Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

NA Cilfone, DE Kirschner, JJ Linderman - Cellular and molecular …, 2015 - Springer
Biologically related processes operate across multiple spatiotemporal scales. For
computational modeling methodologies to mimic this biological complexity, individual scale …

Global sensitivity analysis of biological multiscale models

M Renardy, C Hult, S Evans, JJ Linderman… - Current opinion in …, 2019 - Elsevier
Mathematical models of biological systems need to both reflect and manage the inherent
complexities of biological phenomena. Through their versatility and ability to capture …

Macrophage polarization drives granuloma outcome during Mycobacterium tuberculosis infection

S Marino, NA Cilfone, JT Mattila… - Infection and …, 2015 - Am Soc Microbiol
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), induces formation of
granulomas, structures in which immune cells and bacteria colocalize. Macrophages are …

[HTML][HTML] Lymph nodes are sites of prolonged bacterial persistence during Mycobacterium tuberculosis infection in macaques

SKC Ganchua, AM Cadena, P Maiello… - PLoS …, 2018 - journals.plos.org
Tuberculosis is commonly considered a chronic lung disease, however, extrapulmonary
infection can occur in any organ. Even though lymph nodes (LN) are among the most …

[图书][B] Mathematical immunology of virus infections

Understanding the cellular and molecular mechanisms that control the ability of the immune
system to mount a protective response against pathogen-derived foreign antigens, but avoid …

Iterative community-driven development of a SARS-CoV-2 tissue simulator

M Getz, Y Wang, G An, M Asthana, A Becker… - BioRxiv, 2020 - biorxiv.org
The 2019 novel coronavirus, SARS-CoV-2, is an emerging pathogen of critical significance
to international public health. Knowledge of the interplay between molecular-scale virus …

[HTML][HTML] Spatial Organization and Recruitment of Non-Specific T Cells May Limit T Cell-Macrophage Interactions Within Mycobacterium tuberculosis Granulomas

JA Millar, JR Butler, S Evans, NL Grant… - Frontiers in …, 2021 - frontiersin.org
Tuberculosis (TB) is a worldwide health problem; successful interventions such as vaccines
and treatment require a 2better understanding of the immune response to infection with …

Tuneable resolution as a systems biology approach for multi‐scale, multi‐compartment computational models

DE Kirschner, CA Hunt, S Marino… - … Systems Biology and …, 2014 - Wiley Online Library
The use of multi‐scale mathematical and computational models to study complex biological
processes is becoming increasingly productive. Multi‐scale models span a range of spatial …

[HTML][HTML] A multi-compartment hybrid computational model predicts key roles for dendritic cells in tuberculosis infection

S Marino, DE Kirschner - Computation, 2016 - mdpi.com
Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people
infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The …

Agent‐based models of inflammation in translational systems biology: A decade later

Y Vodovotz, G An - Wiley Interdisciplinary Reviews: Systems …, 2019 - Wiley Online Library
Agent‐based modeling is a rule‐based, discrete‐event, and spatially explicit computational
modeling method that employs computational objects that instantiate the rules and …