Published in J Theor Biol on December 07, 2004
A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol (2008) 5.11
Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PLoS Pathog (2012) 1.84
Agent-based models in translational systems biology. Wiley Interdiscip Rev Syst Biol Med (2010) 1.70
Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. J Immunol (2009) 1.66
Modeling formalisms in Systems Biology. AMB Express (2011) 1.61
A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning. J Theor Biol (2007) 1.45
Agent-based modeling of host-pathogen systems: The successes and challenges. Inf Sci (Ny) (2009) 1.43
After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res (2012) 1.38
Multiscale agent-based cancer modeling. J Math Biol (2008) 1.37
Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation. J Immunol (2011) 1.32
Modeling the Mycobacterium tuberculosis Granuloma - the Critical Battlefield in Host Immunity and Disease. Front Immunol (2013) 1.21
The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor Biol Med Model (2007) 1.14
The tuberculous granuloma: an unsuccessful host defence mechanism providing a safety shelter for the bacteria? Clin Dev Immunol (2012) 1.14
Using uncertainty and sensitivity analyses in socioecological agent-based models to improve their analytical performance and policy relevance. PLoS One (2014) 1.11
A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. J Theor Biol (2011) 1.08
Differential risk of tuberculosis reactivation among anti-TNF therapies is due to drug binding kinetics and permeability. J Immunol (2012) 1.07
Characterizing the dynamics of CD4+ T cell priming within a lymph node. J Immunol (2010) 1.07
A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends Microbiol (2012) 1.03
A multifaceted approach to modeling the immune response in tuberculosis. Wiley Interdiscip Rev Syst Biol Med (2010) 1.03
Modeling lymphocyte homing and encounters in lymph nodes. BMC Bioinformatics (2009) 1.03
Strain specific transcriptional response in Mycobacterium tuberculosis infected macrophages. Cell Commun Signal (2012) 1.02
Within the Enemy's Camp: contribution of the granuloma to the dissemination, persistence and transmission of Mycobacterium tuberculosis. Front Immunol (2013) 1.02
Modeling of wildlife-associated zoonoses: applications and caveats. Vector Borne Zoonotic Dis (2012) 1.02
Mathematical modeling of tuberculosis bacillary counts and cellular populations in the organs of infected mice. PLoS One (2010) 0.98
Sensitivity analysis of infectious disease models: methods, advances and their application. J R Soc Interface (2013) 0.98
An agent-based model of inflammation and fibrosis following particulate exposure in the lung. Math Biosci (2011) 0.98
Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cell Mol Bioeng (2015) 0.97
A virtual look at Epstein-Barr virus infection: simulation mechanism. J Theor Biol (2008) 0.97
Agent-based modeling: a systematic assessment of use cases and requirements for enhancing pharmaceutical research and development productivity. Wiley Interdiscip Rev Syst Biol Med (2013) 0.97
Macrophage polarization drives granuloma outcome during Mycobacterium tuberculosis infection. Infect Immun (2014) 0.96
NF-κB Signaling Dynamics Play a Key Role in Infection Control in Tuberculosis. Front Physiol (2012) 0.96
Functional complexity of the Leishmania granuloma and the potential of in silico modeling. Front Immunol (2013) 0.95
Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. PLoS Pathog (2012) 0.94
Tuberculosis: global approaches to a global disease. Curr Opin Biotechnol (2010) 0.94
Immune control of HIV-1 infection after therapy interruption: immediate versus deferred antiretroviral therapy. BMC Infect Dis (2009) 0.93
Parameter estimation and sensitivity analysis in an agent-based model of Leishmania major infection. J Theor Biol (2009) 0.93
Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis. Theor Biol Med Model (2011) 0.90
An agent-based model to study the epidemiological and evolutionary dynamics of Influenza viruses. BMC Bioinformatics (2011) 0.90
Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models. Wiley Interdiscip Rev Syst Biol Med (2014) 0.90
AGENT-BASED MODELS IN EMPIRICAL SOCIAL RESEARCH. Sociol Methods Res (2015) 0.88
A computational tool integrating host immunity with antibiotic dynamics to study tuberculosis treatment. J Theor Biol (2014) 0.87
Modeling innate immune response to early Mycobacterium infection. Comput Math Methods Med (2012) 0.87
Understanding original antigenic sin in influenza with a dynamical system. PLoS One (2011) 0.86
Targeting the biophysical properties of the myeloma initiating cell niches: a pharmaceutical synergism analysis using multi-scale agent-based modeling. PLoS One (2014) 0.85
Latent Tuberculosis: Models, Computational Efforts and the Pathogen's Regulatory Mechanisms during Dormancy. Front Bioeng Biotechnol (2013) 0.85
Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies. BMC Syst Biol (2012) 0.85
Criticality of timing for anti-HIV therapy initiation. PLoS One (2010) 0.84
Investigating biocomplexity through the agent-based paradigm. Brief Bioinform (2013) 0.84
Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome. PLoS Comput Biol (2016) 0.83
A population model capturing dynamics of tuberculosis granulomas predicts host infection outcomes. Math Biosci Eng (2015) 0.82
A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury. PLoS Comput Biol (2015) 0.82
A multi-scale approach to designing therapeutics for tuberculosis. Integr Biol (Camb) (2015) 0.82
The roles of immune memory and aging in protective immunity and endogenous reactivation of tuberculosis. PLoS One (2013) 0.81
A Multiscale Agent-Based in silico Model of Liver Fibrosis Progression. Front Bioeng Biotechnol (2014) 0.81
Computational Modeling Predicts Simultaneous Targeting of Fibroblasts and Epithelial Cells Is Necessary for Treatment of Pulmonary Fibrosis. Front Pharmacol (2016) 0.80
How the interval between prime and boost injection affects the immune response in a computational model of the immune system. Comput Math Methods Med (2012) 0.80
Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective. BMC Bioinformatics (2013) 0.80
Using an Agent-Based Model to Examine the Role of Dynamic Bacterial Virulence Potential in the Pathogenesis of Surgical Site Infection. Adv Wound Care (New Rochelle) (2013) 0.79
An Agent-Based Modeling Template for a Cohort of Veterans with Diabetic Retinopathy. PLoS One (2013) 0.79
A test of agent-based models as a tool for predicting patterns of pathogen transmission in complex landscapes. BMC Ecol (2013) 0.79
A simple immune system simulation reveals optimal movement and cell density parameters for successful target clearance. Immunology (2007) 0.78
Inoculation dose of Mycobacterium tuberculosis does not influence priming of T cell responses in lymph nodes. J Immunol (2013) 0.78
Mathematical modeling of viral infection dynamics in spherical organs. J Math Biol (2012) 0.78
The Small Breathing Amplitude at the Upper Lobes Favors the Attraction of Polymorphonuclear Neutrophils to Mycobacterium tuberculosis Lesions and Helps to Understand the Evolution toward Active Disease in An Individual-Based Model. Front Microbiol (2016) 0.76
Strategic Priming with Multiple Antigens can Yield Memory Cell Phenotypes Optimized for Infection with Mycobacterium tuberculosis: A Computational Study. Front Microbiol (2016) 0.76
Oxygen Modulates the Effectiveness of Granuloma Mediated Host Response to Mycobacterium tuberculosis: A Multiscale Computational Biology Approach. Front Cell Infect Microbiol (2016) 0.76
A computational model of invasive aspergillosis in the lung and the role of iron. BMC Syst Biol (2016) 0.76
Towards anatomic scale agent-based modeling with a massively parallel spatially explicit general-purpose model of enteric tissue (SEGMEnT_HPC). PLoS One (2015) 0.76
Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions. Infect Immun (2016) 0.75
M2 macrophages or IL-33 treatment attenuate ongoing Mycobacterium tuberculosis infection. Sci Rep (2017) 0.75
Bayesian approach to model CD137 signaling in human M. tuberculosis in vitro responses. PLoS One (2013) 0.75
Modeling the clonal heterogeneity of stem cells. Theor Biol Med Model (2010) 0.75
mlegp: statistical analysis for computer models of biological systems using R. Bioinformatics (2008) 0.75
In silico models of M. tuberculosis infection provide a route to new therapies. Drug Discov Today Dis Models (2014) 0.75
Identifying mechanisms driving formation of granuloma-associated fibrosis during Mycobacterium tuberculosis infection. J Theor Biol (2017) 0.75
A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection. Computation (Basel) (2016) 0.75
The equilibria that allow bacterial persistence in human hosts. Nature (2007) 2.45
Systems biology of persistent infection: tuberculosis as a case study. Nat Rev Microbiol (2008) 1.70
Neutralization of tumor necrosis factor (TNF) by antibody but not TNF receptor fusion molecule exacerbates chronic murine tuberculosis. J Infect Dis (2007) 1.49
A hybrid multi-compartment model of granuloma formation and T cell priming in tuberculosis. J Theor Biol (2011) 1.08
Dynamics of naive and memory CD4+ T lymphocytes in HIV-1 disease progression. J Acquir Immune Defic Syndr (2002) 1.08
Comparing epidemic tuberculosis in demographically distinct heterogeneous populations. Math Biosci (2002) 1.05
On treatment of tuberculosis in heterogeneous populations. J Theor Biol (2003) 0.95
Modeling socio-demography to capture tuberculosis transmission dynamics in a low burden setting. J Theor Biol (2011) 0.95
An agent-based computational approach for representing aspects of in vitro multi-cellular tumor spheroid growth. Conf Proc IEEE Eng Med Biol Soc (2004) 0.82
A population model capturing dynamics of tuberculosis granulomas predicts host infection outcomes. Math Biosci Eng (2015) 0.82
The roles of immune memory and aging in protective immunity and endogenous reactivation of tuberculosis. PLoS One (2013) 0.81
A model for the study of Helicobacter pylori interaction with human gastric acid secretion. J Theor Biol (2004) 0.80
A model for Vibrio cholerae colonization of the human intestine. J Theor Biol (2011) 0.79
Mathematical analysis of the global dynamics of a model for HTLV-I infection and ATL progression. Math Biosci (2002) 0.79
The importance of an inter-compartmental delay in a model for human gastric acid secretion. Bull Math Biol (2003) 0.76
A model for integrative study of human gastric acid secretion. J Appl Physiol (1985) (2002) 0.76
Identifying DNA splice sites using hypernetworks with artificial molecular evolution. Biosystems (2006) 0.75
Fifty years of JTB: past, present and future: a letter from the Editors-in-Chief. J Theor Biol (2010) 0.75