% bmc_article.bib
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@article{blank,
	author  = {}, 
	title   = {},
	journal = {}, 
	year  = {},
	  month = {}, 
	  volume= {}, 
	  number= {}, 
	  pages = {},
	  note  = {} 
}	

@article{bretz2008dose,
  title={Dose finding--a challenge in statistics},
  author={Bretz, Frank and Hsu, Jason and Pinheiro, Jose and Liu, Yi},
  journal={Biometrical Journal: Journal of Mathematical Methods in Biosciences},
  volume={50},
  number={4},
  pages={480--504},
  year={2008},
  publisher={Wiley Online Library}
}

@article{rao2009multiple,
  title={Multiple comparison procedures-a note and a bibliography},
  author={Rao, CV},
  journal={Journal of Statistics},
  volume={16},
  number={1},
  year={2009},
  publisher={Citeseer}
}

@article{hothorn2006multiple,
  title={Multiple comparisons and multiple contrasts in randomized dose-response trials—confidence interval oriented approaches},
  author={Hothorn, Ludwig A},
  journal={Journal of Biopharmaceutical Statistics},
  volume={16},
  number={5},
  pages={711--731},
  year={2006},
  publisher={Taylor \& Francis}
}

@article{bretz2003statistical,
  title={Statistical analysis of monotone or non-monotone dose--response data from in vitro toxicological assays},
  author={Bretz, Frank and Hothorn, Ludwig A},
  journal={Alternatives to Laboratory Animals},
  volume={31},
  number={1\_suppl},
  pages={81--96},
  year={2003},
  publisher={SAGE Publications Sage UK: London, England}
}

@article{jewell2019testing,
  title={Testing for a change in mean after changepoint detection},
  author={Jewell, Sean and Fearnhead, Paul and Witten, Daniela},
  journal={arXiv preprint arXiv:1910.04291},
  year={2019}
}

@article{akacha2017estimandsperspective,
  title={Estimands in clinical trials--broadening the perspective},
  author={Akacha, Mouna and Bretz, Frank and Ruberg, Stephen},
  journal={Statistics in medicine},
  volume={36},
  number={1},
  pages={5--19},
  year={2017},
  publisher={Wiley Online Library}
}

@article{akacha2017estimandstrails,
  title={Estimands and their role in clinical trials},
  author={Akacha, Mouna and Bretz, Frank and Ohlssen, David and Rosenkranz, Gerd and Schmidli, Heinz},
  journal={Statistics in Biopharmaceutical Research},
  volume={9},
  number={3},
  pages={268--271},
  year={2017},
  publisher={Taylor \& Francis}
}

@book{mallinckrodt2019estimands,
  title={Estimands, Estimators and Sensitivity Analysis in Clinical Trials},
  author={Mallinckrodt, Craig and Molenberghs, Geert and Lipkovich, Ilya and Ratitch, Bohdana},
  year={2019},
  publisher={CRC Press},
  address   = {Boca Raton}
}

@article{leuchs2015choosing,
  title={Choosing appropriate estimands in clinical trials},
  author={Leuchs, Ann-Kristin and Zinserling, J{\"o}rg and Brandt, Andreas and Wirtz, Dorothee and Benda, Norbert},
  journal={Therapeutic Innovation \& Regulatory Science},
  volume={49},
  number={4},
  pages={584--592},
  year={2015},
  publisher={SAGE Publications Sage CA: Los Angeles, CA}
}

@article{li2017introduction,
  title={An introduction to multiplicity issues in clinical trials: the what, why, when and how},
  author={Li, Guowei and Taljaard, Monica and Van den Heuvel, Edwin R and Levine, Mitchell AH and Cook, Deborah J and Wells, George A and Devereaux, Philip J and Thabane, Lehana},
  journal={International journal of epidemiology},
  volume={46},
  number={2},
  pages={746--755},
  year={2017},
  publisher={Oxford University Press}
}

@article{alosh2014advanced,
  title={Advanced multiplicity adjustment methods in clinical trials},
  author={Alosh, Mohamed and Bretz, Frank and Huque, Mohammad},
  journal={Statistics in medicine},
  volume={33},
  number={4},
  pages={693--713},
  year={2014},
  publisher={Wiley Online Library}
}

@article{ratitch2020choosing,
  title={Choosing estimands in clinical trials: Putting the ICH E9 (R1) into practice},
  author={Ratitch, Bohdana and Bell, James and Mallinckrodt, Craig and Bartlett, Jonathan W and Goel, Niti and Molenberghs, Geert and O’Kelly, Michael and Singh, Pritibha and Lipkovich, Ilya},
  journal={Therapeutic innovation \& regulatory science},
  volume={54},
  number={2},
  pages={324--341},
  year={2020},
  publisher={Springer}
}

@article{akacha2017estimands,
  title={Estimands and their role in clinical trials},
  author={Akacha, Mouna and Bretz, Frank and Ohlssen, David and Rosenkranz, Gerd and Schmidli, Heinz},
  journal={Statistics in Biopharmaceutical Research},
  volume={9},
  number={3},
  pages={268--271},
  year={2017},
  publisher={Taylor \& Francis}
}

@misc{wasserstein2019moving,
  title={Moving to a world beyond “p< 0.05”},
  author={Wasserstein, Ronald L and Schirm, Allen L and Lazar, Nicole A},
  year={2019},
  publisher={Taylor \& Francis}
}

@article{sneddon2017considering,
  title={Considering aspects of the 3Rs principles within experimental animal biology},
  author={Sneddon, Lynne U and Halsey, Lewis G and Bury, Nic R},
  journal={Journal of Experimental Biology},
  volume={220},
  number={17},
  pages={3007--3016},
  year={2017},
  publisher={The Company of Biologists Ltd}
}

@article{balcombe2013prolonged,
  title={Prolonged pain research in mice: trends in reference to the 3Rs},
  author={Balcombe, Jonathan and Ferdowsian, Hope and Briese, Lauren},
  journal={Journal of applied animal welfare science},
  volume={16},
  number={1},
  pages={77--95},
  year={2013},
  publisher={Taylor \& Francis}
}

@article{goldfeld2020simstudy,
  title={simstudy: Illuminating research methods through data generation},
  author={Goldfeld, Keith and Wujciak-Jens, Jacob},
  journal={Journal of Open Source Software},
  volume={5},
  number={54},
  pages={2763},
  year={2020}
}

@article{barr2013random,
  title={Random effects structure for confirmatory hypothesis testing: Keep it maximal},
  author={Barr, Dale J and Levy, Roger and Scheepers, Christoph and Tily, Harry J},
  journal={Journal of memory and language},
  volume={68},
  number={3},
  pages={255--278},
  year={2013},
  publisher={Elsevier}
}

@article{matuschek2017balancing,
  title={Balancing Type I error and power in linear mixed models},
  author={Matuschek, Hannes and Kliegl, Reinhold and Vasishth, Shravan and Baayen, Harald and Bates, Douglas},
  journal={Journal of memory and language},
  volume={94},
  pages={305--315},
  year={2017},
  publisher={Elsevier}
}

@article{schad2020capitalize,
  title={How to capitalize on a priori contrasts in linear (mixed) models: A tutorial},
  author={Schad, Daniel J and Vasishth, Shravan and Hohenstein, Sven and Kliegl, Reinhold},
  journal={Journal of Memory and Language},
  volume={110},
  pages={104038},
  year={2020},
  publisher={Elsevier}
}

@article{schaarschmidt2009analysis,
  title={Analysis of trials with complex treatment structure using multiple contrast tests},
  author={Schaarschmidt, Frank and Vaas, Lea},
  journal={HortScience},
  volume={44},
  number={1},
  pages={188--195},
  year={2009},
  publisher={American Society for Horticultural Science}
}

@article{hasler2008multiple,
  title={Multiple contrast tests in the presence of heteroscedasticity},
  author={Hasler, Mario and Hothorn, Ludwig A},
  journal={Biometrical Journal: Journal of Mathematical Methods in Biosciences},
  volume={50},
  number={5},
  pages={793--800},
  year={2008},
  publisher={Wiley Online Library}
}


@article{hothorn2008simultaneous,
  title={Simultaneous inference in general parametric models},
  author={Hothorn, Torsten and Bretz, Frank and Westfall, Peter},
  journal={Biometrical Journal: Journal of Mathematical Methods in Biosciences},
  volume={50},
  number={3},
  pages={346--363},
  year={2008},
  publisher={Wiley Online Library}
}

@book{bretz2016multiple,
  title={Multiple comparisons using R},
  author={Bretz, Frank and Hothorn, Torsten and Westfall, Peter},
  year={2016},
  address = {Boca Raton},
  publisher={CRC Press}
}

@article{kruppa2020comparison,
  title={A comparison study on modeling of clustered and overdispersed count data for multiple comparisons},
  author={Kruppa, Jochen and Hothorn, Ludwig},
  journal={Journal of Applied Statistics},
  pages={1--13},
  year={2020},
  publisher={Taylor \& Francis}
}

@article{benvenuto2020application,
  title={Application of the ARIMA model on the COVID-2019 epidemic dataset},
  author={Benvenuto, Domenico and Giovanetti, Marta and Vassallo, Lazzaro and Angeletti, Silvia and Ciccozzi, Massimo},
  journal={Data in brief},
  volume={29},
  pages={105340},
  year={2020},
  publisher={Elsevier}
}

@article{sowell1992modeling,
  title={Modeling long-run behavior with the fractional ARIMA model},
  author={Sowell, Fallaw},
  journal={Journal of monetary economics},
  volume={29},
  number={2},
  pages={277--302},
  year={1992},
  publisher={Elsevier}
}

@article{frye2018rna,
  title={RNA modifications modulate gene expression during development},
  author={Frye, Michaela and Harada, Bryan T and Behm, Mikaela and He, Chuan},
  journal={Science},
  volume={361},
  number={6409},
  pages={1346--1349},
  year={2018},
  publisher={American Association for the Advancement of Science}
}

@article{hu2019emexplorer,
  title={EmExplorer: a database for exploring time activation of gene expression in mammalian embryos},
  author={Hu, Bosu and Zheng, Lei and Long, Chunshen and Song, Mingmin and Li, Tao and Yang, Lei and Zuo, Yongchun},
  journal={Open biology},
  volume={9},
  number={6},
  pages={190054},
  year={2019},
  publisher={The Royal Society}
}

@article{salas2019expression,
  title={The expression of mirnas in human ovaries, oocytes, extracellular vesicles, and early embryos: a systematic review},
  author={Salas-Huetos, Albert and James, Emma R and Aston, Kenneth I and Jenkins, Timothy G and Carrell, Douglas T and Yeste, Marc},
  journal={Cells},
  volume={8},
  number={12},
  pages={1564},
  year={2019},
  publisher={Multidisciplinary Digital Publishing Institute}
}

@article{cho2015multiple,
  title={Multiple-change-point detection for high dimensional time series via sparsified binary segmentation},
  author={Cho, Haeran and Fryzlewicz, Piotr},
  journal={Journal of the Royal Statistical Society: Series B: Statistical Methodology},
  pages={475--507},
  year={2015},
  publisher={JSTOR}
}

@article{fryzlewicz2014wild,
  title={Wild binary segmentation for multiple change-point detection},
  author={Fryzlewicz, Piotr and others},
  journal={Annals of Statistics},
  volume={42},
  number={6},
  pages={2243--2281},
  year={2014},
  publisher={Institute of Mathematical Statistics}
}

@article{sturludottir2017detection,
  title={Detection of a changepoint, a mean-shift accompanied with a trend change, in short time-series with autocorrelation},
  author={Sturludottir, Erla and Gunnlaugsdottir, Helga and Nielsen, Olafur K and Stefansson, Gunnar},
  journal={Communications in Statistics-Simulation and Computation},
  volume={46},
  number={7},
  pages={5808--5818},
  year={2017},
  publisher={Taylor \& Francis}
}

@article{aminikhanghahi2017survey,
  title={A survey of methods for time series change point detection},
  author={Aminikhanghahi, Samaneh and Cook, Diane J},
  journal={Knowledge and information systems},
  volume={51},
  number={2},
  pages={339--367},
  year={2017},
  publisher={Springer}
}

@article{truong2020selective,
  title={Selective review of offline change point detection methods},
  author={Truong, Charles and Oudre, Laurent and Vayatis, Nicolas},
  journal={Signal Processing},
  volume={167},
  pages={107299},
  year={2020},
  publisher={Elsevier}
}

@book{tartakovsky2014sequential,
  title={Sequential analysis: Hypothesis testing and changepoint detection},
  author={Tartakovsky, Alexander and Nikiforov, Igor and Basseville, Michele},
  year={2014},
  address={Boca Raton},
  publisher={CRC Press}
}

@article{menne2005detection,
  title={Detection of undocumented changepoints using multiple test statistics and composite reference series},
  author={Menne, Matthew J and Williams Jr, Claude N},
  journal={Journal of Climate},
  volume={18},
  number={20},
  pages={4271--4286},
  year={2005}
}






@article{hojsgaard_r_2006,
	title = {The {R} {Package} geepack for {Generalized} {Estimating} {Equations}},
	volume = {15/2},
	journal = {J Stat Softw},
	author = {H{\o}jsgaard, S{\"o}ren and Halekoh, Ulrich and Yan, Jun},
	year = {2006},
	pages = {1--11}
}

@article{bates2014fitting,
  title={Fitting linear mixed-effects models using lme4},
  author={Bates, Douglas and M{\"a}chler, Martin and Bolker, Ben and Walker, Steve},
  journal={arXiv preprint arXiv:1406.5823},
  year={2014}
}

@article{lee2004conditional,
  title={Conditional and marginal models: another view},
  author={Lee, Youngjo and Nelder, John A and others},
  journal={Statistical Science},
  volume={19},
  number={2},
  pages={219--238},
  year={2004},
  publisher={Institute of Mathematical Statistics}
}

@article{muff2016marginal,
  title={Marginal or conditional regression models for correlated non-normal data?},
  author={Muff, Stefanie and Held, Leonhard and Keller, Lukas F},
  journal={Methods in Ecology and Evolution},
  volume={7},
  number={12},
  pages={1514--1524},
  year={2016},
  publisher={Wiley Online Library}
}


% simstudy -- no reference found, used citation() in R
@Manual{,
    title = {simstudy: Simulation of Study Data},
    author = {Keith Goldfeld},
    year = {2019},
    note = {R package version 0.1.14},
    url = {https://CRAN.R-project.org/package=simstudy},
  }

% nonparametric approach for multiple change point analysis of multivariate data
@article{matteson2014nonparametric,
  title={A nonparametric approach for multiple change point analysis of multivariate data},
  author={Matteson, David S and James, Nicholas A},
  journal={Journal of the American Statistical Association},
  volume={109},
  number={505},
  pages={334--345},
  year={2014},
  publisher={Taylor \& Francis}
}

@article{lewis2019animal,
  title={Animal experimentation: Implementation and application of the 3Rs},
  author={Lewis, David I},
  journal={Emerging Topics in Life Sciences},
  volume={3},
  number={6},
  pages={675--679},
  year={2019},
  publisher={Portland Press Ltd.}
}

@book{theiler2013house,
  title={The house mouse: atlas of embryonic development},
  author={Theiler, Karl},
  year={2013},
  address={Z\"urich, Switzerland},
  publisher={Springer Science \& Business Media}
}

% STEM 
@article{ernst2006stem,
  title={STEM: a tool for the analysis of short time series gene expression data},
  author={Ernst, Jason and Bar-Joseph, Ziv},
  journal={BMC bioinformatics},
  volume={7},
  number={1},
  pages={191},
  year={2006},
  publisher={Springer}
}



% Bayesian Change Point Approach
@article{barry1993bayesian,
  title={A Bayesian analysis for change point problems},
  author={Barry, Daniel and Hartigan, John A},
  journal={Journal of the American Statistical Association},
  volume={88},
  number={421},
  pages={309--319},
  year={1993},
  publisher={Taylor \& Francis}
}

% muggeo
@article{muggeo2014segmented,
  title={Segmented mixed models with random changepoints: a maximum likelihood approach with application to treatment for depression study},
  author={Muggeo, Vito MR and Atkins, David C and Gallop, Robert J and Dimidjian, Sona},
  journal={Statistical Modelling},
  volume={14},
  number={4},
  pages={293--313},
  year={2014},
  publisher={Sage Publications Sage India: New Delhi, India}
}

% mcdermott contrast test
@article{mcdermott1999generalized,
  title={Generalized orthogonal contrast tests for homogeneity of ordered means},
  author={Mcdermott, Michael P},
  journal={Canadian Journal of Statistics},
  volume={27},
  number={3},
  pages={457--470},
  year={1999},
  publisher={Wiley Online Library}
}



%mother effect
@article{bernardo1996maternal,
  title={Maternal effects in animal ecology},
  author={Bernardo, Joseph},
  journal={American Zoologist},
  volume={36},
  number={2},
  pages={83--105},
  year={1996},
  publisher={Oxford University Press UK}
}