A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness

A systems approach to infectious disease

(2020) Manon Eckhardt et al.   NATURE REVIEWS GENETICS

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence

(2020) Yu-chen Cao et al.   Travel Medicine and Infectious Disease

Towards whole-lung simulations of aerosol deposition: A model of the deep lung

(2020) P.G. Koullapis et al.   JOURNAL OF AEROSOL SCIENCE

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

(2020) Robert Lorenz Chua et al.   NATURE BIOTECHNOLOGY

Mathematical Modeling of RNA Virus Sensing Pathways Reveals Paracrine Signaling as the Primary Factor Regulating Excessive Cytokine Production

(2020) Jordan J. A. Weaver et al.   Processes

COVID-19: unravelling the clinical progression of nature’s virtually perfect biological weapon

(2020) Giuseppe Lippi et al.   Annals of Translational Medicine

Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures

(2019) Andrea Imle et al.   Nature Communications

Global landscape of mouse and human cytokine transcriptional regulation

(2018) Sebastian Carrasco Pro et al.   NUCLEIC ACIDS RESEARCH

Viral Load Affects the Immune Response to HBV in Mice With Humanized Immune System and Liver

(2017) Mathilde Dusséaux et al.   GASTROENTEROLOGY

A Tunable Diffusion-Consumption Mechanism of Cytokine Propagation Enables Plasticity in Cell-to-Cell Communication in the Immune System

(2017) Alon Oyler-Yaniv et al.   IMMUNITY

Spatiotemporal Dynamics of Virus Infection Spreading in Tissues

(2017) Gennady Bocharov et al.   PLoS One

Physiologically based pharmacokinetic models of small molecules and therapeutic antibodies: a mini-review on fundamental concepts and applications

(2016) Gregory Z. Ferl et al.   BIOPHARMACEUTICS & DRUG DISPOSITION

Therapeutic efficacy of the small molecule GS-5734 against Ebola virus in rhesus monkeys

(2016) Travis K. Warren et al.   NATURE

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology

(2014) Jörn Starruß et al.   BIOINFORMATICS

T Cell Responses to Viral Infections – Opportunities for Peptide Vaccination

(2014) Sietske Rosendahl Huber et al.   Frontiers in Immunology

Role of regulatory T cells during virus infection

(2013) Tamara Veiga-Parga et al.   IMMUNOLOGICAL REVIEWS

Chaste: An Open Source C++ Library for Computational Physiology and Biology

(2013) Gary R. Mirams et al.   PLoS Computational Biology

A hybrid stochastic–deterministic computational model accurately describes spatial dynamics and virus diffusion in HIV-1 growth competition assay

(2012) Taina Immonen et al.   JOURNAL OF THEORETICAL BIOLOGY

Competition for IL-2 between Regulatory and Effector T Cells to Chisel Immune Responses

(2012) Thomas Höfer et al.   Frontiers in Immunology

Design considerations in buildingin silicoequivalents of common experimental influenza virus assays

(2011) Benjamin P. Holder et al.   AUTOIMMUNITY

Influenza A virus infection kinetics: quantitative data and models

(2011) Amber M. Smith et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Lipid-Cytokine-Chemokine Cascade Drives Neutrophil Recruitment in a Murine Model of Inflammatory Arthritis

(2010) Richard C. Chou et al.   IMMUNITY

Characterizing the Dynamics of CD4+ T Cell Priming within a Lymph Node

(2010) J. J. Linderman et al.   JOURNAL OF IMMUNOLOGY

Agent-Based Modeling of Endotoxin-Induced Acute Inflammatory Response in Human Blood Leukocytes

(2010) Xu Dong et al.   PLoS One

Micro- and macrorheology of mucus

(2009) Samuel K. Lai et al.   ADVANCED DRUG DELIVERY REVIEWS

Antimony: a modular model definition language

(2009) L. P. Smith et al.   BIOINFORMATICS

Chaste: A test-driven approach to software development for biological modelling

(2009) Joe Pitt-Francis et al.   COMPUTER PHYSICS COMMUNICATIONS

The Pathology of Influenza Virus Infections

(2008) Jeffery K. Taubenberger et al.   Annual Review of Pathology-Mechanisms of Disease

Agent-based modeling of host–pathogen systems: The successes and challenges

(2008) Amy L. Bauer et al.   INFORMATION SCIENCES