For a complete overview of publications by the Popel Systems Biology Laboratory visit:
Selected Publications
Predictive models of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer usingnuclear morphology and tissue architecture;
Cell Reports Medicine 2021;
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway;
npj Systems Biology and Applications 2021;
Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response;
ImmunoInformatics 2021;
A Spatial Quantitative Systems Pharmacology Platform spQSP-IO for Simulations of Tumor—Immune Interactions and Effects of Checkpoint Inhibitor Immunotherapy;
Cancers 2021;
A data-driven computational model enables integrative and mechanistic characterization of dynamic macrophage polarization;
iScience 2021;
Quantitative Systems Pharmacology Modeling of PBMC-Humanized Mouse to Facilitate Preclinical Immuno-oncology Drug Development;
ACS Pharmacol Transl Sci 2020;
Quantitative systems pharmacology model predictions for efficacy of atezolizumab and nab-paclitaxel in triple-negative breast cancer;
J Immunother Cancer 2021;
Peptides that immunoactivate the tumor microenvironment;
Biochim Biophys Acta Rev Cancer 2021;
Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer;
Front Physiol 2020;
Regulation of the tumor immune microenvironment and vascular normalization in TNBC murine models by a novel peptide;
Oncoimmunology 2020;
Combination therapy with T cell engager and PD-L1 blockade enhances the antitumor potency of T cells as predicted by a QSP model;
J Immunother Cancer 2020;
Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer;
Front Physiol 2020;
QSP‐IO: A Quantitative Systems Pharmacology Toolbox for Mechanistic Multiscale Modeling for Immuno‐Oncology Applications;
CPT: pharmacometrics & systems pharmacology 2020;
Regulation of the tumor immune microenvironment and vascular normalization in TNBC murine models by a novel peptide;
Oncoimmunology 2020;
A Quantitative Systems Pharmacology Model of T Cell Engager Applied to Solid Tumor;
The AAPS Journal 2020;
Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy;
Cancer Biol Ther 2020;
Immunoactivating the tumor microenvironment enhances immunotherapy as predicted by integrative computational model;
Proc Natl Acad Sci U S A 2020; PDF
Conducting a Virtual Clinical Trial in HER2-Negative Breast Cancer Using a Quantitative Systems Pharmacology Model With an Epigenetic Modulator and Immune Checkpoint Inhibitors;
Front Bioeng Biotechnol 2020; PDF
A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology;
PLoS Comput Biol. 2019; PDF
Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma;
NPJ Syst Biol Appl. 2019; PDF
A QSP Model for Predicting Clinical Responses to Monotherapy, Combination and Sequential Therapy Following CTLA-4, PD-1, and PD-L1 Checkpoint Blockade;
Sci Rep. 2019; PDF
Anisotropic poly(lactic-co-glycolic acid) microparticles enable sustained release of a peptide for long-term inhibition of ocular neovascularization.;
Acta Biomater. 2019;
A Computational Model of Neoadjuvant PD-1 Inhibition in Non-Small Cell Lung Cancer;
AAPS J. 2019; PDF
In silico simulation of a clinical trial with anti-CTLA-4 and anti-PD-L1 immunotherapies in metastatic breast cancer using a systems pharmacology model;
R Soc Open Sci. 2019; PDF
Tumor Ensemble-Based Modeling and Visualization of Emergent Angiogenic Heterogeneity in Breast Cancer;
Sci Rep. 2019;
Dynamic Changes in Microvascular Flow Conductivity and Perfusion After Myocardial Infarction Shown by Image-Based Modeling;
J Am Heart Assoc. 2019; PDF
Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment;
Processes 2019;
Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases;
Int J Mol Sci 2019; PDF
A collagen IV-derived peptide disrupts α5β1 integrin and potentiates Ang2/Tie2 signaling;
JCI Insight 2019;
Quantitative Characterization of CD8+ T Cell Clustering and Spatial Heterogeneity in Solid Tumors;
Front Oncol. 2019; PDF
Three-Dimensional Transport Model for Intravitreal and Suprachoroidal Drug Injection;
Invest Ophthalmol Vis Sci. 2018; PDF
Modeling triple-negative breast cancer heterogeneity: Effects of stromal macrophages, fibroblasts and tumor vasculature;
J Theor Biol 2018; PDF
Human expression patterns: qualitative and quantitative analysis of thrombospondin-1 under physiological and pathological conditions;
J Cell Mol Med 2018;
Biomimetic peptide display from a polymeric nanoparticle surface for targeting and antitumor activity to human triple-negative breast cancer cells;
J Biomed Mater Res A 2018;
Deciphering microvascular changes after myocardial infarction through 3D fully automated image analysis;
Sci Rep 2018; PDF
Therapeutic potential of an anti-angiogenic multimodal biomimetic peptide in hepatocellular carcinoma;
Oncotarget 2018; PDF
Simultaneous blockade of IL-6 and CCL5 signaling for synergistic inhibition of triple-negative breast cancer growth and metastasis;
Breast Cancer Res 2018; PDF
Computational modeling of synergistic interaction between αVβ3 integrin and VEGFR2 in endothelial cells: implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides;
J Theor Biol 2018;
Computer Simulation of TSP1 Inhibition of VEGF-Akt-eNOS: An Angiogenesis Triple Threat;
Front Physiol 2018; PDF
A computational multiscale agent-based model for simulating spatio-temporal tumour immune response to PD1 and PDL1 inhibition;
J R Soc Interface 2017; PDF
Crosstalk between stromal components and tumor cells of TNBC via secreted factors enhances tumor growth and metastasis;
Oncotarget 2017; PDF
An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia;
BMC Syst Biol 2017; PDF
Tyrosine kinase blocking collagen IV-derived peptide suppresses ocular neovascularization and vascular leakage;
Sci Transl Med 2017; PDF
Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model;
PLoS Comput Biol 2017; PDF