Citations
In this document, we attempt to keep a list of published scientific
work that has reported using nlmixr in some fashion. If you
have used nlmixr or nlmixr2 (or any
mixrverse package) in your work, please let us know so we
can add it to the list.
Publications
2019
Helmlinger G, Sokolov V, Peskov K, Hallow KM, Kosinsky Y, Voronova V, et al. Quantitative Systems Pharmacology: An Exemplar Model-Building Workflow With Applications in Cardiovascular, Metabolic, and Oncology Drug Development. CPT: Pharmacometrics & Systems Pharmacology. 2019;8(6):380–95. 10.1002/psp4.12426
Fidler M, Wilkins JJ, Hooijmaijers R, Post TM, Schoemaker R, Trame MN, et al. Nonlinear Mixed-Effects Model Development and Simulation Using nlmixr and Related R Open-Source Packages. CPT: Pharmacometrics & Systems Pharmacology. 2019;8(9):621–33. 10.1002/psp4.12445
Schoemaker R, Fidler M, Laveille C, Wilkins JJ, Hooijmaijers R, Post TM, et al. Performance of the SAEM and FOCEI Algorithms in the Open-Source, Nonlinear Mixed Effect Modeling Tool nlmixr. CPT: Pharmacometrics & Systems Pharmacology. 2019;8(12):923–30. 10.1002/psp4.12471
2020
Mwandigha LM, Fraser KJ, Racine-Poon A, Mouksassi MS, Ghani AC. Power calculations for cluster randomized trials (CRTs) with right-truncated Poisson-distributed outcomes: a motivating example from a malaria vector control trial. International Journal of Epidemiology. 2020 Jun 1;49(3):954–62. 10.1093/ije/dyz277
2021
Fidler M, Hooijmaijers R, Schoemaker R, Wilkins JJ, Xiong Y, Wang W. R and nlmixr as a gateway between statistics and pharmacometrics. CPT: Pharmacometrics & Systems Pharmacology. 2021;10(4):283–5. 10.1002/psp4.12618
Lombard A, Mistry H, Aarons L, Ogungbenro K. Dose individualisation in oncology using chemotherapy-induced neutropenia: Example of docetaxel in non-small cell lung cancer patients. British Journal of Clinical Pharmacology. 2021;87(4):2053–63. 10.1111/bcp.14614
Lu J, Deng K, Zhang X, Liu G, Guan Y. Neural-ODE for pharmacokinetics modeling and its advantage to alternative machine learning models in predicting new dosing regimens. iScience. 2021 Jul 23;24(7). 10.1016/j.isci.2021.102804
Välitalo PAJ. Pharmacometric estimation methods for aggregate data, including data simulated from other pharmacometric models. J Pharmacokinet Pharmacodyn. 2021 Oct 1;48(5):623–38. 10.1007/s10928-021-09760-1
Goers R, Coman Schmid D, Jäggi VF, Paioni P, Okoniewski MJ, Parker A, et al. SwissPKcdw – A clinical data warehouse for the optimization of pediatric dosing regimens. CPT: Pharmacometrics & Systems Pharmacology. 2021;10(12):1578–87. 10.1002/psp4.12723
Jaisser F, Tan X, Chi S, Liu J, Wang P, Bush M, et al. The Non-Steroidal Mineralocorticoid Receptor Antagonist KBP-5074 Limits Albuminuria and has Improved Therapeutic Index Compared With Eplerenone in a Rat Model With Mineralocorticoid-Induced Renal Injury. Frontiers in Pharmacology. 2021;12. 10.3389/fphar.2021.604928
Medhora M, Phadnis P, Narayanan J, Gasperetti T, Zielonka J, Moulder JE, et al. Radiation Increases Bioavailability of Lisinopril, a Mitigator of Radiation-Induced Toxicities. Frontiers in Pharmacology. 2021;12. 10.3389/fphar.2021.646076
2022
Lee SY. Bayesian Nonlinear Models for Repeated Measurement Data: An Overview, Implementation, and Applications. Mathematics. 2022 Jan;10(6):898. 10.3390/math10060898
Aghamiri SS, Amin R, Helikar T. Recent applications of quantitative systems pharmacology and machine learning models across diseases. J Pharmacokinet Pharmacodyn. 2022 Feb 1;49(1):19–37. 10.1007/s10928-021-09790-9
Soeorg H, Sverrisdóttir E, Andersen M, Lund TM, Sessa M. The PHARMACOM-EPI Framework for Integrating Pharmacometric Modelling Into Pharmacoepidemiological Research Using Real-World Data: Application to Assess Death Associated With Valproate. Clinical Pharmacology & Therapeutics. 2022;111(4):840–56. 10.1002/cpt.2502
Liakopoulos A, Aulin LBS, Buffoni M, Fragkiskou E, Coen van Hasselt JG, Rozen DE. Allele-specific collateral and fitness effects determine the dynamics of fluoroquinolone resistance evolution. Proceedings of the National Academy of Sciences. 2022 May 3;119(18):e2121768119. 10.1073/pnas.2121768119
Mehta K, Guo T, Wallis RS, van der Graaf PH, van Hasselt JGC. Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy. Antimicrobial Agents and Chemotherapy. 2022 Jul 14;66(8):e00366-22. 10.1128/aac.00366-22
Agyeman AA, You T, Chan PLS, Lonsdale DO, Hadjichrysanthou C, Mahungu T, et al. Comparative assessment of viral dynamic models for SARS-CoV-2 for pharmacodynamic assessment in early treatment trials. British Journal of Clinical Pharmacology. 2022;88(12):5428–33. 10.1111/bcp.15518
Aulin LBS, Tandar ST, van Zijp T, van Ballegooie E, van der Graaf PH, Saleh MAA, et al. Physiologically Based Modelling Framework for Prediction of Pulmonary Pharmacokinetics of Antimicrobial Target Site Concentrations. Clin Pharmacokinet. 2022 Dec 1;61(12):1735–48. 10.1007/s40262-022-01186-3
Kloprogge F, Ortiz Canseco J, Phee L, Sadouki Z, Kipper K, Witney AA, et al. Emergence of phenotypic and genotypic antimicrobial resistance in Mycobacterium tuberculosis. Sci Rep. 2022 Dec 11;12(1):21429. 10.1038/s41598-022-25827-6
Voulgarelis D, Bulusu KC, Yates JWT. Comparison of classical tumour growth models for patient derived and cell-line derived xenografts using the nonlinear mixed-effects framework. Journal of Biological Dynamics. 2022 Dec 31;16(1):160–85. 10.1080/17513758.2022.2061615
2023
Mak WY, Ooi QX, Cruz CV, Looi I, Yuen KH, Standing JF. Assessment of the nlmixr R package for population pharmacokinetic modeling: A metformin case study. British Journal of Clinical Pharmacology. 2023;89(1):330–9. 10.1111/bcp.15496
Mehta K, Guo T, van der Graaf PH, van Hasselt JGC. Predictions of Bedaquiline and Pretomanid Target Attainment in Lung Lesions of Tuberculosis Patients using Translational Minimal Physiologically Based Pharmacokinetic Modeling. Clin Pharmacokinet. 2023 Mar 1;62(3):519–32. 10.1007/s40262-023-01217-7
Yang W, Mak W, Gwee A, Gu M, Wu Y, Shi Y, et al. Establishment and Evaluation of a Parametric Population Pharmacokinetic Model Repository for Ganciclovir and Valganciclovir. Pharmaceutics. 2023 Jul;15(7):1801. 10.3390/pharmaceutics15071801
Ibrahim EIK, Karlsson MO, Friberg LE. Assessment of ibrutinib scheduling on leukocyte, lymph node size and blood pressure dynamics in chronic lymphocytic leukemia through pharmacokinetic-pharmacodynamic models. CPT: Pharmacometrics & Systems Pharmacology. 2023;12(9):1305–18. 10.1002/psp4.13010
Zhang S, Agyeman AA, Hadjichrysanthou C, Standing JF. SARS-CoV-2 viral dynamic modeling to inform model selection and timing and efficacy of antiviral therapy. CPT: Pharmacometrics & Systems Pharmacology. 2023;12(10):1450–60. 10.1002/psp4.13022
Barrett JS, Betourne A, Walls RL, Lasater K, Russell S, Borens A, et al. The future of rare disease drug development: the rare disease cures accelerator data analytics platform (RDCA-DAP). J Pharmacokinet Pharmacodyn. 2023 Dec 1;50(6):507–19. 10.1007/s10928-023-09859-7
2024
Kovács L, Ferenci T, Gombos B, Füredi A, Rudas I, Szakács G, et al. Positive Impulsive Control of Tumor Therapy—A Cyber-Medical Approach. IEEE Transactions on Systems, Man, and Cybernetics: Systems. 2024 Jan;54(1):597–608. 10.1109/TSMC.2023.3315637
Lepak AJ, VanScoy B, Rubino C, Ambrose PG, Andes DR. In vivo pharmacodynamic characterization of a next-generation polyene, SF001, in the invasive pulmonary aspergillosis mouse model. Antimicrobial Agents and Chemotherapy. 2024 Feb 6;0(0):e01631-23. 10.1128/aac.01631-23
Standing JF, Buggiotti L, Guerra-Assuncao JA, Woodall M, Ellis S, Agyeman AA, et al. Randomized controlled trial of molnupiravir SARS-CoV-2 viral and antibody response in at-risk adult outpatients. Nat Commun. 2024 Feb 23;15(1):1652. 10.1038/s41467-024-45641-0
Conference Proceedings
2016
Fidler M, Schoemaker R, Xiong Y, Wilkins J, Laveille C, Wang W. W-66. nlmixr: an open-source package for pharmacometric modelling in R. Abstracts accepted for American Conference on Pharmacometrics 2016 (ACoP7). J Pharmacokinet Pharmacodyn. 2016 43(S1):S115. 10.1007/s10928-016-9485-x
2017
Erhardt E, Jacobs T, Gasparini M. Comparison of pharmacokinetic parameters estimated by the experimental R package ‘nlmixr’ and MONOLIX. PAGE 2017 (Budapest, Hungary): Abstr 7247
Schoemaker R, Fidler M, Xiong Y, Wilkins J, Trame MN, Laveille C, Wang W. T-012. nlmixr: an open-source package for pharmacometric modelling in R. Abstracts for American Conference on Pharmacometrics 2017 (ACoP8). J Pharmacokinet Pharmacodyn. 2017 44(S1):S60. 10.1007/s10928-017-9536-y
Schoemaker R, Fidler M, Xiong Y, Wilkins J, Trame M, Laveille C, Wang W. nlmixr: an open-source package for pharmacometric modelling in R. PAGE 2017 (Budapest, Hungary): Abstr 7102
2018
Bartels C, Bieth B, Dumortier T, Baltcheva I, Bhattacharya S, Ludwig I, Demin I, Gassem A, Renard D. ggPMX: a toolbox to easily generate a comprehensive set of model diagnostic plots for population models. PAGE 2018 (Montreux, Switzerland): Abstr 8423
Fidler M, Xiong Y, Schoemaker R, Wilkins J, Trame MN, Post T, Hooijmaijers R, Wang W. W-058. Exploring inductive linearization in population pharmacokinetic and pharmacodynamic models. Abstracts for the Ninth American Conference on Pharmacometrics (ACoP9). J Pharmacokinet Pharmacodyn. 2018 45(S1):S116. 10.1007/s10928-018-9606-9
Hooijmaijers R, Fidler M, Schoemaker R, Trame MN, Wang W, Wilkins J, Xiong Y, Post T. ShinyMixR: A project-centric R/Shiny run management tool for nlmixr. PAGE 2018 (Montreux, Switzerland): Abstr 8452
Erhardt EM, Ursino M, Jacobs T, Biewenga J, Gasparini M. Bayesian knowledge integration for an in vitro–in vivo correlation (IVIVC) model. PAGE 2018 (Montreux, Switzerland): Abstr 8689
2019
Baltcheva I, Bartels C, Dumortier T, Bhattacharya S, Paule I, Ludwig I, Demin I, Gassem A, Renard D, Bieth B. ggPMX: an open-source R package for pharmacometric model diagnostic plots. PAGE 2019 (Stockholm, Sweden): Abstr 9013
Schoemaker S, Fidler M, Laveille C, Wilkins JJ, Hooijmaijers R, Post TM, Trame MN, Xiong Y, Wang W. Performance of the SAEM and FOCEI algorithms in the open-source non-linear mixed effect modelling tool nlmixr. PAGE 2019 (Stockholm, Sweden): Abstr 8978
2021
Aulin LBS, Liakopoulos A, Rozen DE, van Hasselt JGC. Model-based design of innovative treatment strategies to suppress antimicrobial resistance using collateral sensitivity. PAGE 2021 (Virtual): Abstr 9792
Ibrahim E, Karlsson MO, Friberg LE. Pharmacokinetic-pharmacodynamic (PK-PD) modeling of leukocyte dynamics and lymph node size in chronic lymphocytic leukaemia patients treated with ibrutinib. PAGE 2021 (Virtual): Abstr 9682
Jung WJ, Hwang T, Jung S, Savic RM, Chae JW, Yun HY. Web based platform for clinical pharmacokinetic consultation service (CPCS) with Non-linear Mixed Effect Model. PAGE 2021 (Virtual): Abstr 9727
Pham AD, van Hasselt JGC. Modelling rate and extent of resistance development against colistin in Klebsiella pneumoniae. PAGE 2021 (Virtual): Abstr 9774
Tran QT, Lee CH, Kim MG, Kim M, Kim H, Chae JW, Yun HY. Overview of Korean Pharmacometrics Modeling Library and web-based pharmacometrics platform. PAGE 2021 (Virtual): Abstr 9865
Vavilov S, Sokolov V, Zhudenkov K, Stolbov L, Peskov K. Parameter estimation in nonlinear fixed-effects QSP models: benchmark of optimization methods. PAGE 2021 (Virtual): Abstr 9755
2022
Bieth B, Fidler M, Baltcheva I. ggPMX: re-imagine diagnostics plots. PAGE 2022 (Ljubljana, Slovenia): Abstr 9998
Liu C, Cojutti PG, Bussini L, Rosselli Del Turco E, Bartoletti M, Pea F. Comparison of performances of the open-source R package “nlmixr” vs. Monolix for population pharmacokinetics of continuous infusion meropenem in patients with onco-hematological malignancies. PAGE 2022 (Ljubljana, Slovenia): Abstr 10210
Nordgren R, Belin S, Yngman G, Huang Z, Carter SJ, Chen X, Qutishat O, Hamdan A, Wang S, Yang T, Assawasuwannakit P, Buatois S, Abrantes JA, Hooker AC, Karlsson MO. Pharmpy: a versatile open-source library for pharmacometrics. PAGE 2022 (Ljubljana, Slovenia): Abstr 10096
2023
Cheng I, Solas C, Howley E, McGarrity O, Rajani K, Breuer J, Standing J, Kreins A. Favipiravir pharmacokinetics in immunocompromised infants and children with chronic RNA viral infections. PAGE 2023 (A Coruña, Spain): Abstr 10570
Codina MS, Pham AD, van Os W, al Jalali V, Matzneller P, Wölfl-Duchek M, Vychytil A, Reiter B, Stimpfl T, van Hasselt JG, Zeitlinger M. Evaluating ceftazidime-avibactam exposure in patients undergoing automated peritoneal dialysis using population pharmacokinetic modelling. PAGE 2023 (A Coruña, Spain): Abstr 10707
Combes FP, Fidler M, Ochsenbein D, Illis W, Subrahmanyam K, Ho Y-Y. Benchmarking Industrial Computing Environments - Pharmacometrics Study (BICEPS). PAGE 2023 (A Coruña, Spain): Abstr 10604
Duong A, Marsot A. NONMEM versus nlmixr2 : An example of external evaluation of gentamicin Pop-PK models. PAGE 2023 (A Coruña, Spain): Abstr 10602
Fidler M, Denney WS, Harrold J, Hooijmaijers R, Schoemaker R, Taubert M, Trame M, Papathanasiou T, Wilkins J. nlmixr2, rxode2 and NONMEM: interchangeable models using babelmixr2 and nonmem2rx. PAGE 2023 (A Coruña, Spain): Abstr 10313
Huang Z, Standing JF, Kloprogge F. Development and exploration of exhaustive, stepwise, and heuristic algorithms for automated population pharmacokinetic modelling. PAGE 2023 (A Coruña, Spain): Abstr 10704.
Jeon H, Sung T, Jung W, Chae J-W, Yun H-Y. Construction of model-based PK-PD software platform using R package considering compatibility of nlme structured model. PAGE 2023 (A Coruña, Spain): Abstr 10432
Nordgren R, Belin S, Chen X, Borg J, Huang Z, Qutishat O, Shi K, Liu X, Wang S, Mohamed S, Mirasbekov S, Hooker AC, Karlsson MO. Pharmpy: a versatile open-source library for pharmacometrics. PAGE 2023 (A Coruña, Spain): Abstr 10508
Xu C, Yu J, Cao W, Lu H, Yao Z, Sun X, Zhang K, Luo J, Zheng Q, Zheng H. PyMaS: population pharmacometric modeling in Python. PAGE 2023 (A Coruña, Spain): Abstr 10676