Research output per year
Research output per year
- 1 - 50 out of 371 results
Search results
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2024
Chemokine-derived oncolytic peptide induces immunogenic cancer cell death and significantly suppresses tumor growth
Furukawa, N., Yang, W., Chao, A. R., Patil, A., Mirando, A. C., Pandey, N. & Popel, A. S., Dec 2024, In: Cell Death Discovery. 10, 1, 161.Research output: Contribution to journal › Article › peer-review
Open Access -
Eliciting the antitumor immune response with a conditionally activated PD-L1 targeting antibody analyzed with a quantitative systems pharmacology model
Ippolito, A., Wang, H., Zhang, Y., Vakil, V., Bazzazi, H. & Popel, A. S., Jan 2024, In: CPT: Pharmacometrics and Systems Pharmacology. 13, 1, p. 93-105 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Endothelial cells signaling and patterning under hypoxia: a mechanistic integrative computational model including the Notch-Dll4 pathway
Oliveira, R. H. D. M., Annex, B. H. & Popel, A. S., 2024, In: Frontiers in Physiology. 15, 1351753.Research output: Contribution to journal › Article › peer-review
Open Access -
Signaling-biophysical modeling unravels mechanistic control of red blood cell phagocytosis by macrophages in sickle cell disease
Zhang, Y., Qiang, Y., Li, H., Li, G., Lu, L., Dao, M., Karniadakis, G. E., Popel, A. S. & Zhao, C., Feb 1 2024, In: PNAS Nexus. 3, 2, pgae031.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
Anti-angiogenic collagen IV-derived peptide target engagement with αvβ3 and α5β1 in ocular neovascularization models
Lima e Silva, R., Mirando, A. C., Tzeng, S. Y., Green, J. J., Popel, A. S., Pandey, N. B. & Campochiaro, P. A., Feb 17 2023, In: iScience. 26, 2, 106078.Research output: Contribution to journal › Article › peer-review
Open Access -
A transcriptome-informed QSP model of metastatic triple-negative breast cancer identifies predictive biomarkers for PD-1 inhibition
Arulraj, T., Wang, H., Emens, L. A., Santa-Maria, C. A. & Popel, A. S., Jun 2023, In: Science Advances. 9, 26, eadg0289.Research output: Contribution to journal › Article › peer-review
Open Access -
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
Zhang, Y., Popel, A. S. & Bazzazi, H., May 12 2023, In: ACS Pharmacology and Translational Science. 6, 5, p. 710-726 17 p.Research output: Contribution to journal › Article › peer-review
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Erratum: Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces (Cell Systems (2023) 14(4) (285–301.e4), (S2405471223000807), (10.1016/j.cels.2023.03.004))
Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, S., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 others, Aug 16 2023, In: Cell Systems. 14, 8, p. 722 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Experiment-based computational model predicts that IL-6 classic and trans-signaling exhibit similar potency in inducing downstream signaling in endothelial cells
Song, M., Wang, Y., Annex, B. H. & Popel, A. S., Dec 2023, In: npj Systems Biology and Applications. 9, 1, 45.Research output: Contribution to journal › Article › peer-review
Open Access -
Gel-forming therapeutic peptide exhibits sustained delivery and efficacy in a mouse model of triple-negative breast cancer
Patil, A., Mirando, A. C., Liatsou, I., Sgouros, G., Popel, A. S. & Pandey, N. B., Nov 2023, In: Peptides. 169, 171075.Research output: Contribution to journal › Article › peer-review
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Generating immunogenomic data-guided virtual patients using a QSP model to predict response of advanced NSCLC to PD-L1 inhibition
Wang, H., Arulraj, T., Kimko, H. & Popel, A. S., Dec 2023, In: npj Precision Oncology. 7, 1, 55.Research output: Contribution to journal › Article › peer-review
Open Access -
Quantifying Intratumoral Heterogeneity and Immunoarchitecture Generated In-Silico by a Spatial Quantitative Systems Pharmacology Model
Nikfar, M., Mi, H., Gong, C., Kimko, H. & Popel, A. S., May 2023, In: Cancers. 15, 10, 2750.Research output: Contribution to journal › Article › peer-review
Open Access -
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence
Zhang, S., Yuan, L., Danilova, L., Mo, G., Zhu, Q., Deshpande, A., Bell, A. T. F., Elisseeff, J., Popel, A. S., Anders, R. A., Jaffee, E. M., Yarchoan, M., Fertig, E. J. & Kagohara, L. T., Dec 2023, In: Genome Medicine. 15, 1, 72.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces
Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, A. V., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 others, Apr 19 2023, In: Cell Systems. 14, 4, p. 285-301.e4Research output: Contribution to journal › Article › peer-review
Open Access -
Using quantitative systems pharmacology modeling to optimize combination therapy of anti-PD-L1 checkpoint inhibitor and T cell engager
Anbari, S., Wang, H., Zhang, Y., Wang, J., Pilvankar, M., Nickaeen, M., Hansel, S. & Popel, A. S., 2023, In: Frontiers in Pharmacology. 14, 1163432.Research output: Contribution to journal › Article › peer-review
Open Access -
Vascular phenotyping of the invasive front in breast cancer using a 3D angiogenesis atlas
Bhargava, A., Popel, A. S. & Pathak, A. P., Sep 2023, In: Microvascular Research. 149, 104555.Research output: Contribution to journal › Article › peer-review
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2022
Dynamic Multiscale Regulation of Perfusion Recovery in Experimental Peripheral Arterial Disease: A Mechanistic Computational Model
Zhao, C., Heuslein, J. L., Zhang, Y., Annex, B. H. & Popel, A. S., Jan 2022, In: JACC: Basic to Translational Science. 7, 1, p. 28-50 23 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Dynamics of tumor-associated macrophages in a quantitative systems pharmacology model of immunotherapy in triple-negative breast cancer
Wang, H., Zhao, C., Santa-Maria, C. A., Emens, L. & Popel, A. S., Aug 19 2022, In: iScience. 25, 8, 104702.Research output: Contribution to journal › Article › peer-review
Open Access -
Label Cleaning Multiple Instance Learning: Refining Coarse Annotations on Single Whole-Slide Images
Wang, Z., Saoud, C., Wangsiricharoen, S., James, A. W., Popel, A. S. & Sulam, J., Dec 1 2022, In: IEEE transactions on medical imaging. 41, 12, p. 3952-3968 17 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Multi-Scale Spatial Analysis of the Tumor Microenvironment Reveals Features of Cabozantinib and Nivolumab Efficacy in Hepatocellular Carcinoma
Mi, H., Ho, W. J., Yarchoan, M. & Popel, A. S., May 13 2022, In: Frontiers in immunology. 13, 892250.Research output: Contribution to journal › Article › peer-review
Open Access -
Quantitative Spatial Profiling of Immune Populations in Pancreatic Ductal Adenocarcinoma Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers
Mi, H., Sivagnanam, S., Betts, C. B., Liudahl, S. M., Jaffee, E. M., Coussens, L. M. & Popel, A. S., Dec 1 2022, In: Cancer Research. 82, 23, p. 4359-4372 14 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model
Ruiz-Martinez, A., Gong, C., Wang, H., Sove, R. J., Mi, H., Kimko, H. & Popel, A. S., Jul 2022, In: PLoS computational biology. 18, 7, e1010254.Research output: Contribution to journal › Article › peer-review
Open Access -
Systems biology modeling of endothelial cell and macrophage signaling in angiogenesis in human diseases
Zhang, Y., Zhao, C. & Popel, A. S., Jan 1 2022, The Vasculome: From Many, One. Elsevier, p. 163-172 10 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter
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Systems biology of angiogenesis signaling: Computational models and omics
Zhang, Y., Wang, H., Oliveira, R. H. M., Zhao, C. & Popel, A. S., Jul 1 2022, In: WIREs mechanisms of disease. 14, 4, e1550.Research output: Contribution to journal › Review article › peer-review
Open Access -
The tumor microenvironment and triple-negative breast cancer aggressiveness: shedding light on mechanisms and targeting
Furukawa, N., Stearns, V., Santa-Maria, C. A. & Popel, A. S., 2022, In: Expert opinion on therapeutic targets. 26, 12, p. 1041-1056 16 p.Research output: Contribution to journal › Review article › peer-review
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Virtual clinical trials of anti-PD-1 and anti-CTLA-4 immunotherapy in advanced hepatocellular carcinoma using a quantitative systems pharmacology model
Sové, R. J., Verma, B. K., Wang, H., Ho, W. J., Yarchoan, M. & Popel, A. S., Nov 2 2022, In: Journal for immunotherapy of cancer. 10, 11, e005414.Research output: Contribution to journal › Article › peer-review
Open Access -
2021
A data-driven computational model enables integrative and mechanistic characterization of dynamic macrophage polarization
Zhao, C., Medeiros, T. X., Sové, R. J., Annex, B. H. & Popel, A. S., Feb 19 2021, In: iScience. 24, 2, 102112.Research output: Contribution to journal › Article › peer-review
Open Access -
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, A. S., Aug 1 2021, In: Cancers. 13, 15, 3751.Research output: Contribution to journal › Article › peer-review
Open Access -
A systems biology model of junctional localization and downstream signaling of the Ang–Tie signaling pathway
Zhang, Y., Kontos, C. D., Annex, B. H. & Popel, A. S., Dec 2021, In: npj Systems Biology and Applications. 7, 1, 34.Research output: Contribution to journal › Article › peer-review
Open Access -
Peptides that immunoactivate the tumor microenvironment
Furukawa, N. & Popel, A. S., Jan 2021, In: Biochimica et Biophysica Acta - Reviews on Cancer. 1875, 1, 188486.Research output: Contribution to journal › Review article › peer-review
1 Scopus citations -
Predictive models of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer using nuclear morphology and tissue architecture
Mi, H., Bivalacqua, T. J., Kates, M., Seiler, R., Black, P. C., Popel, A. S. & Baras, A. S., Sep 21 2021, In: Cell Reports Medicine. 2, 9, 100382.Research output: Contribution to journal › Article › peer-review
Open Access -
Protocol for simulating macrophage signal transduction and phenotype polarization using a large-scale mechanistic computational model
Zhao, C. & Popel, A., Sep 17 2021, In: STAR Protocols. 2, 3, 100739.Research output: Contribution to journal › Article › peer-review
Open Access -
Quantitative Systems Pharmacology Modeling of PBMC-Humanized Mouse to Facilitate Preclinical Immuno-oncology Drug Development
Ma, H., Pilvankar, M., Wang, J., Giragossian, C. & Popel, A. S., Feb 12 2021, In: ACS Pharmacology and Translational Science. 4, 1, p. 213-225 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Quantitative systems pharmacology model predictions for efficacy of atezolizumab and nab-paclitaxel in triple-negative breast cancer
Wang, H., Ma, H., Sové, R. J., Emens, L. A. & Popel, A. S., Feb 12 2021, In: Journal for immunotherapy of cancer. 9, 2, e002100.Research output: Contribution to journal › Article › peer-review
Open Access -
2020
A Quantitative Systems Pharmacology Model of T Cell Engager Applied to Solid Tumor
Ma, H., Wang, H., Sove, R. J., Jafarnejad, M., Tsai, C. H., Wang, J., Giragossian, C. & Popel, A. S., Jul 1 2020, In: AAPS Journal. 22, 4, 85.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
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, R. J., Wang, J., Giragossian, C. & Popel, A. S., Aug 27 2020, In: Journal for immunotherapy of cancer. 8, 2, e001141.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
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, R. J., Jafarnejad, M., Rahmeh, S., Jaffee, E. M., Stearns, V., Torres, E. T. R., Connolly, R. M. & Popel, A. S., Feb 25 2020, In: Frontiers in Bioengineering and Biotechnology. 8, 141.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy
Malone, M. K., Smrekar, K., Park, S., Blakely, B., Walter, A., Nasta, N., Park, J., Considine, M., Danilova, L. V., Pandey, N. B., Fertig, E. J., Popel, A. S. & Jin, K., Jun 2 2020, In: Cancer Biology and Therapy. 21, 6, p. 560-569 10 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
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, E. J., Szalay, A. S., Jaffee, E. M., Stearns, V., Emens, L., Cimino-Mathews, A. M. & Popel, A. S., Oct 19 2020, In: Frontiers in Physiology. 11, 583333.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Immunoactivating the tumor microenvironment enhances immunotherapy as predicted by integrative computational model
Popel, A. S., Mar 3 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 9, p. 4447-4449 3 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access10 Scopus citations -
QSP-IO: A Quantitative Systems Pharmacology Toolbox for Mechanistic Multiscale Modeling for Immuno-Oncology Applications
Sové, R. J., Jafarnejad, M., Zhao, C., Wang, H., Ma, H. & Popel, A. S., Sep 1 2020, In: CPT: Pharmacometrics and Systems Pharmacology. 9, 9, p. 484-497 14 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Regulation of the tumor immune microenvironment and vascular normalization in TNBC murine models by a novel peptide
Mirando, A. C., Patil, A., Rafie, C. I., Christmas, B. J., Pandey, N. B., Stearns, V., Jaffee, E. M., Roussos Torres, E. T. & Popel, A. S., Jan 1 2020, In: OncoImmunology. 9, 1, 1760685.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Suppression of ocular vascular inflammation through peptide-mediated activation of angiopoietin-tie2 signaling
Mirando, A. C., E Silva, R. L., Chu, Z., Campochiaro, P. A., Pandey, N. B. & Popel, A. S., Jul 2 2020, In: International journal of molecular sciences. 21, 14, p. 1-20 20 p., 5142.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
2019
A collagen IV-derived peptide disrupts α5β1 integrin and potentiates Ang2/Tie2 signaling
Mirando, A. C., Shen, J., Silva, R. L. E., Chu, Z., Sass, N. C., Lorenc, V. E., Green, J. J., Campochiaro, P. A., Popel, A. S. & Pandey, N. B., Feb 21 2019, In: JCI Insight. 4, 4Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
A Computational Model of Neoadjuvant PD-1 Inhibition in Non-Small Cell Lung Cancer
Jafarnejad, M., Gong, C., Gabrielson, E., Bartelink, I. H., Vicini, P., Wang, B., Narwal, R., Roskos, L. & Popel, A. S., Sep 1 2019, In: AAPS Journal. 21, 5, 79.Research output: Contribution to journal › Article › peer-review
Open Access19 Scopus citations -
A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology
Zhao, C., Mirando, A. C., Sové, R. J., Medeiros, T. X., Annex, B. H. & Popel, A. S., 2019, In: PLoS computational biology. 15, 11, e1007468.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Angiopoietin-Tie Signaling Pathway in Endothelial Cells: A Computational Model
Zhang, Y., Kontos, C. D., Annex, B. H. & Popel, A. S., Oct 25 2019, In: iScience. 20, p. 497-511 15 p.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
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, R. B., Mirando, A. C., Tzeng, S. Y., Pandey, N. B., Ben-Akiva, E., Popel, A. S., Campochiaro, P. A. & Green, J. J., Oct 1 2019, In: Acta Biomaterialia. 97, p. 451-460 10 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
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, I. H., Wang, B., Vicini, P., Narwal, R., Roskos, L. & Popel, A. S., Dec 1 2019, In: Scientific reports. 9, 1, 11286.Research output: Contribution to journal › Article › peer-review
Open Access25 Scopus citations -
Dynamic changes in microvascular flow conductivity and perfusion after myocardial infarction shown by image-based modeling
Gkontra, P., El-Bouri, W. K., Norton, K. A., Santos, A., Popel, A. S., Payne, S. J. & Arroyo, A. G., 2019, In: Journal of the American Heart Association. 8, 7, e011058.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations