Selected Publications

A data-driven computational model enables integrative and mechanistic characterization of dynamic macrophage polarization; Zhao C, Medeiros TX, Sové RJ, Annex BH, Popel AS; iScience 2021;
Quantitative Systems Pharmacology Modeling of PBMC-Humanized Mouse to Facilitate Preclinical Immuno-oncology Drug Development; Ma H, Pilvankar M, Wang J, Giragossian C, Popel AS; ACS Pharmacol Transl Sci 2020;
Quantitative systems pharmacology model predictions for efficacy of atezolizumab and nab-paclitaxel in triple-negative breast cancer; Wang H, Ma H, Sové RJ, Emens LA, Popel AS; J Immunother Cancer 2021;
Peptides that immunoactivate the tumor microenvironment; Furukawa N, Popel AS; 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; Mi H, Gong C, Sulam J, Fertig EJ, Szalay AS, Jaffee EM, Stearns V, Emens LA, Cimino-Mathews AM, Popel AS; Front Physiol 2020;
Regulation of the tumor immune microenvironment and vascular normalization in TNBC murine models by a novel peptide; Mirando AC, Patil A, Rafie CI, Christmas BJ, Pandey NB, Stearns V, Jaffee EM, Roussos Torres ET, Popel AS; 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; Ma H, Wang H, Sové RJ, Wang J, Giragossian C, Popel AS.; J Immunother Cancer 2020;
Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer; Mi H, Gong C, Sulam J, Fertig EJ, Szalay AS, Jaffee EM, Stearns V, Emens LA, Cimino-Mathews AM, Popel AS.; Front Physiol 2020;
QSP‐IO: A Quantitative Systems Pharmacology Toolbox for Mechanistic Multiscale Modeling for Immuno‐Oncology Applications; Sove RJ, Jafarnejad M, Zhao C, Wang H, Ma H, Popel AS; CPT: pharmacometrics & systems pharmacology 2020;
Regulation of the tumor immune microenvironment and vascular normalization in TNBC murine models by a novel peptide; Mirando AC, Patil A, Rafie CI, Christmas BJ, Pandey NB, Stearns V, Jaffee EM, Roussos Torres ET, Popel AS; Oncoimmunology 2020;
A Quantitative Systems Pharmacology Model of T Cell Engager Applied to Solid Tumor; Ma H, Wang H, Sove RJ, Jafarnejad M, Tsai C, Wang J, Giragossian C, Popel AS; The AAPS Journal 2020;
Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy; Malone MK, Smrekar K, Park S, Blakely B, Walter A, Nasta N, Park J, Considine M, Danilova LV, Pandey NB, Fertig EJ, Popel AS, Jin K; Cancer Biol Ther 2020;
Immunoactivating the tumor microenvironment enhances immunotherapy as predicted by integrative computational model; Popel AS; 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; Wang H, Sové RJ, Jafarnejad M, Rahmeh S, Jaffee EM, Stearns V, Roussos Torres ET, Connolly RM, Popel AS; Front Bioeng Biotechnol 2020; PDF
A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology; Zhao C, Mirando AC, Sové RJ, Medeiros TX, Annex BH, Popel AS; PLoS Comput Biol. 2019; PDF
Angiopoietin-Tie Signaling Pathway in Endothelial Cells: A Computational Model; Zhang Y, Kontos CD, Annex BH, Popel AS; iScience 2019; PDF
Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma; Jafarnejad M, Sové RJ, Danilova L, Mirando AC, Zhang Y, Yarchoan M, Tran PT, Pandey NB, Fertig EJ, Popel AS; 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; Milberg O, Gong C, Jafarnejad M, Bartelink IH, Wang B, Vicini P, Narwal R, Roskos L, Popel AS; Sci Rep. 2019; PDF
Anisotropic poly(lactic-co-glycolic acid) microparticles enable sustained release of a peptide for long-term inhibition of ocular neovascularization.; Kim J, Lima E Silva R, Shmueli RB, Mirando AC, Tzeng SY, Pandey NB, Ben-Akiva E, Popel AS, Campochiaro PA, Green JJ.; Acta Biomater. 2019;
A Computational Model of Neoadjuvant PD-1 Inhibition in Non-Small Cell Lung Cancer; Jafarnejad M, Gong C, Gabrielson E, Bartelink IH, Vicini P, Wang B, Narwal R, Roskos L, Popel AS; 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; Wang H, Milberg O, Bartelink IH, Vicini P, Wang B, Narwal R, Roskos L, Santa-Maria CA, Popel AS; R Soc Open Sci. 2019; PDF
Tumor Ensemble-Based Modeling and Visualization of Emergent Angiogenic Heterogeneity in Breast Cancer; Stamatelos SK, Bhargava A, Kim E, Popel AS, Pathak AP; Sci Rep. 2019;
Dynamic Changes in Microvascular Flow Conductivity and Perfusion After Myocardial Infarction Shown by Image-Based Modeling; Gkontra P, El-Bouri WK, Norton KA, Santos A, Popel AS, Payne SJ, Arroyo AG; J Am Heart Assoc. 2019; PDF
Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment; Norton KA, Gong C, Jamalian S, Popel AS; Processes 2019;
Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases; Zhao C, Zhang Y, Popel AS; Int J Mol Sci 2019; PDF
A collagen IV-derived peptide disrupts α5β1 integrin and potentiates Ang2/Tie2 signaling; Mirando AC, Shen J, Silva RLE, Chu Z, Sass NC, Lorenc VE, Green JJ, Campochiaro PA, Popel AS, Pandey NB; JCI Insight 2019;
Quantitative Characterization of CD8+ T Cell Clustering and Spatial Heterogeneity in Solid Tumors; Gong C, Anders RA, Zhu Q, Taube JM, Green B, Cheng W, Bartelink IH, Vicini P, Wang B, Popel AS; Front Oncol. 2019; PDF
Three-Dimensional Transport Model for Intravitreal and Suprachoroidal Drug Injection; Zhang Y, Bazzazi H, Lima E Silva R, Pandey NB, Green JJ, Campochiaro PA, Popel AS; Invest Ophthalmol Vis Sci. 2018; PDF
Modeling triple-negative breast cancer heterogeneity: Effects of stromal macrophages, fibroblasts and tumor vasculature; Norton KA, Jin K, Popel AS; J Theor Biol 2018; PDF
Human expression patterns: qualitative and quantitative analysis of thrombospondin-1 under physiological and pathological conditions; Zhao C, Isenberg JS, Popel AS; 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; Bressler EM, Kim J, Shmueli RB, Mirando AC, Bazzazi H, Lee E, Popel AS, Pandey NB, Green JJ; J Biomed Mater Res A 2018;
Deciphering microvascular changes after myocardial infarction through 3D fully automated image analysis; Gkontra P, Norton KA, Żak MM, Clemente C, Agüero J, Ibáñez B, Santos A, Popel AS, Arroyo AG; Sci Rep 2018; PDF
Therapeutic potential of an anti-angiogenic multimodal biomimetic peptide in hepatocellular carcinoma; Barbhuiya MA, Mirando AC, Simons BW, Lemtiri-Chlieh G, Green JJ, Popel AS, Pandey NB, Tran PT; Oncotarget 2018; PDF
Simultaneous blockade of IL-6 and CCL5 signaling for synergistic inhibition of triple-negative breast cancer growth and metastasis; Jin K, Pandey NB, Popel AS; 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; Bazzazi H, Zhang Y, Jafarnejad M, Popel AS; J Theor Biol 2018;
Computer Simulation of TSP1 Inhibition of VEGF-Akt-eNOS: An Angiogenesis Triple Threat; Bazzazi H, Zhang Y, Jafarnejad M, Isenberg JS, Annex BH, Popel AS; Front Physiol 2018; PDF
A computational multiscale agent-based model for simulating spatio-temporal tumour immune response to PD1 and PDL1 inhibition; Gong C, Milberg O, Wang B, Vicini P, Narwal R, Roskos L, Popel AS; J R Soc Interface 2017; PDF
Crosstalk between stromal components and tumor cells of TNBC via secreted factors enhances tumor growth and metastasis; Jin K, Pandey NB, Popel AS; Oncotarget 2017; PDF
An agent-based model of triple-negative breast cancer: the interplay between chemokine receptor CCR5 expression, cancer stem cells, and hypoxia; Norton KA, Wallace T, Pandey NB, Popel AS; BMC Syst Biol 2017; PDF
Tyrosine kinase blocking collagen IV-derived peptide suppresses ocular neovascularization and vascular leakage; Silva RLE, Kanan Y, Mirando AC, Kim J, Shmueli RB, Lorenc VE, Fortmann SD, Sciamanna J, Pandey NB, Green JJ, Popel AS, Campochiaro PA; Sci Transl Med 2017; PDF
Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model; Zhao C, Isenberg JS, Popel AS; PLoS Comput Biol 2017; PDF