Selected Publications

Dynamics of tumor-associated macrophages in a quantitative systems pharmacology model of immunotherapy in triple-negative breast cancer; Hanwen Wang, Chen Zhao, Cesar A Santa-Maria, Leisha A Emens, Aleksander S Popel; Iscience 2022;
Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model; Alvaro Ruiz-Martinez, Chang Gong, Hanwen Wang, Richard J Sové, Haoyang Mi, Holly Kimko, Aleksander S Popel; PLoS computational biology 2022;
Systems biology of angiogenesis signaling: Computational models and omics; Yu Zhang, Hanwen Wang, Rebeca Hannah M Oliveira, Chen Zhao, Aleksander S Popel; WIREs mechanisms of disease 2022;
Multi-scale spatial analysis of the tumor microenvironment reveals features of cabozantinib and nivolumab efficacy in hepatocellular carcinoma; Haoyang Mi, Won Jin Ho, Mark Yarchoan, Aleksander S Popel; Frontiers in immunology 2022;
Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model; Richard J Sové, Babita K Verma, Hanwen Wang, Won Jin Ho, Mark Yarchoan, Aleksander S Popel; Journal for immunotherapy of cancer 2022;
Systems biology modeling of endothelial cell and macrophage signaling in angiogenesis in human diseases; Yu Zhang, Chen Zhao, Aleksander S Popel; The Vasculome, Academic Press 2022;
A transcriptome-informed QSP model of metastatic triple-negative breast cancer identifies predictive biomarkers for PD-1 inhibition; Theinmozhi Arulraj, Hanwen Wang, Leisha A Emens, Cesar A Santa-Maria, Aleksander S Popel; Science Advances 2023;
Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition; Hanwen Wang, Theinmozhi Arulraj, Holly Kimko, Aleksander S Popel; NPJ Precision Oncology 2023;
Vascular phenotyping of the invasive front in breast cancer using a 3D angiogenesis atlas; Akanksha Bhargava, Aleksander S Popel, Arvind P Pathak; Microvascular Research 2023;
Quantifying Intratumoral Heterogeneity and Immunoarchitecture Generated In-Silico by a Spatial Quantitative Systems Pharmacology Model; Mehdi Nikfar, Haoyang Mi, Chang Gong, Holly Kimko, Aleksander S Popel; Cancers 2023;
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces; Atul Deshpande, Melanie Loth, Dimitrios N Sidiropoulos, Shuming Zhang, Long Yuan, Alexander TF Bell, Qingfeng Zhu, Won Jin Ho, Cesar Santa-Maria, Daniele M Gilkes, Stephen R Williams, Cedric R Uytingco, Jennifer Chew, Andrej Hartnett, Zachary W Bent, Alexander V Favorov, Aleksander S Popel, Mark Yarchoan, Ashley Kiemen, Pei-Hsun Wu, Kohei Fujikura, Denis Wirtz, Laura D Wood, Lei Zheng, Elizabeth M Jaffee, Robert A Anders, Ludmila Danilova, Genevieve Stein-O’Brien, Luciane T Kagohara, Elana J Fertig; Cell Systems 2023;
Combining Multikinase Tyrosine Kinase Inhibitors Targeting the Vascular Endothelial Growth Factor and Cluster of Differentiation 47 Signaling Pathways Is Predicted to Increase the Efficacy of Antiangiogenic Combination Therapies; Yu Zhang, Aleksander S Popel, Hojjat Bazzazi; ACS Pharmacology & Translational Science 2023;
Anti-angiogenic collagen IV-derived peptide target engagement with αvβ3 and α5β1 in ocular neovascularization models; Raquel Lima e Silva, Adam C Mirando, Stephany Y Tzeng, Jordan J Green, Aleksander S Popel, Niranjan B Pandey, Peter A Campochiaro; Iscience 2023;
Using quantitative systems pharmacology modeling to optimize combination therapy of anti-PD-L1 checkpoint inhibitor and T cell engager; Samira Anbari, Hanwen Wang, Yu Zhang, Jun Wang, Minu Pilvankar, Masoud Nickaeen, Steven Hansel, Aleksander S Popel; Frontiers in Pharmacology 2023;
The tumor microenvironment and triple-negative breast cancer aggressiveness: shedding light on mechanisms and targeting; Natsuki Furukawa, Vered Stearns, Cesar A Santa-Maria, Aleksander S Popel; Expert opinion on therapeutic targets 2022;
Quantitative spatial profiling of immune populations in pancreatic ductal adenocarcinoma reveals tumor microenvironment heterogeneity and prognostic biomarkers; Haoyang Mi, Shamilene Sivagnanam, Courtney B Betts, Shannon M Liudahl, Elizabeth M Jaffee, Lisa M Coussens, Aleksander S Popel; Cancer research 2022;
Label cleaning multiple instance learning: Refining coarse annotations on single whole-slide images; Zhenzhen Wang, Carla Saoud, Sintawat Wangsiricharoen, Aaron W James, Aleksander S Popel, Jeremias Sulam; IEEE transactions on medical imaging 2022;
Dynamic multiscale regulation of perfusion recovery in experimental peripheral arterial disease: a mechanistic computational model; Chen Zhao, Joshua L Heuslein, Yu Zhang, Brian H Annex, Aleksander S Popel; Basic to Translational Science 2022;
Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response; Shuming Zhang, Chang Gong, Alvaro Ruiz-Martinez, Hanwen Wang, Emily Davis-Marcisak, Atul Deshpande, Aleksander S Popel, Elana J Fertig; Immunoinformatics 2021;
Predictive models of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer usingnuclear morphology and tissue architecture; Mi H, Bivalacqua TJ, Kates M, Seiler R, Black PC, Popel AS, Baras AS; Cell Reports Medicine 2021;
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway; Zhang Y, Kontos CD, Annex BH, Popel AS; 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; Zhang S, Gong C, Ruiz-Martinez A, Wang H, Davis-Marcisak E, Desphande A, Popel AS, Fertig EJ; ImmunoInformatics 2021;
A Spatial Quantitative Systems Pharmacology Platform spQSP-IO for Simulations of Tumor—Immune Interactions and Effects of Checkpoint Inhibitor Immunotherapy; Gong C, Ruiz-Martinez A, Kimko H, Popel AS; Cancers 2021;
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