@ARTICLE{dawson2021qsar,
  title = {Designing QSARs for Parameters of High-Throughput Toxicokinetic Models Using Open-Source Descriptors},
  author = {Dawson, Daniel E. and Ingle, Brandall L. and Phillips, Katherine A. and Nichols, John W. and Wambaugh, John F. and Tornero-Velez, Rogelio},
  journal = {Environmental Science \& Technology},
  volume = {55},
  number = {9},
  pages = {6505-6517},
  year = {2021},
  doi = {10.1021/acs.est.0c06117},
  note ={PMID: 33856768},
  URL = {https://doi.org/10.1021/acs.est.0c06117},
  eprint = {https://doi.org/10.1021/acs.est.0c06117}
}

@article{kapraun2019empirical,
  doi = {10.1371/journal.pone.0215906},
  author = {Kapraun, Dustin F. AND Wambaugh, John F. AND Setzer, R. Woodrow AND Judson, Richard S.},
  journal = {PLOS ONE},
  publisher = {Public Library of Science},
  title = {Empirical models for anatomical and physiological changes in a human mother and fetus during pregnancy and gestation},
  year = {2019},
  month = {05},
  volume = {14},
  url = {https://doi.org/10.1371/journal.pone.0215906},
  pages = {1-56},
  number = {5}
}

@ARTICLE{linakis2020development,
  title={Development and evaluation of a high-throughput inhalation model for organic chemicals},
  author={Linakis, Matthew W and Sayre, Risa R and Pearce, Robert G and Sfeir, Mark A and Sipes, Nisha S and Pangburn, Heather A and Gearhart, Jeffery M and Wambaugh, John F},
  journal={Journal of exposure science \& environmental epidemiology},
  volume={30},
  number={5},
  pages={866--877},
  year={2020},
  publisher={Nature Publishing Group}
}

@ARTICLE{pearce2017httk,
  title={Httk: R package for high-throughput toxicokinetics},
  author={Pearce, Robert G and Setzer, R Woodrow and Strope, Cory L and Wambaugh, John F and Sipes, Nisha S},
  journal={Journal of Statistical Software},
  volume={79},
  number={4},
  pages={1},
  year={2017},
  publisher={NIH Public Access}
}

@article{pradeep2020chemstr,
  title = {Using chemical structure information to develop predictive models for in vitro toxicokinetic parameters to inform high-throughput risk-assessment},
  journal = {Computational Toxicology},
  volume = {16},
  pages = {100136},
  year = {2020},
  issn = {2468-1113},
  doi = {https://doi.org/10.1016/j.comtox.2020.100136},
  url = {https://doi.org/10.1016/j.comtox.2020.100136},
  author = {Pradeep, Prachi and Patlewicz, Grace and Pearce, Robert and Wambaugh, John and Wetmore, Barbara and Judson, Richard},
  keywords = {HTTK, Fub, Clearance, QSAR, IVIVE, Toxicokinetics}
}

@article{Aylward2014matfet,
  title={Relationships of chemical concentrations in maternal and cord blood: a review of available data},
  author={Aylward, LL and Hays, Sean M and Kirman, CR and Marchitti, SA and Kenneke, JF and English, C and Mattison, DR and Becker, RA},
  journal={Journal of Toxicology and Environmental Health, Part B},
  volume={17},
  number={3},
  pages={175--203},
  year={2014},
  publisher={Taylor \& Francis},
  doi = {https://doi.org/10.1080/10937404.2014.884956}
}

@article{dallmann2018pregpbtk,
  title={A physiologically based pharmacokinetic model for pregnant women to predict the pharmacokinetics of drugs metabolized via several enzymatic pathways},
  author={Dallmann, Andre and Ince, Ibrahim and Coboeken, Katrin and Eissing, Thomas and Hempel, Georg},
  journal={Clinical pharmacokinetics},
  volume={57},
  number={6},
  pages={749--768},
  year={2018},
  publisher={Springer}
}

@article{Csanady2002fetalpc,
  title={Distribution and unspecific protein binding of the xenoestrogens bisphenol A and daidzein},
  author={Csanady, G and Oberste-Frielinghaus, H and Semder, B and Baur, C and Schneider, K and Filser, J},
  journal={Archives of toxicology},
  volume={76},
  number={5-6},
  pages={299--305},
  year={2002},
  publisher={Springer}
}

@article{Curley1969fetalpc,
  title={Chlorinated hydrocarbon insecticides in organs of stillborn and blood of newborn babies},
  author={Curley, August and Copeland, M Frank and Kimbrough, Renate D},
  journal={Archives of Environmental Health: An International Journal},
  volume={19},
  number={5},
  pages={628--632},
  year={1969},
  publisher={Taylor \& Francis}
}

@article{Weijs2013fetalpc,
  title={Application of Bayesian population physiologically based pharmacokinetic (PBPK) modeling and Markov chain Monte Carlo simulations to pesticide kinetics studies in protected marine mammals: DDT, DDE, and DDD in harbor porpoises},
  author={Weijs, Liesbeth and Yang, Raymond SH and Das, Krishna and Covaci, Adrian and Blust, Ronny},
  journal={Environmental science \& technology},
  volume={47},
  number={9},
  pages={4365--4374},
  year={2013},
  publisher={ACS Publications}
}

@article{Wang2018matbloodnta,
author = {Aolin Wang  and Roy R. Gerona  and Jackie M. Schwartz  and Thomas Lin  and Marina Sirota  and Rachel Morello-Frosch  and Tracey J. Woodruff },
title = {A Suspect Screening Method for Characterizing Multiple Chemical Exposures among a Demographically Diverse Population of Pregnant Women in San Francisco},
journal = {Environmental Health Perspectives},
volume = {126},
number = {7},
pages = {077009},
year = {2018},
doi = {10.1289/EHP2920},
URL = {https://doi.org/10.1289/EHP2920},
}

@article{Ring2017SEEM,
  title={Consensus modeling of median chemical intake for the US population based on predictions of exposure pathways},
  author={Ring, Caroline L and Arnot, Jon A and Bennett, Deborah H and Egeghy, Peter P and Fantke, Peter and Huang, Lei and Isaacs, Kristin K and Jolliet, Olivier and Phillips, Katherine A and Price, Paul S and others},
  journal={Environmental science \& technology},
  volume={53},
  number={2},
  pages={719--732},
  year={2018},
  publisher={ACS Publications}
}

@misc{
  HondaUnpublishedCaco2,
  author = {Honda, Gregory and Kenyon, Elaina M and Davidson-Fritz, Sarah E and Dinallo, Roger and El-Masri, Hisham and Korel-Bexell, Evgenia and Li, Li and Paul-Friedman, Katie and Pearce, Robert and Sayre, Risa and Strock, Christopher and Thomas, Russell and Wetmore, Barbara A and Wambaugh, John F},
  title  = {Impact of Gut Permeability on Estimation of Oral Bioavailability for Chemicals in Commerce and the Environment},
  year   = {2023},
  howpublished = {Unpublished}
}

@misc{DavidsonFritzUnpublishedModelAdding,
  author = {Davidson-Fritz, Sarah E and Evans, Marina V and Chang, Xiaoqing and Breen, Miyuki and Honda, Gregory S and Kenyon, Elaina and Linakis, Matthew W and Meade, Annabel and Pearce, Robert G and Purucker, Tom and Ring, Caroline L and Sfeir, Mark A and Setzer, R. Woodrow and Sluka, James P and Vitense, Kelsey and Devito, Michael J and Wambaugh, John F},
  title  = {Transparent and Evaluated Toxicokinetic Models for Bioinformatics and Public Health Risk Assessment},
  year   = {2023},
  howpublished = {Unpublished}
}

@article{sipes2017intuitive,
  title={An intuitive approach for predicting potential human health risk with the Tox21 10k library},
  author={Sipes, Nisha S and Wambaugh, John F and Pearce, Robert and Auerbach, Scott S and Wetmore, Barbara A and Hsieh, Jui-Hua and Shapiro, Andrew J and Svoboda, Daniel and DeVito, Michael J and Ferguson, Stephen S},
  journal={Environmental science \& technology},
  volume={51},
  number={18},
  pages={10786--10796},
  year={2017},
  publisher={ACS Publications}
}

@article{kapraun2022fetalmodel,
  title={Evaluation of a rapid, generic human gestational dose model},
  author={Kapraun, Dustin F and Sfeir, Mark and Pearce, Robert G and Davidson-Fritz, Sarah E and Lumen, Annie and Dallmann, Andre and Judson, Richard S and Wambaugh, John F},
  journal={Reproductive Toxicology},
  volume={113},
  pages={172--188},
  year={2022},
  publisher={Elsevier}
}

@article{darwich2010interplay,
  title={Interplay of metabolism and transport in determining oral drug absorption and gut wall metabolism: a simulation assessment using the 'Advanced Dissolution, Absorption, Metabolism (ADAM)' model},
  author={S Darwich, A and Neuhoff, S and Jamei, Masoud and Rostami-Hodjegan, Amin},
  journal={Current drug metabolism},
  volume={11},
  number={9},
  pages={716--729},
  year={2010},
  publisher={Bentham Science Publishers}
}

@article{yang2007prediction,
  title={Prediction of intestinal first-pass drug metabolism},
  author={Yang, Jiansong and Jamei, Masoud and Yeo, Karen R and Tucker, Geoffrey T and Rostami-Hodjegan, Amin},
  journal={Current drug metabolism},
  volume={8},
  number={7},
  pages={676--684},
  year={2007},
  publisher={Bentham Science Publishers}
}

@article{obringer2016suitability,
  title={Suitability of the in vitro Caco-2 assay to predict the oral absorption of aromatic amine hair dyes},
  author={Obringer, Cindy and Manwaring, John and Goebel, Carsten and Hewitt, Nicola J and Rothe, Helga},
  journal={Toxicology in Vitro},
  volume={32},
  pages={1--7},
  year={2016},
  publisher={Elsevier}
}

@article{lanevskij2019physicochemical,
  title={Physicochemical QSAR analysis of passive permeability across Caco-2 monolayers},
  author={Lanevskij, Kiril and Didziapetris, Remigijus},
  journal={Journal of Pharmaceutical Sciences},
  volume={108},
  number={1},
  pages={78--86},
  year={2019},
  publisher={Elsevier}
}

@article{gaulton2012chembl,
  title={ChEMBL: a large-scale bioactivity database for drug discovery},
  author={Gaulton, Anna and Bellis, Louisa J and Bento, A Patricia and Chambers, Jon and Davies, Mark and Hersey, Anne and Light, Yvonne and McGlinchey, Shaun and Michalovich, David and Al-Lazikani, Bissan and others},
    journal = {Nucleic Acids Research},
  volume={40},
  number={D1},
  pages={D1100--D1107},
  year={2012},
  publisher={Oxford University Press}
}

@article{breen2022simulating,
  title={Simulating toxicokinetic variability to identify susceptible and highly exposed populations},
  author={Breen, Miyuki and Wambaugh, John F and Bernstein, Amanda and Sfeir, Mark and Ring, Caroline L},
  journal={Journal of Exposure Science \& Environmental Epidemiology},
  volume={32},
  number={6},
  pages={855--863},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

@article{ring2017identifying,
  title={Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability},
  author={Ring, Caroline L and Pearce, Robert G and Setzer, R Woodrow and Wetmore, Barbara A and Wambaugh, John F},
  journal={Environment International},
  volume={106},
  pages={105--118},
  year={2017},
  publisher={Elsevier}
}

@article{armitage2013development,
  title={Development and evaluation of a mechanistic bioconcentration model for ionogenic organic chemicals in fish},
  author={Armitage, James M and Arnot, Jon A and Wania, Frank and Mackay, Don},
  journal={Environmental toxicology and chemistry},
  volume={32},
  number={1},
  pages={115--128},
  year={2013},
  publisher={Wiley Online Library}
}

@article{honda2019using,
  title={Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions},
  author={Honda, Gregory S and Pearce, Robert G and Pham, Ly L and Setzer, RW and Wetmore, Barbara A and Sipes, Nisha S and Gilbert, Jon and Franz, Briana and Thomas, Russell S and Wambaugh, John F},
  journal={PloS one},
  volume={14},
  number={5},
  pages={e0217564},
  year={2019},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{wambaugh2015toxicokinetic,
  title={Toxicokinetic triage for environmental chemicals},
  author={Wambaugh, John F and Wetmore, Barbara A and Pearce, Robert and Strope, Cory and Goldsmith, Rocky and Sluka, James P and Sedykh, Alexander and Tropsha, Alex and Bosgra, Sieto and Shah, Imran and others},
  journal={Toxicological Sciences},
  volume={147},
  number={1},
  pages={55--67},
  year={2015},
  publisher={Oxford University Press}
}

@article{rowland1973clearance,
  title={Clearance concepts in pharmacokinetics},
  author={Rowland, Malcolm and Benet, Leslie Z and Graham, Garry G},
  journal={Journal of pharmacokinetics and biopharmaceutics},
  volume={1},
  number={2},
  pages={123--136},
  year={1973},
  publisher={Springer}
}

@article{kilford2008hepatocellular,
  title={Hepatocellular binding of drugs: correction for unbound fraction in hepatocyte incubations using microsomal binding or drug lipophilicity data},
  author={Kilford, Peter J and Gertz, Michael and Houston, J Brian and Galetin, Aleksandra},
  journal={Drug Metabolism and Disposition},
  volume={36},
  number={7},
  pages={1194--1197},
  year={2008},
  publisher={ASPET}
}

@article{wetmore2015incorporating,
  title={Incorporating high-throughput exposure predictions with dosimetry-adjusted in vitro bioactivity to inform chemical toxicity testing},
  author={Wetmore, Barbara A and Wambaugh, John F and Allen, Brittany and Ferguson, Stephen S and Sochaski, Mark A and Setzer, R Woodrow and Houck, Keith A and Strope, Cory L and Cantwell, Katherine and Judson, Richard S and others},
  journal={Toxicological Sciences},
  volume={148},
  number={1},
  pages={121--136},
  year={2015},
  publisher={Oxford University Press}
}

@article{wambaugh2019assessing,
  title={Assessing toxicokinetic uncertainty and variability in risk prioritization},
  author={Wambaugh, John F and Wetmore, Barbara A and Ring, Caroline L and Nicolas, Chantel I and Pearce, Robert G and Honda, Gregory S and Dinallo, Roger and Angus, Derek and Gilbert, Jon and Sierra, Teresa and others},
  journal={Toxicological Sciences},
  volume={172},
  number={2},
  pages={235--251},
  year={2019},
  publisher={Oxford University Press}
}

@article{schmitt2008general,
  title={General approach for the calculation of tissue to plasma partition coefficients},
  author={Schmitt, Walter},
  journal={Toxicology in vitro},
  volume={22},
  number={2},
  pages={457--467},
  year={2008},
  publisher={Elsevier}
}

@article{schmitt2008corrigendum,
  title={Corrigendum to:'General approach for the calculation of tissue to plasma partition coefficients'[Toxicology in Vitro 22 (2008) 457--467]},
  author={Schmitt, Walter},
  journal={Toxicology in Vitro},
  volume={22},
  number={6},
  pages={1666},
  year={2008},
  publisher={Oxford; New York: Pergamon, 1987-}
}

@article{pearce2017evaluation,
  title={Evaluation and calibration of high-throughput predictions of chemical distribution to tissues},
  author={Pearce, Robert G and Setzer, R Woodrow and Davis, Jimena L and Wambaugh, John F},
  journal={Journal of pharmacokinetics and pharmacodynamics},
  volume={44},
  pages={549--565},
  year={2017},
  publisher={Springer}
}

@article{peyret2010unified,
  title={A unified algorithm for predicting partition coefficients for PBPK modeling of drugs and environmental chemicals},
  author={Peyret, Thomas and Poulin, Patrick and Krishnan, Kannan},
  journal={Toxicology and applied pharmacology},
  volume={249},
  number={3},
  pages={197--207},
  year={2010},
  publisher={Elsevier}
}

@article{poulin2012advancing,
  title={Advancing prediction of tissue distribution and volume of distribution of highly lipophilic compounds from a simplified tissue-composition-based model as a mechanistic animal alternative method},
  author={Poulin, Patrick and Haddad, Sami},
  journal={Journal of pharmaceutical sciences},
  volume={101},
  number={6},
  pages={2250--2261},
  year={2012},
  publisher={Elsevier}
}

@article{birnbaum1994physiological,
  title={Physiological parameter values for PBPK models},
  author={Birnbaum, L and Brown, R and Bischoff, K and Foran, J and Blancato, J and Clewell, H and Dedrick, R},
  journal={International Life Sciences Institute, Risk Science Institute, Washington, DC},
  year={1994}
}

@article{ruark2014predicting,
  title={Predicting passive and active tissue: plasma partition coefficients: interindividual and interspecies variability},
  author={Ruark, Christopher D and Hack, C Eric and Robinson, Peter J and Mahle, Deirdre A and Gearhart, Jeffery M},
  journal={Journal of pharmaceutical sciences},
  volume={103},
  number={7},
  pages={2189--2198},
  year={2014},
  publisher={Elsevier}
}

@article{snyder1974report,
  title={Report of the task group on reference man},
  author={Snyder, Walter S},
  journal={ICRP publication},
  year={1974}
}

@article{rotroff2010incorporating,
  title={Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening},
  author={Rotroff, Daniel M and Wetmore, Barbara A and Dix, David J and Ferguson, Stephen S and Clewell, Harvey J and Houck, Keith A and LeCluyse, Edward L and Andersen, Melvin E and Judson, Richard S and Smith, Cornelia M and others},
  journal={Toxicological Sciences},
  volume={117},
  number={2},
  pages={348--358},
  year={2010},
  publisher={Oxford University Press}
}

@article{wetmore2012integration,
  title={Integration of dosimetry, exposure, and high-throughput screening data in chemical toxicity assessment},
  author={Wetmore, Barbara A and Wambaugh, John F and Ferguson, Stephen S and Sochaski, Mark A and Rotroff, Daniel M and Freeman, Kimberly and Clewell III, Harvey J and Dix, David J and Andersen, Melvin E and Houck, Keith A and others},
  journal={Toxicological Sciences},
  volume={125},
  number={1},
  pages={157--174},
  year={2012},
  publisher={Oxford University Press}
}

@article{yang2007misuse,
  title={Misuse of the well-stirred model of hepatic drug clearance},
  author={Yang, Jiansong and Jamei, Masoud and Yeo, Karen R and Rostami-Hodjegan, Amin and Tucker, Geoffrey T},
  journal={Drug Metabolism and Disposition},
  volume={35},
  number={3},
  pages={501--502},
  year={2007},
  publisher={ASPET}
}

@article{ito2004comparison,
  title={Comparison of the use of liver models for predicting drug clearance using in vitro kinetic data from hepatic microsomes and isolated hepatocytes},
  author={Ito, Kiyomi and Houston, J Brian},
  journal={Pharmaceutical research},
  volume={21},
  pages={785--792},
  year={2004},
  publisher={Springer}
}

@article{carlile1997scaling,
  title={Scaling factors to relate drug metabolic clearance in hepatic microsomes, isolated hepatocytes, and the intact liver: studies with induced livers involving diazepam},
  author={Carlile, David J and Zomorodi, Katayoun and Houston, J Brian},
  journal={Drug metabolism and disposition},
  volume={25},
  number={8},
  pages={903--911},
  year={1997},
  publisher={ASPET}
}

@article{sayre2020database,
  title={Database of pharmacokinetic time-series data and parameters for 144 environmental chemicals},
  author={Sayre, Risa R and Wambaugh, John F and Grulke, Christopher M},
  journal={Scientific data},
  volume={7},
  number={1},
  pages={122},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{yu1999compartmental,
  title={A compartmental absorption and transit model for estimating oral drug absorption},
  author={Yu, Lawrence X and Amidon, Gordon L},
  journal={International journal of pharmaceutics},
  volume={186},
  number={2},
  pages={119--125},
  year={1999},
  publisher={Elsevier}
}

@article{davies1993physiological,
  title={Physiological parameters in laboratory animals and humans},
  author={Davies, Brian and Morris, Tim},
  journal={Pharmaceutical research},
  volume={10},
  number={7},
  pages={1093--1095},
  year={1993},
  publisher={Springer}
}

@article{brown1997physiological,
  title={Physiological parameter values for physiologically based pharmacokinetic models},
  author={Brown, Ronald P and Delp, Michael D and Lindstedt, Stan L and Rhomberg, Lorenz R and Beliles, Robert P},
  journal={Toxicology and industrial health},
  volume={13},
  number={4},
  pages={407--484},
  year={1997},
  publisher={Sage Publications Sage CA: Thousand Oaks, CA}
}

@article{reece201514,
  title={14 Body Temperature and Its Regulation},
  author={Reece, William O},
  journal={Dukes' physiology of domestic animals},
  pages={149},
  year={2015},
  publisher={John Wiley \& Sons}
}

@article{stammers1926blood,
  title={The blood count and body temperature in normal rats},
  author={Stammers, Arthur Dighton},
  journal={The Journal of Physiology},
  volume={61},
  number={3},
  pages={329},
  year={1926},
  publisher={Wiley}
}

@article{jordan1995temperature,
  title={Temperature regulation in laboratory rodents},
  author={Jordan, David},
  journal={Journal of anatomy},
  volume={186},
  number={Pt 1},
  pages={228},
  year={1995},
  publisher={Wiley}
}

@article{grandoni2019building,
  title={Building in-house PBPK modelling tools for oral drug administration from literature information},
  author={Grandoni, Silvia and Cesari, Nicola and Brogin, Giandomenico and Puccini, Paola and Magni, Paolo},
  journal={ADMET and DMPK},
  volume={7},
  number={1},
  pages={4--21},
  year={2019},
  publisher={Me{\dj}unarodna udruga fizikalnih kemi{\v{c}}ara}
}

@article{griffin2008models,
  title={Models of the small intestine},
  author={Griffin, Brendan and O’Driscoll, Caitriona},
  journal={Drug Absorption Studies: In Situ, In Vitro and In Silico Models},
  pages={34--76},
  year={2008},
  publisher={Springer}
}

@article{lennernas1997human,
  title={Human jejunal effective permeability and its correlation with preclinical drug absorption models},
  author={Lennern{\"A}s, Hans},
  journal={Journal of Pharmacy and Pharmacology},
  volume={49},
  number={7},
  pages={627--638},
  year={1997},
  publisher={Wiley Online Library}
}