The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena

Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success

(2016) Thomas E. Yankeelov et al.   ANNALS OF BIOMEDICAL ENGINEERING

Merging trait-based and individual-based modelling: An animal functional type approach to explore the responses of birds to climatic and land use changes in semi-arid African savannas

(2016) Cédric Scherer et al.   ECOLOGICAL MODELLING

InSTREAM-Gen: Modelling eco-evolutionary dynamics of trout populations under anthropogenic environmental change

(2016) Daniel Ayllón et al.   ECOLOGICAL MODELLING

Reproducibility in Computational Neuroscience Models and Simulations

(2016) Robert A. McDougal et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments

(2016) Andrew K. Smith et al.   PLoS Computational Biology

A multi-scale approach to designing therapeutics for tuberculosis

(2015) Jennifer J. Linderman et al.   Integrative Biology

Molecular mechanism matters: Benefits of mechanistic computational models for drug development

(2015) Lindsay E. Clegg et al.   PHARMACOLOGICAL RESEARCH

Ten Simple Rules for Experiments’ Provenance

(2015) Toni Kazic   PLoS Computational Biology

A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases

(2015) Chuan Xue et al.   PLoS Computational Biology

Tolerance to Acetaminophen Hepatotoxicity in the Mouse Model of Autoprotection Is Associated with Induction of Flavin-Containing Monooxygenase-3 (FMO3) in Hepatocytes

(2014) Swetha Rudraiah et al.   TOXICOLOGICAL SCIENCES

Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)

(2014) Chase Cockrell et al.   PLoS Computational Biology

Ketamine Disrupts Theta Modulation of Gamma in a Computer Model of Hippocampus

(2011) S. A. Neymotin et al.   JOURNAL OF NEUROSCIENCE

The Explanatory Force of Dynamical and Mathematical Models in Neuroscience: A Mechanistic Perspective*

(2011) David Michael Kaplan et al.   PHILOSOPHY OF SCIENCE

A Computational Model to Predict the Effects of Class I Anti-Arrhythmic Drugs on Ventricular Rhythms

(2011) J. D. Moreno et al.   Science Translational Medicine

What is a mechanism? Thinking about mechanisms across the sciences

(2011) Phyllis McKay Illari et al.   European Journal for Philosophy of Science

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

(2010) Jonathan Tang et al.   PLoS Computational Biology

Current Concepts of Mechanisms in Drug-Induced Hepatotoxicity

(2009) Stefan Russmann et al.   CURRENT MEDICINAL CHEMISTRY

A 2D mechanistic model of breast ductal carcinoma in situ (DCIS) morphology and progression

(2009) Kerri-Ann Norton et al.   JOURNAL OF THEORETICAL BIOLOGY

Thinking Again about Biological Mechanisms

(2009) Lindley Darden   PHILOSOPHY OF SCIENCE

Therapeutically Targeting ErbB3: A Key Node in Ligand-Induced Activation of the ErbB Receptor-PI3K Axis

(2009) B. Schoeberl et al.   Science Signaling

Multiscale modeling for biologists

(2009) Martin Meier-Schellersheim et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Agent-based simulation of notch-mediated tip cell selection in angiogenic sprout initialisation

(2007) Katie Bentley et al.   JOURNAL OF THEORETICAL BIOLOGY