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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 Aug 16;5:29. doi: 10.1038/s41540-019-0107-2. eCollection 2019.


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 Aug 2;9(1):11286. doi: 10.1038/s41598-019-47802-4.


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 Jul 30. pii: S1742-7061(19)30543-4. doi: 10.1016/j.actbio.2019.07.054. [Epub ahead of print]


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 Jun 24;21(5):79. doi: 10.1208/s12248-019-0350-x.


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 May 22;6(5):190366. doi: 10.1098/rsos.190366. eCollection 2019 May.


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 Mar 27;9(1):5276. doi: 10.1038/s41598-019-40888-w.


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 Apr 2;8(7):e011058. doi: 10.1161/JAHA.118.011058.


Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment.

Norton KA, Gong C, Jamalian S, Popel AS.

Processes (Basel). 2019 Jan;7(1). pii: 37. doi: 10.3390/pr7010037. Epub 2019 Jan 13.


Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases.

Zhao C, Zhang Y, Popel AS.

Int J Mol Sci. 2019 Jan 19;20(2). pii: E421. doi: 10.3390/ijms20020421. Review.


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 Feb 21;4(4). pii: 122043. doi: 10.1172/jci.insight.122043. eCollection 2019 Feb 21.


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 Jan 7;8:649. doi: 10.3389/fonc.2018.00649. eCollection 2018.


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 Oct 1;59(12):5266-5276. doi: 10.1167/iovs.17-23632.


Author Correction: 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 Sep 25;8(1):14563. doi: 10.1038/s41598-018-32598-6.


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 Oct 14;455:212-221. doi: 10.1016/j.jtbi.2018.06.029. Epub 2018 Jul 20.


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 May 30;9:644. doi: 10.3389/fphys.2018.00644. eCollection 2018.


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 Jun 14;20(1):54. doi: 10.1186/s13058-018-0981-3.


Modeling triple-negative breast cancer heterogeneity: Effects of stromal macrophages, fibroblasts and tumor vasculature.

Norton KA, Jin K, Popel AS.

J Theor Biol. 2018 Sep 7;452:56-68. doi: 10.1016/j.jtbi.2018.05.003. Epub 2018 May 8.


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 Apr;22(4):2086-2097. doi: 10.1111/jcmm.13565. Epub 2018 Feb 14. Review.


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 Jun;106(6):1753-1764. doi: 10.1002/jbm.a.36360. Epub 2018 Feb 23.


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 Jan 30;8(1):1854. doi: 10.1038/s41598-018-19758-4. Erratum in: Sci Rep. 2018 Sep 25;8(1):14563.


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. 2017 Sep 21;8(60):101520-101534. doi: 10.18632/oncotarget.21148. eCollection 2017 Nov 24.


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 Jul 21;8(36):60210-60222. doi: 10.18632/oncotarget.19417. eCollection 2017 Sep 1.


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 Sep;14(134). pii: 20170320. doi: 10.1098/rsif.2017.0320.


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 Jul 11;11(1):68. doi: 10.1186/s12918-017-0445-x.


Corrigendum: Inhibition of VEGFR2 Activation and Its Downstream Signaling to ERK1/2 and Calcium by Thrombospondin-1 (TSP1): In silico Investigation.

Bazzazi H, Isenberg JS, Popel AS.

Front Physiol. 2017 Mar 7;8:147. doi: 10.3389/fphys.2017.00147. eCollection 2017.


Inhibition of VEGFR2 Activation and Its Downstream Signaling to ERK1/2 and Calcium by Thrombospondin-1 (TSP1): In silico Investigation.

Bazzazi H, Isenberg JS, Popel AS.

Front Physiol. 2017 Feb 6;8:48. doi: 10.3389/fphys.2017.00048. eCollection 2017. Erratum in: Front Physiol. 2017 Mar 07;8:147.


Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells.

Bazzazi H, Popel AS.

PLoS Comput Biol. 2017 Feb 8;13(2):e1005332. doi: 10.1371/journal.pcbi.1005332. eCollection 2017 Feb.


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 Jan 18;9(373). pii: eaai8030. doi: 10.1126/scitranslmed.aai8030.


Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model.

Zhao C, Isenberg JS, Popel AS.

PLoS Comput Biol. 2017 Jan 3;13(1):e1005272. doi: 10.1371/journal.pcbi.1005272. eCollection 2017 Jan.


The Angiogenic Secretome in VEGF overexpressing Breast Cancer Xenografts.

Dore-Savard L, Lee E, Kakkad S, Popel AS, Bhujwalla ZM.

Sci Rep. 2016 Dec 20;6:39460. doi: 10.1038/srep39460.


Gene delivery nanoparticles to modulate angiogenesis.

Kim J, Mirando AC, Popel AS, Green JJ.

Adv Drug Deliv Rev. 2017 Sep 15;119:20-43. doi: 10.1016/j.addr.2016.11.003. Epub 2016 Nov 30. Review.


A multiscale computational model predicts distribution of anti-angiogenic isoform VEGF165b in peripheral arterial disease in human and mouse.

Chu LH, Ganta VC, Choi MH, Chen G, Finley SD, Annex BH, Popel AS.

Sci Rep. 2016 Nov 17;6:37030. doi: 10.1038/srep37030.


Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.

Yankeelov TE, An G, Saut O, Luebeck EG, Popel AS, Ribba B, Vicini P, Zhou X, Weis JA, Ye K, Genin GM.

Ann Biomed Eng. 2016 Sep;44(9):2626-41. doi: 10.1007/s10439-016-1691-6. Epub 2016 Jul 6. Review.


Endothelial cells decode VEGF-mediated Ca2+ signaling patterns to produce distinct functional responses.

Noren DP, Chou WH, Lee SH, Qutub AA, Warmflash A, Wagner DS, Popel AS, Levchenko A.

Sci Signal. 2016 Feb 23;9(416):ra20. doi: 10.1126/scisignal.aad3188.


Multiscale Modeling in the Clinic: Drug Design and Development.

Clancy CE, An G, Cannon WR, Liu Y, May EE, Ortoleva P, Popel AS, Sluka JP, Su J, Vicini P, Zhou X, Eckmann DM.

Ann Biomed Eng. 2016 Sep;44(9):2591-610. doi: 10.1007/s10439-016-1563-0. Epub 2016 Feb 17. Review.


Pharmacokinetics of Anti-VEGF Agent Aflibercept in Cancer Predicted by Data-Driven, Molecular-Detailed Model.

Finley SD, Angelikopoulos P, Koumoutsakos P, Popel AS.

CPT Pharmacometrics Syst Pharmacol. 2015 Nov;4(11):641-9. doi: 10.1002/psp4.12040. Epub 2015 Oct 9.


Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer.

Zhao C, Popel AS.

PLoS Comput Biol. 2015 Nov 20;11(11):e1004612. doi: 10.1371/journal.pcbi.1004612. eCollection 2015 Nov.


Computational drug repositioning for peripheral arterial disease: prediction of anti-inflammatory and pro-angiogenic therapeutics.

Chu LH, Annex BH, Popel AS.

Front Pharmacol. 2015 Aug 25;6:179. doi: 10.3389/fphar.2015.00179. eCollection 2015.


Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes.

Fertig EJ, Lee E, Pandey NB, Popel AS.

Sci Rep. 2015 Jul 15;5:12133. doi: 10.1038/srep12133.


Heterogeneity of chemokine cell-surface receptor expression in triple-negative breast cancer.

Norton KA, Popel AS, Pandey NB.

Am J Cancer Res. 2015 Mar 15;5(4):1295-307. eCollection 2015.


PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease.

Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS.

Physiol Genomics. 2015 Aug;47(8):331-43. doi: 10.1152/physiolgenomics.00125.2014. Epub 2015 Jun 9.


Crosstalk between cancer cells and blood endothelial and lymphatic endothelial cells in tumour and organ microenvironment.

Lee E, Pandey NB, Popel AS.

Expert Rev Mol Med. 2015 Jan 30;17:e3. doi: 10.1017/erm.2015.2. Review.


Inhibition of breast cancer growth and metastasis by a biomimetic peptide.

Lee E, Lee SJ, Koskimaki JE, Han Z, Pandey NB, Popel AS.

Sci Rep. 2014 Nov 20;4:7139. doi: 10.1038/srep07139.


Vasculature-specific MRI reveals differential anti-angiogenic effects of a biomimetic peptide in an orthotopic breast cancer model.

Kim E, Lee E, Plummer C, Gil S, Popel AS, Pathak AP.

Angiogenesis. 2015 Apr;18(2):125-36. doi: 10.1007/s10456-014-9450-5. Epub 2014 Nov 19.


A biomimetic collagen derived peptide exhibits anti-angiogenic activity in triple negative breast cancer.

Rosca EV, Penet MF, Mori N, Koskimaki JE, Lee E, Pandey NB, Bhujwalla ZM, Popel AS.

PLoS One. 2014 Nov 10;9(11):e111901. doi: 10.1371/journal.pone.0111901. eCollection 2014.


Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

Chu LH, Lee E, Bader JS, Popel AS.

PLoS One. 2014 Oct 16;9(10):e110871. doi: 10.1371/journal.pone.0110871. eCollection 2014.


Computational systems biology approaches to anti-angiogenic cancer therapeutics.

Finley SD, Chu LH, Popel AS.

Drug Discov Today. 2015 Feb;20(2):187-97. doi: 10.1016/j.drudis.2014.09.026. Epub 2014 Oct 5. Review.


Antiangiogenic cancer drug sunitinib exhibits unexpected proangiogenic effects on endothelial cells.

Norton KA, Han Z, Popel AS, Pandey NB.

Onco Targets Ther. 2014 Sep 9;7:1571-82. doi: 10.2147/OTT.S65055. eCollection 2014.


An agent-based model of cancer stem cell initiated avascular tumour growth and metastasis: the effect of seeding frequency and location.

Norton KA, Popel AS.

J R Soc Interface. 2014 Nov 6;11(100):20140640. doi: 10.1098/rsif.2014.0640.

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