@Book{rootSolve,
    title = {A Practical Guide to Ecological Modelling: Using \proglang{R} as a Simulation Platform},
    publisher = {Springer-Verlag},
    year = {2009},
    author = {Karline Soetaert and Peter M. J. Herman},
}
  
@Manual{rPython,
  title = {\pkg{rPython}: Package Allowing \proglang{R} to Call \proglang{Python}},
  author = {Carlos J. Gil Bellosta},
  year = {2015},
  note = {\proglang{R} package version 0.0-6},
  url = {https://CRAN.R-project.org/package=rPython},
}

@Manual{parallel,
  title =	 {\proglang{R}: {A} Language and Environment for
                  Statistical Computing},
  author =	 {{\proglang{R} Core Team}},
  organization = {\proglang{R} Foundation for Statistical Computing},
  address =	 {Vienna, Austria},
  year =	 2019,
  url =		 {https://www.R-project.org/}
}

@Article{raue2009structural,
  title = {Structural and Practical Identifiability Analysis of Partially Observed Dynamical Models by Exploiting the Profile Likelihood},
  author = {Andreas Raue and Clemens Kreutz and Thomas Maiwald and Julie Bachmann and Marcel Schilling and Ursula Klingm{\"u}ller and Jens Timmer},
  journal = {Bioinformatics},
  volume = {25},
  number = {15},
  pages = {1923--1929},
  year = {2009},
  publisher = {Oxford Univ Press},
  doi = {10.1093/bioinformatics/btp358},
}

@Article{raue2011addressing,
  title = {Addressing Parameter Identifiability by Model-Based Experimentation},
  author = {Andreas Raue and Clemens Kreutz and Thomas Maiwald and Ursula Klingm{\"u}ller and Jens Timmer},
  journal = {IET Systems Biology},
  volume = {5},
  number = {2},
  pages = {120--130},
  year = {2011},
  publisher = {IET},
  doi = {10.1049/iet-syb.2010.0061},
}

@Article{maiwald2016driving,
  title = {Driving the Model to Its Limit: Profile Likelihood Based Model Reduction},
  author = {Tim Maiwald and Helge Hass and Bernhard Steiert and Joep Vanlier and Raphael Engesser and Andreas Raue and Friederike Kipkeew and Hans H Bock and Daniel Kaschek and Clemens Kreutz and Jens Timmer},
  journal = {PloS ONE},
  volume = {11},
  number = {9},
  pages = {e0162366},
  year = {2016},
  publisher = {Public Library of Science},
  doi = {10.1371/journal.pone.0162366},
}

@Article{raue2013lessons,
  title = {Lessons Learned from Quantitative Dynamical Modeling in Systems Biology},
  author = {Andreas Raue and Marcel Schilling and Julie Bachmann and Andrew Matteson and Max Schelker and Daniel Kaschek and Sabine Hug and Clemens Kreutz and Brian D Harms and Fabian J Theis and Ursula Klingm{\"u}ller and Jens Timmer},
  journal = {PloS ONE},
  volume = {8},
  number = {9},
  pages = {e74335},
  year = {2013},
  publisher = {Public Library of Science},
  doi = {10.1371/journal.pone.0074335},
}

@Article{merkt2015higher,
  title = {Higher-Order Lie Symmetries in Identifiability and Predictability Analysis of Dynamic Models},
  author = {Benjamin Merkt and Jens Timmer and Daniel Kaschek},
  journal = {Physical Review E},
  volume = {92},
  number = {1},
  pages = {012920},
  year = {2015},
  publisher = {APS},
  doi = {10.1103/physreve.92.012920},
}

@Article{rosenblatt2016customized,
  title = {Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models},
  author = {Marcus Rosenblatt and Jens Timmer and Daniel Kaschek},
  journal = {Frontiers in Cell and Developmental Biology},
  volume = {4},
  year = {2016},
  publisher = {Frontiers Media SA},
  doi = {10.3389/fcell.2016.00041},
}

@Article{squire1998using,
  title = {Using Complex Variables to Estimate Derivatives of Real Functions},
  author = {William Squire and George Trapp},
  journal = {SIAM Review},
  volume = {40},
  number = {1},
  pages = {110--112},
  year = {1998},
  publisher = {SIAM},
  doi = {10.1137/s003614459631241x},
}

@Article{raue2013joining,
  title = {Joining Forces of Bayesian and Frequentist Methodology: A Study for Inference in the Presence of Non-Identifiability},
  author = {Andreas Raue and Clemens Kreutz and Fabian Joachim Theis and Jens Timmer},
  journal = {Philosophical Transactions of the Royal Society A},
  volume = {371},
  number = {1984},
  pages = {20110544},
  year = {2013},
  publisher = {The Royal Society},
  doi = {10.1098/rsta.2011.0544},
}

@Article{kreutz2013profile,
  title = {Profile Likelihood in Systems Biology},
  author = {Clemens Kreutz and Andreas Raue and Daniel Kaschek and Jens Timmer},
  journal = {FEBS Journal},
  volume = {280},
  number = {11},
  pages = {2564--2571},
  year = {2013},
  publisher = {John Wiley \& Sons},
  doi = {10.1111/febs.12276},
}

@Article{kreutz2012likelihood,
  title = {Likelihood Based Observability Analysis and Confidence Intervals for Predictions of Dynamic Models},
  author = {Clemens Kreutz and Andreas Raue and Jens Timmer},
  journal = {BMC Systems Biology},
  volume = {6},
  number = {1},
  pages = {120},
  year = {2012},
  publisher = {BioMed Central Ltd},
  doi = {10.1186/1752-0509-6-120},
}

@Article{murphy2000profile,
  title = {On Profile Likelihood},
  author = {Susan A Murphy and Aad W {Van der Vaart}},
  journal = {Journal of the American Statistical Association},
  volume = {95},
  number = {450},
  pages = {449--465},
  year = {2000},
  publisher = {Taylor \& Francis Group},
  doi = {10.1080/01621459.2000.10474219},
}

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

@Article{wright1999numerical,
  title = {Numerical Optimization},
  author = {Stephen Wright and Jorge Nocedal},
  journal = {Springer-Verlag},
  volume = {35},
  pages = {67--68},
  year = {1999},
  doi = {10.1007/b98874},
}

@Article{hass2016fast,
  title = {Fast Integration-Based Prediction Bands for Ordinary Differential Equation Models},
  author = {Helge Hass and Clemens Kreutz and Jens Timmer and Daniel Kaschek},
  journal = {Bioinformatics},
  volume = {32},
  number = {8},
  pages = {1204--1210},
  year = {2016},
  publisher = {Oxford Univ Press},
  doi = {10.1093/bioinformatics/btv743},
}

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

@Article{venzon1988method,
  title = {A Method for Computing Profile-Likelihood-Based Confidence Intervals},
  author = {D J Venzon and S H Moolgavkar},
  journal = {Applied Statistics},
  pages = {87--94},
  year = {1988},
  publisher = {JSTOR},
  doi = {10.2307/2347496},
}