SimBiology

 

Modeling and Simulation in Drug Development with SimBiology and MATLAB

Selected publications with SimBiology and MATLAB

QSP, PBPK, and PK/PD Modeling and Analysis

 

Quantitative systems pharmacology model-based investigation of adverse gastrointestinal events associated with prolonged treatment with PI3-kinase inhibitors

Gadkar, Kapil, Genentech et al., CPT Pharmacometrics Syst Pharmacol (2022)
Code: Supplementary material

Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model

Richard J. Sove et al., John Hopkins University School of Medicine, J. Immunother. Cancer (2022)
Code

A Mechanistic Site-Of-Action Model: A Tool for Informing Right Target, Right Compound, And Right Dose for Therapeutic Antagonistic Antibody Programs

Kapitanov, Georgi I. et al, Pfizer, Front. Bioinform (2021)
Code

Quantitative systems pharmacology model predictions for efficacy of atezolizumab and nab-paclitaxel in triple-negative breast cancer

Hanwen Wang et al., John Hopkins University, J.  Immunother. Cancer (2021)

Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modeling

Iraj Hosseini et al., Genentech, npj Syst Biol Appl (2020)
Code

A Dynamic Quantitative Systems Pharmacology Model of Inflammatory Bowel Disease: Part 1 – Model Framework

Katharine V. Rogers et al, Pfizer, Clin Transl Sci (2020)
Code

Quantification of IgG monoclonal antibody clearance in tissues

Miro J. Eigenmann et al, Roche, MAbs (2017)

A Mechanistic Systems Pharmacology Model for Prediction of LDL Cholesterol Lowering by PCSK9 Antagonism in Human Dyslipidemic Populations

K Gadkar et al, Genentech, CPT Pharmacometrics Syst Pharmacol (2014)

A Kinetic Proofreading Model for Bispecific Protein Degraders

Derek Bartlett, Pfizer, et al., J Pharmacokinet Pharmacodyn (2021)
Code

Virtual clinical trial simulations for a novel KRASG12C inhibitor (ASP2453) in non-small cell lung cancer

Hiroyuki Sayama et al., Astellas, CPT Pharmacometrics Syst Pharmacol (2021)
Code

Mechanistic Modeling of Intra‐Tumor Spatial Distribution of Antibody‐Drug Conjugates: Insights into Dosing Strategies in Oncology.

Jared Weddell et al, AbbVie, Clin Transl Sci (2020)
Code

Conducting a Virtual Clinical Trial in HER2-Negative Breast Cancer Using a Quantitative Systems Pharmacology Model With an Epigenetic Modulator and Immune Checkpoint Inhibitors

Hanwen Wang et al, John Hopkins University, Front. Bioeng. Biotechnol., (2020)
Code

Modeling bispecific monoclonal antibody interaction with two cell membrane targets indicates the importance of surface diffusion

Bram G. Sengers et al, GlaxoSmithKline, MAbs (2016)

Cross-species/cross-modality physiologically based pharmacokinetics for biologics: 89Zr-labelled albumin-binding domain antibody GSK3128349 in humans

Armin Sepp et al, GlaxoSmithKline, mAbs (2020)
Code

An in vitro quantitiative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias

Jennifer L. Wilson et al, Genentech, PLoS Comput Biol (2020)
Code

Quantitative Systems Pharmacology Model for Alzheimer Disease Indicates Targeting Sphingolipid Dysregulation as Potential Treatment Option

Diana Clausznitzer et al, AbbVie, CPT Pharmacometrics Syst Pharmacol (2018)

A Systems Pharmacology Model for Predicting Effects of Factor Xa Inhibitors in Healthy Subjects: Assessment of Pharmacokinetics and Binding Kinetics

X Zhou et. al., Janssen, CPT Pharmacometrics Syst Pharmacol (2015)

SimBiology Based Apps and Modeling Frameworks

 

Biologics PBPK model builder for MATLAB SimBiology

Armin Sepp, GlaxoSmithKline (2021)

gQSPSim: A SimBiology-Based GUI for Standardized QSP Model Development and Application

Iraj Hosseini et al, Genentech, CPT Pharmacometrics Syst Pharmacol (2020)
Code

QSP Toolbox: Computational Implementation of Integrated Workflow Components for Deploying Multi-Scale Mechanistic Models

Yougan Cheng et al, Bristol Myers Squibb, The AAPS Journal (2017)
Code

QSP‐IO: A Quantitative Systems Pharmacology Toolbox for Mechanistic Multiscale Modeling for Immuno‐Oncology Applications

Richard J. Sové et al, John Hopkins University, CPT Pharmacometrics Syst Pharmacol (2020)
Code

Quantitative Systems Pharmacology (QSP) tools to aid in model development and communication: Vantage QSP Modeling Tools (VQM-Tools)

Madhav Channavazzala et al, Vantage, PAGE 28 (2019)

gPKPDSim: a SimBiology®-based GUI application for PKPD modeling in drug development

Iraj Hosseini et al, Genentech, J Pharmacokinet Pharmacodyn (2018)
Code