Publications

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Although a new software in the field, Pumas products have already been used in a variety of projects. Here is a list of publications, posters and presentations that used Pumas to perform modeling & simulation.

To cite Pumas in your publications:
Rackauckas, Chris, Yingbo Ma, Andreas Noack, Vaibhav Dixit, Patrick Kofod Mogensen, Simon Byrne, Shubham Maddhashiya, et al. “Accelerated Predictive Healthcare Analytics with Pumas, a High Performance Pharmaceutical Modeling and Simulation Platform.” BioRxiv, November 30, 2020, 2020.11.28.402297. https://doi.org/10.1101/2020.11.28.402297 .
2023

Bhavatharini P A, Mahendra Joshi, Archana Kakkar, Ivaturi V, et al.. “Bioequivalence Study Followed by Model Informed Dose Optimization of a Powder for Oral Suspension of 6-Mercaptopurine.”

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CONSULTING

Mohamed Tarek (1,2), Jose Storopoli (1,3), Casey Davis (4), Chris Elrod (1,5), Vijay Ivaturi (1,6). A Complete Bayesian Workflow in Pumas

Poster

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PUMAS

Pawan Kumar Gupta, Bev Incledon, Jogarao V. S. Gobburu, Roberto Gomeni. A convolution-based in vitro-in vivo correlation model for methylphenidate hydrochloride delayed-release and extended-release capsule

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CONSULTING

Erik R. Strauss, Shuhui Li, Reney Henderson, Ross Carpenter, Dong Guo, Kiruphagaran Thangaraju, Upendra Katneni, Paul W. Buehler, Jogarao V.S. Gobburu, Kenichi A. Tanaka. “A Pharmacokinetic and Plasmin-Generation Pharmacodynamic Assessment of a Tranexamic Acid Regimen Designed for Cardiac Surgery With Cardiopulmonary Bypass”

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CONSULTING

Mohamed Tarek, Jose Storopoli, Casey Davis, Chris Elrod, Julius Krumbiegel, Chris Rackauckas, Vijay Ivaturi. A Practitioner's Guide to Bayesian Inference in Pharmacometrics using Pumas

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PUMAS

Bunn HT, Gobburu JVS, Floryance LM. “Bayesian model-guided antimicrobial therapy in pediatrics. Front Pharmacol.”

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CONSULTING

Selig DJ, Kress AT, Nadeau RJ, DeLuca JP. Beta-Lactam Probability of Target Attainment Success: Cefepime as a Case Study. Antibiotics.

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CONSULTING

Zhengqi Tan (1), Ayyappa Chaturvedula (1), Julie Desrochers (2), Kirsten Riber Bergmann (2), Yassine Kamal Lyauk (2), Rune Viig Overgaard (2). “Comparison of Pumas and NONMEM in parameter estimation of a complex pharmacodynamic model”

Poster

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PUMAS

Niklas Korsbo, Mohamed Tarek, Chris Elrod, Antoine Soubret, Francesco Brizzi, Christopher Rackauckas, Jogarao Gobburu, Vijay Ivaturi. “DeepPumas for automatic discovery of individualizable functions governing longitudinal patient outcomes”

Poster

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DEEPPUMAS

Gledys Reynaldo Fernandez, Leyanis Rodriguez-Vera, Jorge Duconge, Daniel Amaro, Joaquin Solozábal, Victor Mangas-Sanjuan, Iñaki Troconiz, Valvanera Vozmediano. Enlightenment on the strategic selection of pegylated rHuEPO candidates using a mechanistic model-driven extrapolation approach of the pharmacokinetics and pharmacodynamics.

SELECT

Beumer JH, Kennard BC, Holleran JL, Moore N, Zlott J, Miller BM, Kummar S, Chen A, Doroshow J, Park W, Gobburu J, Dunn A. “Evaluating the indotecan-neutropenia relationship in patients with solid tumors by population pharmacokinetic modeling and sigmoidal Emax regressions. Cancer Chemother Pharmacol.”

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CONSULTING

Mohamed Tarek [1, 2], Many Francis [3], Anastasios Panagiotelis [2]. “Fast cross-validation for Bayesian inference using proposals on a linear subspace”

Poster

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SELECT

Leyanis Rodriguez, Monica Rodriguez, John C Lukas, Cameron Durrant, Dale Chappell, Valvanera Vozmediano. “First-in-Pediatric Dose Selection of Lenzilumab in Rare Juvenile Myelomonocytic Leukemia”

SELECT

Amira Soliman, Leyanis Rodriguez, Ana Alarcia Lacalle, Parsshava Mehta, Valvanera Vozmediano. Leveraging PBPK/PD modeling to inform drug-drug interactions and specific recommendations for pediatric labeling: Omeprazole case example

SELECT

Parsshava Mehta, Serge Guzy, Valvanera Vozmediano. “Link of T-Cell Modulation and Disability Progression with High Dose Corticosteroids in Relapsing-Remitting Multiple Sclerosis using an integrative PK-semi-mechanistic PD/MBMA approach”

SELECT

Mohamed Tarek, Jose Storopoli, Chris Elrod, Joga Gobbur, Vijay Ivaturi. Marginal Markov Chain Monte Carlo (MCMC)

SELECT

Mohamed Tarek [1, 2], ose Storopoli [1, 3], Chris Elrod [1, 4], Joga Gobburu [1, 5], Vijay Ivaturi [1, 5]. “Marginal No-U-Turn Sampler for Bayesian Analysis in Pharmacometrics”

Poster

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SELECT

Salem, AM, Dvergsten, E, Karovic, S, Maitland, ML, Gopalakrishnan, M. “Model-based approach to identify predictors of paclitaxel-induced myelosuppression in “real-world” administration. CPT Pharmacometrics Syst Pharmacol.”

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CONSULTING

Pawan Kumar Gupta, Bev Incledon, Jogarao V. S. Gobburu, Roberto Gomeni. “Novel concolution-base in vitro-In vivo correlation (IVIVC) model with time scaling and bioavailability sub-models for, JORNAY PM, a methylphenidate hydrochloride delayed-release and extended-release capsule. “

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CONSULTING

Andreas Noack, Patrick Kofod Mogensen, Vijay Ivaturi. “On the error of the Laplace approximation when lags and duration parameters have between-subject variation”

Poster

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SELECT

Jarugula P, Akcan-Arikan A, Munoz-Rivas F, Moffett BS, Ivaturi V, Rios D. “Optimizing Vancomycin Dosing and Monitoring in Neonates and Infants Using Population Pharmacokinetic Modeling.”

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CONSULTING

Matcha, S., Raj, E.A., Mahadevan, R., et al.. “Pharmacometric approach to assist dosage regimen design in neonates undergoing therapeutic hypothermia.”

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CONSULTING

Saikumar Matcha, Jayashree Dillibatcha, Arun Prasath Raju, Bhim Bahadur Chaudhari, Sudheer Moorkoth, Leslie E. Lewis, Surulivelrajan Mallayasamy. “Predictive Performance of Population Pharmacokinetic Models for Amikacin in Term Neonates”

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CONSULTING

Husain Attarwala, Matthew Lumley, Min Liang, Vijay Ivaturi, Joe Senn. “Translational Pharmacokinetic/Pharmacodynamic Model for mRNA-3927, an Investigational Therapeutic for the Treatment of Propionic Acidemia. “

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CONSULTING
2022

Salem AM, Moffett BS, Gopalakrishnan M. “A Full Bayesian Approach for Population Pharmacokinetic/Pharmacodynamic Modeling of Unfractionated Heparin in Pediatrics.”

Poster

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CONSULTING

Chris Rackauckas, Yingbo Ma, Andreas Noack, Vaibhav Dixit, Patrick Kofod Mogensen, Chris Elrod, Mohammad Tarek, Simon Byrne, Shubham Maddhashiya, José Bayoán Santiago Calderón, Michael Hatherly, Joakim Nyberg, Jogarao V.S. Gobburu, Vijay Ivaturi. “Accelerated Predictive Healthcare Analytics with Pumas, A High Performance Pharmaceutical Modeling and Simulation Platform”

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PUMAS

Parsshava Mehta, Leyanis Rodriguez, Vijay Siripuram, Paula Muniz, Monica Rodriguez, Emili-González-Pérez3, Marta ForcadelI, Valvanera Vomediano. “Application of interspecies PBPK modeling to characterize BBB permeability using levetiracetam and acetaminophen as model drug”

SELECT

Goyal RK, McManus JL, Gopalakrishnan M. “Application of Machine Learning Analysis to Inform Medical Countermeasure Development – A Case Study Using Random Forest Ensemble to Identify Predictive Biomarkers of Mortality for Hematopoietic Acute Radiation Syndrome and Confirmation of Benefit with Leukine® Across Myeloid Lineages”

Poster

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SELECT

Greene S, Attarwala H, Ivaturi V, Guglieri-Lopez B, Kramarczyk JF, Panther L, Natenshon, A. “Immunostimulatory/Immunodynamic Model of an mRNA-Based Vaccine Against Cytomegalovirus Infection to Guide Vaccine Dose Selection”

Poster

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CONSULTING

Gordon O, Brosnan MK, Yoon S, Jung D, Littlefield K, Ganesan A, Caputo CA, Li M, Morgenlander WR, Henson SN, Ordonez AA, De Jesus P, Tucker EW, Peart Akindele N, Ma Z, Wilson J, Ruiz-Bedoya CA, Younger MEM, Bloch EM, Shoham S, Sullivan D, Tobian AA, Cooke KR, Larman B, Gobburu JV, Casadevall A, Pekosz A, Lederman HM, Klein SL, Jain SK. “Pharmacokinetics of high-titer anti-SARS-CoV-2 human convalescent plasma in high-risk children”

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CONSULTING

Jung D, Roem J, Ng DK, Procaccini D, Bembea MM, Gobburu JVS. “Pharmacokinetics of Plasma-derived Antithrombin III in Critically Ill Pediatric Patients Supported on Extracorporeal Membrane Oxygenation”

Poster

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Submit a Request

CONSULTING

Li S, Feng K, Lee J, Gong Y, Wu F, Newman B, Yoon M, Fang L, Zhao L, Gobburu JVS. “Unsupervised Hierarchical Clustering Analysis for the Characterization of Sequence of Pancytopenia in Male and Female Non-human Primates Post Total Body Irradiation”

Poster

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CONSULTING

Li, S., Dvorak, C.C., Lu, Y., Chan, D., Gobburu, J.V.S., Long-Boyle, J. and Apsel Winger, B.. “Population Pharmacokinetics of Melphalan for Pediatric Patients Undergoing Hematopoietic Cell Transplantation.”

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CONSULTING

Goyal RK, Moffett BS, Gobburu JVS, Al Mohajer M. “Population Pharmacokinetics of Vancomycin in Pregnant Women.”

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CONSULTING

Roesch E, Jain A, Micluta-Campeanu S, Rackauckas C. Pumas-QSP: A high-performance and easy-to-use modeling tool for Advanced Pharmaceutical Sciences

Poster

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PUMASCP

Dunn A, Beumer JH, Gobburu JVS. “The Effect of Liver Dysfunction on the Pharmacokinetic Disposition of Belinostat and its Metabolites in Patients with Advanced Cancers”

Poster

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CONSULTING

Husain Attarwala, Matthew Lumley, Min Liang, Vijay Ivaturi, Joe Senn. “Translational Pharmacokinetic/Pharmacodynamic Model for mRNA-3927, an Investigational Therapeutic for the Treatment of Propionic Acidemia”

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CONSULTING

Goyal RK, McManus JL, Gopalakrishnan M. “Unsupervised Hierarchical Clustering Analysis for the Characterization of Sequence of Pancytopenia in Male and Female Non-human Primates Post Total Body Irradiation”

Poster

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CONSULTING
2021

Chris Elrod, Andreas Noack, Patrick Kofod Mogensen, Vaibhav Dixit, Vijay Ivaturi. “SAEM in Pumas – A systematic evaluation and benchmarking”

Poster

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PUMAS

Mohamed Tarek, Christopher Rackauckas, Patrick K. Mognesen, Vijay Ivaturi, Andreas Noack. “Analysis of Laplace Approximation for Pharmaceutical Nonlinear Mixed Effects Models”

Poster

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SELECT

Raj Dandekar, Vaibhav Dixit, Mohamed Tarek, Aslan Garcia Valadez, Chris Rackauckas. “Bayesian Neural Ordinary Differential Equations”

Poster

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SELECT

Allison Dunn, Brady S. Moffett, Vijay Ivaturi, Jogarao V. S. Gobburu. “Characterization of drug–drug interactions on the pharmacokinetic disposition of busulfan in paediatric patients during haematopoietic stem cell transplantation conditioning”

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CONSULTING

Rackauckas, Christopher Vincent, Vaibhav Dixit, Adam R. Gerlach, Vijay Ivaturi. “Efficient Precision Dosing Under Estimated Uncertainties via Koopman Expectations of Bayesian Posteriors with Pumas.”

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PUMAS

Andreas Noack, Patrick Kofod Mogensen, Joakim Nyberg, Vijay Ivaturi. “Generalized FOCE with Pumas”

Poster

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Submit a Request

PUMAS

Rackauckas, C.. “Generalizing Automatic Differentiation to Automatic Sparsity, Uncertainty, Stability, and Parallelism,”

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CONSULTING

Ma, Yingbo, Shashi Gowda, Ranjan Anantharaman, Chris Laughman, Viral Shah, Chris Rackauckas. ModelingToolkit: A Composable Graph Transformation System For Equation-Based Modeling.

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CONSULTING

Mohamed Tarek, Vijay Ivaturi, Andreas Noack. “Non-Gaussian random effects in nonlinear mixed effects models in Pumas”

Poster

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PUMAS

Mohamed Tarek, Joakim Nyberg, Vijay Ivaturi, Andreas Noack. “Nonlinear mixed effects model based optimal design of experiments using mathematical programming in Pumas”

Poster

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PUMAS

Pal, Avik, Yingbo Ma, Viral Shah, Christopher Rackauckas. Opening the Blackbox: Accelerating Neural Differential Equations by Regularizing Internal Solver Heuristics.

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CONSULTING

Mohamed Tarek, Manu Francis, Vijay Ivaturi. “Parallel hierarchical Gibbs-NUTS MCMC algorithm for Nonlinear Mixed Effects models in Pumas”

Poster

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PUMAS

Kalaria, Shamir N., Michael Armahizer, Paul McCarthy, Neeraj Badjatia, Jogarao V. Gobburu, Mathangi Gopalakrishnan. “A Prospective, Real-World, Clinical Pharmacokinetic Study to Inform Lacosamide Dosing in Critically Ill Patients Undergoing Continuous Venovenous Haemofiltration (PADRE-02).”

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CONSULTING

Manu Francis, Vijay Ivaturi, Mohamed Tarek. “Subspace MCMC algorithm for Bayesian parameter estimation of hierarchical PK/PD models in Pumas”

PUMAS

Praneeth Jarugula, Sarah Scott, Vijay Ivaturi, Andreas Noack, Brady S. Moffet, Adnan Bhutta, Jogarao V.S. Gobburu. Understanding the Role of Pharmacometrics-Based Clinical Decision Support Systems in Pediatric Patient Management: A Case Study Using Lyv Software

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CONSULTING

Rackauckas, Christopher Vincent, Vaibhav Dixit, Adam R. Gerlach, Vijay Ivaturi. “Efficient Precision Dosing Under Estimated Uncertainties via Koopman Expectations of Bayesian Posteriors with Pumas.”

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Pumas-NLME Pumas-OD

Kalaria, Shamir N., Michael Armahizer, Paul McCarthy, Neeraj Badjatia, Jogarao V. Gobburu, Mathangi Gopalakrishnan. “A Prospective, Real-World, Clinical Pharmacokinetic Study to Inform Lacosamide Dosing in Critically Ill Patients Undergoing Continuous Venovenous Haemofiltration (PADRE-02).”

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Pumas-NCA Pumas-NLME

Rackauckas C. “Generalizing Automatic Differentiation to Automatic Sparsity, Uncertainty, Stability, and Parallelism”

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Pumas-PBPK Pumas-QsP

Ma Yingbo, Shashi Gowda, Ranjan Anantharaman, Chris Laughman, Viral Shah, Chris Rackauckas. “ModelingToolkit: A Composable Graph Transformation System For Equation-Based Modeling.”

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Pumas-PBPK Pumas-QsP

Pal, Avik, Yingbo Ma, Viral Shah, Christopher Rackauckas. “Opening the Blackbox: Accelerating Neural Differential Equations by Regularizing Internal Solver Heuristics.”

General

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Pumas-DeepNLME Pumas-NLME
2020

Davis C, Sandeep Dutta, Khamir Mehta. “A Bayesian Approach to PK/PD Modeling – A Comparison of Stan and Pumas in Julia.”

Poster

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Submit a Request

PUMAS

Strauss, Erik R., Elyes Dahmane, Miranda Judd, Dong Guo, Brittney Williams, Michael Meyer, James S. Gammie, et al.. “A Pharmacokinetic and Pharmacodynamic Investigation of an ε-Aminocaproic Acid Regimen Designed for Cardiac Surgery With Cardiopulmonary Bypass.”

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CONSULTING

Kalaria, Shamir N., Michael Armahizer, Paul McCarthy, Neeraj Badjatia, Jogarao V. Gobburu, Mathangi Gopalakrishnan. “A Practice-Based, Clinical Pharmacokinetic Study to Inform Levetiracetam Dosing in Critically Ill Patients Undergoing Continuous Venovenous Hemofiltration (PADRE-01).”

General

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CONSULTING

Rackauckas, Chris, Yingbo Ma, Andreas Noack, Vaibhav Dixit, Patrick Kofod Mogensen, Simon Byrne, Shubham Maddhashiya, et al.. “Accelerated Predictive Healthcare Analytics with Pumas, a High Performance Pharmaceutical Modeling and Simulation Platform.”

General

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PUMAS

Miszta, Adam, Homa K. Ahmadzia, Naomi L. C. Luban, Shuhui Li, Dong Guo, Lori A. Holle, Jeffrey S. Berger, et al.. “Application of a Plasmin Generation Assay to Define Pharmacodynamic Effects of Tranexamic Acid in Women Undergoing Cesarean Delivery.”

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CONSULTING

Dandekar, Raj, Vaibhav Dixit, Mohamed Tarek, Aslan Garcia-Valadez, Chris Rackauckas. “Bayesian Neural Ordinary Differential Equations,”

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CONSULTING

Dunn A, Ivaturi V, Paek H, Gillespie A, Brady Moffett, Gobburu J, Krance R. Characterization of Drug-Drug Interactions on the Pharmacokinetic Disposition of Busulfan in the Pediatric Hematopoietic Stem Cell Transplantation Patient

Poster

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Submit a Request

CONSULTING

Wansu Park, Gobburu J, Lo L, Chonchol M, Devalaraja M. Pharmacokinetic analysis of Ziltivekimab, anti-Interleukin-6 monoclonal antibody in chronic kidney disease patients.

Poster

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Submit a Request

CONSULTING

Sumar A, Takebe N, Chen A, Kummar S, Piekarz R, Kiesel B, Moore N, Doroshow J, Beumer J, Gobburu J. Population Pharmacokinetic Modeling of Belinostat and its Major Metabolite in Advanced Cancer Patients with varying degrees of Liver Dysfunction

Poster

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Submit a Request

CONSULTING

Jayesh Patel, Dvorak C, Melton A, Highan C, Lu Y, Winger B, Gobburu J, Long-Boyle J. Population Pharmacokinetics of Thiotepa and its Active Metabolite, Tepa in Pediatric Patients Undergoing Hematopoietic Cell Transplantation (HCT)

Poster

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Submit a Request

CONSULTING

Strauss, Erik R, Elyes Dahmane, Miranda Judd, Dong Guo, Brittney Williams, Michael Meyer, James S. Gammie. “A Pharmacokinetic and Pharmacodynamic Investigation of an ε-Aminocaproic Acid Regimen Designed for Cardiac Surgery With Cardiopulmonary Bypass.”

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Pumas-NLME Pumas-NCA

Miszta, Adam, Homa K. Ahmadzia, Naomi L. C. Luban, Shuhui Li, Dong Guo, Lori A. Holle, Jeffrey S. Berger. “Application of a Plasmin Generation Assay to Define Pharmacodynamic Effects of Tranexamic Acid in Women Undergoing Cesarean Delivery.”

General

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Pumas-NCA Pumas-NLME

Kalaria, Shamir N., Michael Armahizer, Paul McCarthy, Neeraj Badjatia, Jogarao V. Gobburu, Mathangi Gopalakrishnan. “A Practice-Based, Clinical Pharmacokinetic Study to Inform Levetiracetam Dosing in Critically Ill Patients Undergoing Continuous Venovenous Hemofiltration (PADRE-01).”

General

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Pumas-NLME Pumas-NCA

Rackauckas, Chris, Yingbo Ma, Andreas Noack, Vaibhav Dixit, Patrick Kofod Mogensen, Simon Byrne, Shubham Maddhashiya. “Accelerated Predictive Healthcare Analytics with Pumas, a High Performance Pharmaceutical Modeling and Simulation Platform.”

General

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Pumas-NLME Pumas-NCA Pumas-BE Pumas-OD Pumas-PBPK

Dandekar, Raj, Vaibhav Dixit, Mohamed Tarek, Aslan Garcia-Valadez, Chris Rackauckas. “Bayesian Neural Ordinary Differential Equations.”

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Pumas-DeepNLME
2019

Rackauckas C, Ivaturi V. Bayesian-Koopman Techniques for Optimization of Intervention with Respect to Uncertainty in PuMaS.jl.

Poster

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Submit a Request

PUMAS

Santiago Calderón JB, Gopalakrishnan M, Ivaturi V. Bioequivalence.jl: A suite of routines for bioequivalence (BE) analysis for the Julia language as part of the PuMaS ecosystem.

Poster

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Submit a Request

PUMAS

Byrne S, Noack A, Nyberg J, Rackauckas C, Ivaturi V. Comparison of Bayesian Functionality between PuMaS and NONMEM.

Poster

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Submit a Request

PUMAS

Ma Y, Guglieri-Lopez B, Gobburu J, Denney W, Ivaturi V. Comparison of non-compartmental analysis results between PKNCA, PuMaS.NCA and Phoenix WinNonlin.

Poster

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Submit a Request

PUMAS

Noack A, Ivaturi V, Nyberg J. Fast evaluation of experimental designs in non-linear mixed effects models with the PuMaS package.

Poster

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Submit a Request

PUMAS

Widmann D, Ivaturi V, Rackauckas C. Handling Steady-state Dosing in Stiff State-Dependent Delay Differential Equations in PuMaS.jl.

Poster

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Submit a Request

PUMAS

Rackauckas C, Ivaturi V. Neural-embedded nonlinear mixed effects models (NENLME) in PuMaS.jl.

Poster

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Submit a Request

PUMAS

Park W, Noack A, Mogenson P, Dixit V, Rackauckas C, Gobburu J, Nyberg J, Ivaturi V. Numerical and Performance comparison for Maximum Likelihood estimation methods between PuMaS.jl and industry standard software.

Poster

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Submit a Request

PUMAS

Jarugula P, Dixit V, Rackauckas C, Gobburu J, Ivaturi V. Physiologically-based Pharmacokinetic (PBPK) Modeling Workflow in PuMaS.

Poster

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Submit a Request

PUMAS

Hechuan Wang, Aksana K. Jones, Christopher C. Dvorak, Liusheng Huang, Paul Orchard, Vijay Ivaturi, Janel Long-Boyle. “Population Pharmacokinetics of Clofarabine as Part of Pretransplantation Conditioning in Pediatric Subjects before Hematopoietic Cell Transplantation”

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CONSULTING
2018

Rackauckas, Christopher, Joakim Nyberg, Pao CSVijay Ivaturi. PKPDSimulator.Jl : A Simulation Engine for Drug Development and Clinical Therapeutics in Julia.

Poster

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Submit a Request

CONSULTING

Perrone R, Gobburu J, Czerwiec FS, Pao CS, Ivaturi V. Estimating Short-Term Risk of Disease-Related Outcomes in ADPKD: A Prediction Model Based on Longitudinal Data From the OVERTURE Study

CONSULTING
2017

Vijay Ivaturi, Christopher C. Dvorak, Danna Chan, Tao Liu, Morton J. Cowan, Justin Wahlstrom, Melisa Stricherz, Cathryn Jennissen, Paul J. Orchard, Jakub Tolar, Sung-Yun Pai, Liusheng Huang, Francesca Aweeka, Janel Long-Boyle. “Pharmacokinetics and Model-Based Dosing to Optimize Fludarabine Therapy in Pediatric Hematopoietic Cell Transplant Recipients”

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CONSULTING

Danna Chan, Vijay Ivaturi, Janel Long-Boyle. The time is now: model-based dosing to optimize drug therapy

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CONSULTING
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Dover, DE 19901
Email: info@pumas.ai
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Pumas-AI Inc.
3500 South Dupont Highway
Suite GT-101
Dover, DE 19901
Email: info@pumas.ai
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