Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity

Physiologically based pharmacokinetic (PBPK) modelling tools: how to fit with our needs?

(2012) François Bouzom et al.   BIOPHARMACEUTICS & DRUG DISPOSITION

Utility of a physiologically-based pharmacokinetic (PBPK) modeling approach to quantitatively predict a complex drug-drug-disease interaction scenario for rivaroxaban during the drug review process: implications for clinical practice

(2012) Joseph A. Grillo et al.   BIOPHARMACEUTICS & DRUG DISPOSITION

Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: Incorporating EGFR signaling pathway and angiogenesis

(2012) Xiaoqiang Sun et al.   BMC BIOINFORMATICS

Physiologically Based Pharmacokinetics Joined With In Vitro–In Vivo Extrapolation of ADME: A Marriage Under the Arch of Systems Pharmacology

(2012) A Rostami-Hodjegan   CLINICAL PHARMACOLOGY & THERAPEUTICS

Drugs that target pathogen public goods are robust against evolved drug resistance

(2012) John W. Pepper   Evolutionary Applications

Use of physiologically based pharmacokinetic modeling for assessment of drug–drug interactions

(2012) Guillaume Baneyx et al.   Future Medicinal Chemistry

Agent-based model of macrophage action on endocrine pancreas

(2012) Ignacio V. Martínez et al.   International Journal of Data Mining and Bioinformatics

Differential Risk of Tuberculosis Reactivation among Anti-TNF Therapies Is Due to Drug Binding Kinetics and Permeability

(2012) M. Fallahi-Sichani et al.   JOURNAL OF IMMUNOLOGY

Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells

(2012) P. Mina et al.   Journal of the Royal Society Interface

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

Complexity in a brain-inspired agent-based model

(2012) Karen E. Joyce et al.   NEURAL NETWORKS

Merging Systems Biology with Pharmacodynamics

(2012) R. Iyengar et al.   Science Translational Medicine

Individualized, discrete event, simulations provide insight into inter- and intra-subject variability of extended-release, drug products

(2012) Sean HJ Kim et al.   Theoretical Biology and Medical Modelling

Integration of TGF-β- and EGFR-based signaling pathways using an agent-based model of epithelial restitution

(2012) Jordan R. Stern et al.   WOUND REPAIR AND REGENERATION

The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation

(2012) Haiyang Zhang et al.   PLoS Computational Biology

Modeling Protective Anti-Tumor Immunity via Preventative Cancer Vaccines Using a Hybrid Agent-based and Delay Differential Equation Approach

(2012) Peter S. Kim et al.   PLoS Computational Biology

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

(2012) Yael Artzy-Randrup et al.   eLife

An Agent-Based Model of Income Inequalities in Diet in the Context of Residential Segregation

(2011) Amy H. Auchincloss et al.   AMERICAN JOURNAL OF PREVENTIVE MEDICINE

Physiologically-Based Pharmacokinetics in Drug Development and Regulatory Science

(2011) Malcolm Rowland et al.   Annual Review of Pharmacology and Toxicology

Agent-based simulation of reactions in the crowded and structured intracellular environment: Influence of mobility and location of the reactants

(2011) Michael T Klann et al.   BMC Systems Biology

Can the flow of medicines be improved? Fundamental pharmacokinetic and pharmacological principles toward improving Phase II survival

(2011) Paul Morgan et al.   DRUG DISCOVERY TODAY

Enabling Clearance Predictions to Emerge from In Silico Actions of Quasi-Autonomous Hepatocyte Components

(2011) S. Sheikh-Bahaei et al.   DRUG METABOLISM AND DISPOSITION

Trade-off between road avoidance and attraction by roadside salt pools in moose: An agent-based model to assess measures for reducing moose-vehicle collisions

(2011) Paul D. Grosman et al.   ECOLOGICAL MODELLING

Have physiologically-based pharmacokinetic models delivered?

(2011) Andrea N Edginton et al.   Expert Opinion on Drug Metabolism & Toxicology

Phenotypic transition maps of 3D breast acini obtained by imaging-guided agent-based modeling

(2011) Jonathan Tang et al.   Integrative Biology

The role of predictive biopharmaceutical modeling and simulation in drug development and regulatory evaluation

(2011) Wenlei Jiang et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Multiscale Computational Modeling Reveals a Critical Role for TNF-  Receptor 1 Dynamics in Tuberculosis Granuloma Formation

(2011) M. Fallahi-Sichani et al.   JOURNAL OF IMMUNOLOGY

From the Special Issue Editors: Agent-Based Modeling of Innovation Diffusion*

(2011) Rosanna Garcia et al.   JOURNAL OF PRODUCT INNOVATION MANAGEMENT

A hybrid multi-compartment model of granuloma formation and T cell priming in Tuberculosis

(2011) Simeone Marino et al.   JOURNAL OF THEORETICAL BIOLOGY

Believe it or not: how much can we rely on published data on potential drug targets?

(2011) Florian Prinz et al.   NATURE REVIEWS DRUG DISCOVERY

Systems Pharmacology: Bridging Systems Biology and Pharmacokinetics-Pharmacodynamics (PKPD) in Drug Discovery and Development

(2011) Piet H. van der Graaf et al.   PHARMACEUTICAL RESEARCH

Distributed Real-Time Software for Cyber–Physical Systems

(2011) John C. Eidson et al.   PROCEEDINGS OF THE IEEE

Data-parallel techniques for simulating a mega-scale agent-based model of systemic inflammatory response syndrome on graphics processing units

(2011) Samuel Alberts et al.   SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL

Relational grounding facilitates development of scientifically useful multiscale models

(2011) C Anthony Hunt et al.   Theoretical Biology and Medical Modelling

Application of PBPK modelling in drug discovery and development at Pfizer

(2011) Hannah M Jones et al.   XENOBIOTICA

A multifaceted approach to modeling the immune response in tuberculosis

(2011) Simeone Marino et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

MDCK Cystogenesis Driven by Cell Stabilization within Computational Analogues

(2011) Jesse A. Engelberg et al.   PLoS Computational Biology

Tutorial on agent-based modelling and simulation

(2011) C M Macal et al.   Journal of Simulation

Cloud computing and validation of expandable in silico livers

(2010) Glen EP Ropella et al.   BMC Systems Biology

Improving Productivity With Model-Based Drug Development: An Enterprise Perspective

(2010) T H Grasela et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Next-Generation Model-Based Drug Discovery and Development: Quantitative and Systems Pharmacology

(2010) S R B Allerheiligen   CLINICAL PHARMACOLOGY & THERAPEUTICS

Multiscale Modeling in Drug Discovery and Development: Future Opportunities and Present Challenges

(2010) P Vicini   CLINICAL PHARMACOLOGY & THERAPEUTICS

Moving beyond in silico tools to in silico science in support of drug development research

(2010) C. Anthony Hunt et al.   DRUG DEVELOPMENT RESEARCH

In silico augmentation of the drug development pipeline: examples from the study of acute inflammation

(2010) Gary An et al.   DRUG DEVELOPMENT RESEARCH

The current role of model-based drug development

(2010) Satyendra Suryawanshi et al.   Expert Opinion on Drug Discovery

Model-Based Drug Development: Strengths, Weaknesses, Opportunities, and Threats for Broad Application of Pharmacometrics in Drug Development

(2010) Jeffrey D. Wetherington et al.   JOURNAL OF CLINICAL PHARMACOLOGY

Computational experiments reveal plausible mechanisms for changing patterns of hepatic zonation of xenobiotic clearance and hepatotoxicity

(2010) Shahab Sheikh-Bahaei et al.   JOURNAL OF THEORETICAL BIOLOGY

Novel opportunities for computational biology and sociology in drug discovery

(2010) Lixia Yao et al.   TRENDS IN BIOTECHNOLOGY

Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research

(2010) Gary C. An   WOUND REPAIR AND REGENERATION

Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion

(2010) Jonathan Tang et al.   PLoS Computational Biology

Model-based approaches to increase efficiency of drug development in schizophrenia: a can't miss opportunity

(2009) Gianluca Nucci et al.   Expert Opinion on Drug Discovery

Simulation of the vegetation structure and function in a Malaysian tropical rain forest using the individual-based dynamic vegetation model SEIB-DGVM

(2009) Hisashi Sato   FOREST ECOLOGY AND MANAGEMENT

Agent-based simulation of T-cell activation and proliferation within a lymph node

(2009) Gib Bogle et al.   IMMUNOLOGY AND CELL BIOLOGY

Mechanistic Insight from In Silico Pharmacokinetic Experiments: Roles of P-glycoprotein, Cyp3A4 Enzymes, and Microenvironments

(2009) T. N. Lam et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

At the Biological Modeling and Simulation Frontier

(2009) C. Anthony Hunt et al.   PHARMACEUTICAL RESEARCH

In silico toxicology for the pharmaceutical sciences☆

(2009) Luis G. Valerio Jr.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Computational modeling of epithelial tissues

(2009) Rod Smallwood   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Agent-based models in translational systems biology

(2009) Gary An et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

In silico models of cancer

(2009) Lucas B. Edelman et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin

(2009) Alexander M. Bailey et al.   PLoS Computational Biology

Concepts and Challenges in Quantitative Pharmacology and Model-Based Drug Development

(2008) Liping Zhang et al.   AAPS Journal

Quantitative Disease, Drug, and Trial Models

(2008) Jogarao V.S. Gobburu et al.   Annual Review of Pharmacology and Toxicology

Development of Translational Pharmacokinetic–Pharmacodynamic Models

(2008) DE Mager et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Discovering Plausible Mechanistic Details of Hepatic Drug Interactions

(2008) T. N. Lam et al.   DRUG METABOLISM AND DISPOSITION

An individual-based model to describe a bullhead population dynamics including temperature variations

(2008) Sandrine Charles et al.   ECOLOGICAL MODELLING

Heterogeneous composition of models of computation

(2008) Antoon Goderis et al.   Future Generation Computer Systems-The International Journal of eScience

Computational Strategies Unravel and Trace How Liver Disease Changes Hepatic Drug Disposition

(2008) S. Park et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Introducing Spatial Information into Predictive NF-κB Modelling – An Agent-Based Approach

(2008) Mark Pogson et al.   PLoS One

A Patient-Specific in silico Model of Inflammation and Healing Tested in Acute Vocal Fold Injury

(2008) Nicole Y. K. Li et al.   PLoS One

Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation

(2008) Gary An   Theoretical Biology and Medical Modelling

Symmetric competition causes population oscillations in an individual-based model of forest dynamics

(2007) Paul Caplat et al.   ECOLOGICAL MODELLING