Systems Biology Laboratory

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SELECTED PUBLICATIONS (2000 - present)

Tan WH, Popel AS, Mac Gabhann F. Computational model of VEGFR2 pathway to ERK activation and modulation through receptor trafficking. Cell Signal. 2013 Dec;25(12):2496-510. [Abstract]

Lee E, Pandey NB, Popel AS. Pre-treatment of mice with tumor-conditioned media accelerates metastasis to lymph nodes and lungs: a new spontaneous breast cancer metastasis model. Clin Exp Metastasis. 2013 Aug 21. [Abstract]

Finley SD, Dhar M, Popel AS. Compartment model predicts VEGF secretion and investigates the effects of VEGF trap in tumor-bearing mice. Front Oncol. 2013 Jul 30;3:196. [Abstract]

Shmueli RB, Ohnaka M, Miki A, Pandey NB, Lima e Silva R, Koskimaki JE, Kim J, Popel AS, Campochiaro PA, Green JJ. Long-term suppression of ocular neovascularization by intraocular injection of biodegradable polymeric particles containing a serpin-derived peptide. Biomaterials. 2013 Oct;34(30):7544-51. [Abstract]

Tan WH, Popel AS, Mac Gabhann F. Computational Model of Gab1/2-Dependent VEGFR2 Pathway to Akt Activation. PLoS One. 2013 Jun 21;8(6):e67438. [Abstract]

Lee E, Koskimaki JE, Pandey NB, Popel AS. Inhibition of lymphangiogenesis and angiogenesis in breast tumor xenografts and lymph nodes by a peptide derived from transmembrane protein 45A. Neoplasia. 2013 Feb;15(2):112-24. [Abstract]

Imoukhuede PI, Dokun AO, Annex BH, Popel AS. Endothelial cell-by-cell profiling reveals the temporal dynamics of VEGFR1 and VEGFR2 membrane localization after murine hindlimb ischemia. Am J Physiol Heart Circ Physiol. 2013 Apr 15;304(8):H1085-93. [Abstract]

Koskimaki JE, Lee E, Chen W, Rivera CG, Rosca EV, Pandey NB, Popel AS. Synergy between a collagen IV mimetic peptide and a somatotropin-domain derived peptide as angiogenesis and lymphangiogenesis inhibitors. Angiogenesis. 2013 Jan;16(1):159-70. [Abstract]

Rivera CG, Chu LH, Popel AS, Bader JS. Chapter 9, Systems Biology in Cancer Research and Drug Discovery, in Applications of Network Bioinformatics for Cancer Angiogenesis, 2012, Part 2, 229-244. [Abstract]

Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the angiome: a global angiogenesis protein interaction network. Physiol Genomics. 2012 Oct 2;44(19):915-24. [Abstract]

Koskimaki, J.E., Lee, E., Chen, W., Rivera, C.G., Rosca, E.V., Pandey, N.B., Popel, A.S., Synergy between a collagen IV mimetic peptide and a somatotropin-domain containing peptide as angiogenesis and lymphangiogenesis inhibitors, Angiogenesis. 2012 Sep 29. [Abstract]

Koskimaki, J.E., Rosca, E.V., Rivera, C., Lee, E., Chen, W., Pandey, N.B., Popel, A.S., Serpin-derived peptides are anti-angiogenic and suppress breast tumor growth in vivo. Transl Oncol, 5:92-7, 2012 [Abstract]

Finley, S.D. and Popel, A.S. (2012)Predicting the effects of anti-angiogenic agents targeting specific VEGF isoforms. The AAPS Journal. 14(3), 500-509. [Abstract]

Kim E., Stamatelos S.K., Cebulla J., Bhujwalla Z.M., Popel A.S., Pathak A.P., Multiscale Imaging and Computational Modeling of Blood Flow in the Tumor Vasculature. Ann Biomed Eng. 2012. Epub 2012 May 9th. [Abstract]

Finley SD, Engel-Stefanini MO, Imoukhuede PI, Popel AS. Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies. BMC Syst Biol. 2011 Nov 21;5:193. [Abstract]

Yen P, Finley SD, Engel-Stefanini MO, Popel AS. A two-compartment model of VEGF distribution in the mouse. PLoS One. 2011;6(11):e27514. Epub 2011 Nov 8. [Abstract]

Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS. Analysis of VEGF-A Regulated Gene Expression in Endothelial Cells to Identify Genes Linked to Angiogenesis.PLoS One. 2011;6(9):e24887. Epub 2011 Sep 13. [Abstract]

Lee E, Rosca EV, Pandey NB, Popel AS. Small peptides derived from somatotropin domain-containing proteins inhibit blood and lymphatic endothelial cell proliferation, migration, adhesion and tube formation.Int J Biochem Cell Biol. 2011 Sep 6. [Epub ahead of print] [Abstract]

Rosca EV, Koskimaki JE, Pandey NB, Wolff AC, Popel AS. Development of a biomimetic peptide derived from collagen IV with anti-angiogenic activity in breast cancer.Cancer Biol Ther. 2011 Nov 1;12(9). [Epub ahead of print] [Abstract]

Rivera CG, Rosca EV, Pandey NB, Koskimaki JE, Bader JS, Popel AS. Novel Peptide-Specific Quantitative Structure-Activity Relationship (QSAR) Analysis Applied to Collagen IV Peptides with Antiangiogenic Activity. J Med Chem. 2011 Oct 13;54(19):6492-500. Epub 2011 Sep 13. [Abstract]

Rivera CG, Bader JS, Popel AS. Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins. Ann Biomed Eng. 2011 Aug;39(8):2213-22. Epub 2011 May 18. [Abstract]

Vempati P, Popel AS, Mac Gabhann F. Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis. BMC Syst Biol. 2011 May 2;5:59. [Abstract]

Rosca EV, Koskimaki JE, Rivera CG, Pandey NB, Tamiz AP, Popel AS. Anti-angiogenic peptides for cancer therapeutics. Curr Pharm Biotechnol. 2011 Aug;12(8):1101-16. Review. [Abstract]

Liu G, Qutub AA, Vempati P, Mac Gabhann F, Popel AS. Module-based multiscale simulation of angiogenesis in skeletal muscle. Theor Biol Med Model. 2011 Apr 4;8:6. [Abstract]

Stefanini MO, Qutub AA, Mac Gabhann F, Popel AS. Computational models of VEGF-associated angiogenic processes in cancer. Math Med Biol. 2011 Sep 22. [Epub ahead of print] [Abstract]

Imoukhuede PI, Popel AS. Quantification and cell-to-cell variation of vascular endothelial growth factor receptors. Exp Cell Res. 2010 Dec 23. [Epub ahead of print] [Abstract]

Stefanini MO, Wu FT, Mac Gabhann F, Popel AS. Increase of plasma VEGF after intravenous administration of bevacizumab is predicted by a pharmacokinetic model. Cancer Res. 2010 Dec 1;70(23):9886-94. Epub 2010 Nov 30. [Abstract]

Fedosov DA, Caswell B, Popel AS, Karniadakis GE. Blood flow and cell-free layer in microvessels. Microcirculation. 2010 Nov;17(8):615-28. doi: 10.1111/j.1549-8719.2010.00056.x. [Abstract]

Waters SL, Alastruey J, Beard DA, Bovendeerd PH, Davies PF, Jayaraman G, Jensen OE, Lee J, Parker KH, Popel AS, Secomb TW, Siebes M, Sherwin SJ, Shipley RJ, Smith NP, van de Vosse FN. Theoretical models for coronary vascular biomechanics: Progress & challenges. Prog Biophys Mol Biol. 2010 Oct 30. [Epub ahead of print] [Abstract]

Mac Gabhann F, Qutub AA, Annex BH, Popel AS. Systems biology of pro-angiogenic therapies targeting the VEGF system. Wiley Interdiscip Rev Syst Biol Med. 2010 Nov-Dec;2(6):694-707. [Abstract]

Mac Gabhann F, Annex BH, Popel AS. Gene therapy from the perspective of systems biology. Curr Opin Mol Ther. 2010 Oct;12(5):570-7. [Abstract]

Popel AS, Hunter PJ. Systems biology and Physiome Projects. Wiley Interdiscip Rev Syst Biol Med. 2009 Sep-Oct;1(2):153-8. [Abstract]

Vempati P, Mac Gabhann F, Popel AS. Quantifying the proteolytic release of extracellular matrix-sequestered VEGF with a computational model. PLoS One. 2010 Jul 29;5(7):e11860. [Abstract]

Wu FT, Stefanini MO, Mac Gabhann F, Kontos CD, Annex BH, Popel AS. VEGF and soluble VEGF receptor-1 (sFlt-1) distributions in peripheral arterial disease: an in silico model. Am J Physiol Heart Circ Physiol. 2010 Jun;298(6):H2174-91. Epub 2010 Apr 9. [Abstract]

J.E. Koskimaki, E.D. Karagiannis, B.C.Tang, H. Hammers, D.N. Watkins, R. Pili, A.S. Popel., Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model. BMC Cancer. 2010 Feb 1;10:29. [Abstract],[Full Text(pdf)]

M.O. Stefanini, F.T. Wu, F.M. Gabhann, A.S. Popel, The presence of VEGF receptors on the luminal surface of endothelial cells affects VEGF distribution and VEGF signaling. PLoS Comput Biol. 2009 Dec;5(12):e1000622. Epub 2009 Dec 24. [Abstract],[Full Text(pdf)]

J.E. Koskimaki, E.D. Karagiannis, E.V. Rosca, F. Vesuna, P.T. Jr Winnard, V. Raman, Z.M. Bhujwalla, A.S. Popel, Peptides derived from type IV collagen, CXC chemokines, and thrombospondin-1 domain-containing proteins inhibit neovascularization and suppress tumor growth in MDA-MB-231 breast cancer xenografts. Neoplasia. 2009 Dec;11(12):1285-91 [Abstract],[Full Text(pdf)]

K.R. Schumacher, A.S. Popel, B Anvari, W.E Brownell, A.A. Spector., Computational analysis of the tether-pulling experiment to probe plasma membrane-cytoskeleton interaction in cells. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4):041905. Epub. [Abstract],[Full Text(pdf)]

F.T. Wu, M.O. Stefanini, F.M. Gabhann, C.D. Kontos, B.H. Annex, A.S. Popel, Modeling of growth factor-receptor systems from molecular-level protein interaction networks to whole-body compartment models. Methods Enzymol. 2009 467:461-97 [Abstract],[Full Text(pdf)]

F.T. Wu, M.O. Stefanini, F.M. Gabhann, C.D. Kontos, B.H. Annex, A.S. Popel, A systems biology perspective on sVEGFR1: its biological function, pathogenic role and therapeutic use. J Cell Mol Med. 2009 Oct 16, Epub ahead of print [Abstract],[Full Text(pdf)],

B Chung, S. Kim, P.C. Johnson, A.S. Popel, Computational fluid dynamics of aggregating red blood cells in postcapillary venules. Comput Methods Biomech Biomed Engin. 2009;12(4):385-97. [Abstract],[Full Text(pdf)]

K. Chen, A.S. Popel, Nitric oxide production pathways in erythrocytes and plasma. Biorheology. 2009;46(2):107-19. [Abstract],[Full Text(pdf)]

F.T. Wu, M.O. Stefanini, F. Mac Gabhann, A.S. Popel, A compartment model of VEGF distribution in humans in the presence of soluble VEGF receptor-1 acting as a ligand trap. PloS ONE. 2009;4(4):e5108. Epub 2009 Apr 8. [Abstract],[Full Text(pdf)]

F.T. Wu, M.O. Stefanini, F. Mac Gabhann, C.D. Kontos, B.H. Annex, A.S. Popel, A computational kinetic model of VEGF trapping by soluble VEGF receptor-1: Effects of transendothelial and lymphatic macromolecular transport. Physiol Genomics. 2009 Apr 7. [Epub ahead of print] [Abstract],[Full Text(pdf)]

J. Zhang, P.C. Johnson, A.S. Popel, Effects of erythrocyte deformability and aggregation on the cell free layer and apparent viscosity of microscopic blood flows. Microvasc Res. 2009 Feb 4. [Epub ahead of print] [Abstract],[Full Text(pdf)]

M.D. Cano, E. Karagiannis,M Soliman, B Bakir,W Zhuang,A.S. Popel,P. Gehlbach, A Peptide Derived from Type 1 Thrombospondin Repeat-containing Protein WISP-1 Inhibits Corneal and Choroidal Neovascularization.Invest Ophthalmol Vis Sci. 2009 Mar 11. [Epub ahead of print] [Abstract],[Full Text(pdf)]

K. Chen, R.N. Pittman, A.S. Popel, hemorrhagic shock and nitric oxide release from erythrocytic nitric oxide synthase: A quantitative analysis. Microvasc Res 2009 Mar 10. [Epub ahead of print] [Abstract],[Full Text(pdf)]

A.A. Qutub, F. Mac Gabhann, E.D. Karagiannis; P. Vempati, A.S. Popel, Multiscale models of angiogenesis.Engineering in Medicine and Biology Magazine, IEEE, 28(2):14-31 2009[Abstract],[Full Text(pdf)]

A.A. Qutub, G. Liu, P. Vempati, A.S. Popel, Integration of angiogenesis modules at multiple scales: from molecular to tissue. Pac Symp Biocomput. 2009:316-27 [Abstract],[Full Text(pdf)]

A.A. Qutub and A.S. Popel, Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting. BMC Syst Biol.Jan 26 3(1):13. 2009 [Abstract],[Full Text(pdf)]

E.D. Karagiannis, A.S. Popel, A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells. Proc Natl Acad Sci U S A. Sep 16;105(37):13775-80. 2008 Epub 2008 Sep 9, [Abstract],[Full Text(pdf)]

M.O.Stefanini, F.T.Wu, F. Mac Gabhann, A.S.Popel, A compartment model of VEGF distribution in blood, healthy and diseased tissues.BMC Syst Biol. Aug 19;2(1):77. 2008 [Abstract],[Full Text(pdf)]

K. Chen, B. Piknova, R.N. Pittman, A.N. Schechter and A.S. Popel, Nitric oxide from nitrite reduction by hemoglobin in the plasma and erythrocytes. Nitric Oxide, 18 (1):47-60.2008a. [Abstract],[Full Text(pdf)]

K. Chen, R.N. Pittman and A.S. Popel, Nitric oxide in the vasculature: where does it come from and where does it go? A quantitative perspective. Antioxid Redox Signal, 10 (7):1185-1198.2008b [Abstract],[Full Text(pdf)]

A.M. Demetriades, T. Deering, H. Liu, L. Lu, P. Gehlbach, J.D. Packer, F.M. Gabhann, A.S. Popel, L.L Wei and P.A. Campochiaro, Trans-scleral delivery of antiangiogenic proteins. J Ocul Pharmacol Ther, 24 (1):70-79. 2008 [Abstract],[Full Text(pdf)]

F.M. Gabhann, and A.S. Popel., Systems Biology of Vascular Endothelial Growth Factors. Microcirculation, Nov;15(8):715-38 2008 [Abstract],[Full Text(pdf)]

E.D. Karagiannis and A.S. Popel, Novel anti-angiogenic peptides derived from ELR-containing CXC chemokines. J Cell Biochem, 104 (4):1356-1363, 2008 [Abstract], [Full Text(pdf)]

A.A. Qutub and A.S. Popel, Reactive Oxygen Species Regulate Hypoxia-Inducible Factor HIF1{alpha} Differentially in Cancer and Ischemia. Mol Cell Biol. 28(16):5106-19 2008 Epub Jun 16 [Abstract],[FullText(pdf)]

K.R. Schumacher, A.S. Popel, B. Anvari, W.E. Brownell, and A.A. Spector, Modeling the mechanics of tethers pulled from the cochlear outer hair cell membrane. J Biomech Eng, 130 (3):031007, 2008. [Abstract],[Full Text(pdf)]

M. Sharan, E.P.Vovenko, A. Vadapalli, A.S. Popel and R.N. Pittman. Experimental and theoretical studies of oxygen gradients in rat pial microvessels. J Cereb Blood Flow Metab., 28(9): 1957-604 2008. [Abstract],[Full Text(pdf)]

J. Zhang, P.C. Johnson, A.S. Popel. Red blood cell aggregation and dissociation in shear flows simulated by lattice Boltzmann method. J. Biomech., 41 (1):47-55, 2008. [Abstract], [Full Text (pdf)]

C. Kut, F. Mac Gabhann, A.S. Popel. Where is VEGF in the body? A meta-analysis of VEGF distribution in cancer. Br. J. Cancer. 97: 978-985, 2007. [Abstract], [Full Text (pdf)], [Supplement (pdf)]

Z. Liao, S. Feng, A.S. Popel, W.E. Brownell, A.A. Spector. Outer hair cell active force generation in the cochlear environment. J. Acoust. Soc. Am. 122: 2215-2225, 2007. [Abstract], [Full Text (pdf)]

J.W. Ji, F. Mac Gabhann, A.S. Popel. Skeletal Muscle VEGF Gradients in Peripheral Arterial Disease: Simulations of Rest and Exercise. Am. J. Physiol. Heart Circ. Physiol. Dec; 293(6): H3740-9 Epub Sep 21, 2007. [Abstract], [Full Text (pdf)]

P. Vempati, E.D. Karagiannis, A.S. Popel. A biochemical model of the matrix metalloproteinase 9 activation and inhibition. J. Biol. Chem. Dec 28; 282(52): 37585 - 37596, 2007. [Abstract], [Full Text (pdf)]

S. Hazarika, A.O. Dokun, Y. Li, A.S. Popel, C.D. Kontos, B.H. Annex. Impaired Angiogenesis Following Hindlimb Ischemia in Type 2 Diabetes Mellitus. Differential Regulation of Vascular Endothelial Growth Factor Receptor 1 and Soluble VEGFR-1. Circ. Res. Oce 26; 101(9): 948-56, 2007. Epud 2007 Sep 6 [Abstract], [Full Text (pdf)]

A.A. Qutub, A.S. Popel. Three autocrine feedback loops determine HIF1alpha expression in chronic hypoxia. Biochim. Biophys. Acta. Oct; 1773(10):1511-1525 2007 Epub Jul. 20 [Abstract], [Full Text (pdf)]

E.D. Karagiannis, A.S. Popel. Peptides derived from type I thrombospondin repeat-containing proteins of the CCN family inhibit proliferation and migration of endothelial cells. Int. J. Biochem. Cell. Biol. 39: 2314-2323, 2007. [Abstract], [Full Text (pdf)]

N.M. Tsoukias, D. Goldman, A. Vadapalli, R.N. Pittman, A.S. Popel. A computational model of oxygen delivery by hemoglobin-based oxygen carriers in three-dimensional microvascular networks. J. Theor. Biol. 248: 657-674, 2007. [Abstract], [Full Text (pdf)]

S. Kim, J. Zhen, A.S. Popel, M. Intaglietta, P.C. Johnson. Contributions of collision rate and collision efficiency to erythrocyte aggregation in postcapillary venules at low flow rates. Am. J. Physiol. Heart Circ.Physiol Sep; 293(3): H1947-54 2007 Epub Jul 6. [Abstract], [Full Text (pdf)]

K. Chen, R.N. Pittman, A.S. Popel. Vascular Smooth Muscle NO Exposure from Intraerythrocytic SNOHb: A Mathematical Model. Antioxid Redox Signal Antioxid. Redox. Signal. 9: 1097-1110, 2007. [Abstract], [Full Text (pdf)]

E.D. Karagiannis, A.S. Popel. Anti-angiogenic peptides identified in thrombospondin type I domains. Biochem. Biophys. Res. Commun. 359: 63-69, 2007. [Abstract], [Full Text (pdf)]

S. Kim, R.L. Kong, A.S. Popel, M. Intaglietta, P.C. Johnson. Temporal and spatial variations of cell-free layer width in arterioles. Am. J. Physiol. Heart Circ. Physiol. 293: H1526-H1535, 2007. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, A.S. Popel. Dimerization of VEGF receptors and implications for signal transduction: A computational study. Biophys. Chem. 128: 125-139, 2007. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, A.S. Popel. Protein transport to choroid and retina following periocular injection: theoretical and experimental study.. Ann. Biomed. Eng. Apr; 35(4): 615-30, 2007 Epub Feb.3. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, J.W. Ji, A.S. Popel. Multi-scale Computational Models of Pro-angiogenic Treatments in Peripheral Arterial Disease. Ann. Biomed. Eng. 35: 982-994, 2007. [Abstract], [Full Text (pdf)]

M. Zhi, J.T. Ratnanather, E. Ceyhan, A.S. Popel, W.E. Brownell. Hypotonic swelling of salicylate-treated cochlear outer hair cells. Hear. Res. 228: 95-104, 2007. [Abstract], [Full Text (pdf)]

B. Das, J.J. Bishop, S. Kim, H.J. Meiselman, P.C. Johnson, A.S. Popel. Red blood cell velocity profiles in skeletal muscle venules at low flow rates are described by the Casson model. Clin. Hemorheol. Microcirc. 36:217-33, 2007. [Abstract], [Full Text (pdf)]

K. Chen, A.S. Popel. Vascular and perivascular nitric oxide release and transport: biochemical pathways of neuronal nitric oxide synthase (NOS1) and endothelial nitric oxide synthase (NOS3). Free Radic. Biol. Med. 42: 811-822, 2007. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, A.M. Demetriades, T. Deering, J.D. Packer, S.M. Shah, E. Duh, P.A. Campochiaro, A.S. Popel. Protein transport to choroid and retina following periocular injection: theoretical and experimental study. Ann. Biomed. Eng. 35: 615-630, 2007. [Abstract], [Full Text (pdf)]  

E.D. Karagiannis, A.S. Popel. Identification of novel short peptides derived from the alpha 4, alpha 5, and alpha 6 fibrils of type IV collagen with anti-angiogenic properties. Biochem Biophys Res Commun. 354: 434-439, 2007. [Abstract], [Full Text (pdf)]

B. Chung, P.C. Johnson, A.S. Popel. Application of Chimera grid to modelling cell motion and aggregation in a narrow tube. Int. J. Numer. Meth. Fluids 53: 105-128, 2007. [Abstract], [Full Text (pdf)]

F.M. Gabhann, A.S. Popel. Interactions of VEGF isoforms with VEGFR-1, VEGFR-2, and neuropilin in vivo: a computational model of human skeletal muscle. Am. J. Physiol. Heart. Circ. Physiol. 292: H459-H474, 2007. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, J.W. Ji, A.S. Popel. VEGF gradients, receptor activation, and sprout guidance in resting and exercising skeletal muscle. J. Appl. Physiol. 102: 722-734, 2007. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, A.S. Popel. Targeting Neuropilin-1 to Inhibit VEGF Signaling in Cancer: Comparison of Therapeutic Approaches. PLoS Comp. Biol. 2: 1649-1662, 2006. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, J.W. Ji, A.S. Popel. Computational model of vascular endothelial growth factor spatial distribution in muscle and pro-angiogenic cell therapy. PLoS Comp. Biol. 2: 1107-1120, 2006. [Abstract], [Full Text (pdf)]

S. Kim, R.L. Kong, A.S. Popel, M. Intaglietta, P.C. Johnson. A computer-based method for determination of the cell-free layer width in microcirculation. Microcirculation 13: 199-207, 2006. [Abstract], [Full Text (pdf)]

A.A. Qutub, A.S. Popel. A computational model of intracellular oxygen sensing by hypoxia-inducible factor HIF1 alpha.
J. Cell. Sci. 119: 3467-80, 2006. [Abstract], [Full Text (pdf)]

K. Chen, A.S. Popel. Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells.
Free Radic. Biol. Med. 41: 668-680, 2006. [Abstract], [Full Text (pdf)]

S. Kim, A.S. Popel, M. Intaglietta, and P.C. Johnson. Effect of erythrocyte aggregation at normal human levels on functional capillary density in rat spinotrapezius muscle. Am. J. Physiol. Heart Circ. Physiol. 290: H941-H947, 2006. [Abstract], [Full Text (pdf)]

J.W. Ji, N.M. Tsoukias, D. Goldman, and A.S. Popel. A computational model of oxygen transport in skeletal muscle for sprouting and splitting modes of angiogenesis. J. Theor. Biol. 241: 94-108. [Abstract], [Full Text (pdf)]

M. Kavdia and A.S. Popel. Venular endothelium derived NO can affect paired arteriole:  a computational model. Am. J. Physiol. Heart Circ. Physiol. 290: H716-H723, 2006. [Abstract], [Full Text (pdf)]

E.D. Karagiannis and A.S. Popel. Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: Insights from a computational model. J. Theor. Biol., 238:124-145, 2006. [Abstract], [Full Text (pdf)]

D.R. Murdock, S.A. Ermilov, A.A. Spector, A.S. Popel, W.E. Brownell, and B. Anvari. Effects of chlorpromazine on mechanical properties of the outer hair cell plasma membrane. Biophys. J. 89:4090-4095, 2005. [Abstract], [Full Text (pdf)]

Z. Liao, A.S. Popel, W.E. Brownell, and A.A. Spector. Effect of voltage-dependent membrane properties on active force generation in cochlear outer hair cell. J. Acoust. Soc. Am. 118: 3737-3746, 2005. [Abstract], [Full Text (pdf)]

A.A. Spector, A.S. Popel, R.A. Eatock, and W.E. Brownell. Mechanosensitive channels in the lateral wall can enhance the cochlear outer hair cell frequency response. Ann. Biomed. Eng. 33:991-1002, 2005. [Abstract], [Full Text (pdf)]

F. Mac Gabhann, M.T. Yang, A.S. Popel. Monte Carlo simulations of VEGF binding to cell surface receptors in vitro. Biochimica et Biophysica Acta - Molecular Cell Research, 1746:95-107, 2005. [Abstract], [Full Text (pdf)]

Z. Liao, A.S. Popel, W.E. Brownell, and A.A. Spector. High-frequency force generation in the constrained cochlear outer hair cell: A model study. J. Assoc. Res. Otolaryngol. (JARO), 6: 378-389, 2005. [Abstract], [Full Text (pdf)]

P. Bagchi, P.C. Johnson, and A.S. Popel. Computational fluid dynamic simulation of aggregation of deformable cells in a shear flow. J. Biomech. Eng., 127:1070-1080, 2005. [Abstract], [Full Text (pdf)]

A.S. Popel. Mathematical and Computational Models of the Microcirculation. In: Microvascular Research: Biology and Pathology. D. Shepro, Editor-in-Chief; P.A. D'Amore, C.M. Black, J.G.N. Garcia, D.N. Granger, C. Haudenschild, H.B. Hechtman,  R.K. Jain, and J.A. Madri, Editors, Chapter 164, pp.1123-1129, Elsevier, New York, 2005. 

Z. Liao, A.S. Popel, W.E. Brownell, and A.A. Spector. Modeling high-frequency electromotility of cochlear outer hair cell in microchamber experiment. J. Acoust. Soc. Am. 117: 2147-2157, 2005. [Abstract], [Full Text (pdf)

F. Mac Gabhann and A.S. Popel. Differential binding of VEGF isoforms to VEGF Receptor 2 in the presence of Neuropilin-1: a computational model. Am. J. Physiol. (Heart Circ. Physiol.). 288(6):H2851-60, 2005. [Abstract], [Full Text (pdf)

A.S. Popel and P.C. Johnson. Microcirculation and hemorheology. Ann. Rev. Fluid Mechanics, 37:43-69, 2005. [Full Text (pdf)]

R.J. Filion and A.S. Popel. Intracoronary administration of FGF-2: a computational model of myocardial deposition and retention. Am. J. Physiol. (Heart Circ. Physiol.), 288:H263-279, 2005. [Abstract], [Full Text (pdf)

S. Kim, A.S. Popel, M. Intaglietta, and P.C. Johnson. Aggregate formation of erythrocytes in postcapillary venules. Am. J. Physiol. (Heart Circ. Physiol.), 288:H584-90, 2005. [Abstract], [Full Text (pdf)

E.D. Karagiannis and A. S. Popel. A theoretical model of type I collagen proteolysis by matrix metalloproteinase (MMP) 2 and membrane type 1 MMP in the presence of tissue inhibitor of metalloproteinase 2. J. Biol. Chem. 279:39105-39114, 2004. [Abstract], [Full Text (pdf)]

A.S. Popel, M. Kavdia, and N.M. Tsoukias. Effect of hemoglobin-based blood substitutes on nitric oxide transport: Mathematical models. In: Artificial Oxygen Carrier: Its Frontline. K. Kobayashi, Ed. Springer Verlag, Tokyo, 2004.

F. Mac Gabhann and A.S. Popel.  Model of competitive binding of vascular endothelial growth factor and placental growth factor to VEGF receptors on endothelial cells. Am. J. Physiol. (Heart Circ. Physiol.), 286:H153-164, 2004. [Abstract], [Full Text (pdf)]

J.J. Bishop, P.R. Nance, A.S. Popel, M. Intaglietta, and P.C. Johnson. Relationship between erythrocyte aggregate size and flow rate in skeletal muscle venules. Am. J. Physiol. (Heart Circ. Physiol.), 286:H113-120, 2004. [Abstract], [Full Text (pdf)]

N.M. Tsoukias, M. Kavdia, and A.S. Popel. A theoretical model of nitric oxide transport in arterioles: Frequency vs amplitude dependent control of cGMP production. Am. J. Physiol. (Heart Circ. Physiol.), 286:H1043-H1056, 2004. [Abstract], [Full Text (pdf)]

M. Kavdia and A.S. Popel. Contribution of nNOS and eNOS derived NO to microvascular smooth muscle NO exposure. J. Appl. Physiol., 97:293-301, 2004. [Abstract], [Full Text (pdf)]

R.J. Filion and A.S. Popel. A reaction-diffusion model of basic fibroblast growth factor interactions with cell surface receptors. Ann. Biomed. Eng., 32:645-663, 2004. [Abstract], [Full Text (pdf)]

A.S. Popel. Biomechanical Measurements in Cells. 2004 McGraw-Hill Yearbook of Science and Technology, McGraw-Hill, New York, pp. 37-40.

A.A. Spector, W.E. Brownell, and A.S. Popel. Effect of outer hair cell piezoelectricity on high-frequency receptor potentials. J. Acoust. Soc. Am., 113:453-461, 2003. [Abstract], [Full Text (pdf)]

A.S. Popel, D. Goldman, and A. Vadapalli. Modeling of oxygen diffusion from the blood vessels to intracellular organelles. Adv. Exp. Med. Biol., 530:485-495, 2003. [Abstract]

M. Kavdia and A.S. Popel. Wall shear stress differentially affects NO level in arterioles for volume expanders & Hb-based O2 carriers. Microvasc. Res., 66:49-58, 2003. [Abstract], [Full Text (pdf)]

A.A. Spector, W.E. Brownell, and A.S. Popel. Piezoelectric properties enhance outer hair cell high-frequency response. In: The Biophysics of the Cochlea: From Molecules to Models. A.W. Gummer, Ed., World Scientific, Singapore, 2003, pp.152-160.

N.M. Tsoukias and A.S. Popel. A model of nitric oxide capillary exchange. Microcirculation, 10: 479-495, 2003. [Abstract], [Full Text (pdf)]

M. Kavdia, R.N. Pittman and A.S. Popel. Theoretical analysis of the effects of blood substitute affinity and cooperativity on organ oxygen transport. J. Appl. Physiol., 93:2122-2128, 2002. [Abstract], [Full Text (pdf)]

J.J. Bishop, A.S. Popel, M. Intaglietta, and P.C. Johnson. Effect of aggregation and shear rate on the dispersion of red blood cells flowing in venules. Am. J. Physiol. (Heart Circ. Physiol.), 283:H1985-H1996, 2002. [Abstract], [Full Text (pdf)]

M. Sharan and A.S. Popel. A compartmental model for oxygen transport in brain microcirculation in the presence of blood substitutes. J. Theor. Biol., 216: 479-500, 2002. [Abstract], [Full Text (pdf)]

N.M. Tsoukias and A.S. Popel. Erythrocyte consumption of nitric oxide in the presence and absence of plasma-based hemoglobin. Am. J. Physiol. (Heart Circ. Physiol.), 282: H2265-2277, 2002. [Abstract], [Full Text (pdf)]

M. Kavdia, N.M. Tsoukias, and A.S. Popel. A model of nitric oxide diffusion in an arteriole: Impact of hemoglobin-based blood substitutes. Am. J. Physiol. (Heart Circ. Physiol.), 282: H2245-2253, 2002. [Abstract], [Full Text (pdf)]

A.A. Spector, M. Ameen, P.G. Charalambides, and A.S. Popel. Nanostructure, effective properties, and deformation pattern of the cochlear outer hair cell cytoskeleton. J. Biomech. Eng., 124:180-187, 2002. [Abstract], [Full Text (pdf)]

A. Vadapalli, D. Goldman, and A.S. Popel. Calculations of oxygen transport by red blood cells and hemoglobin solutions in capillaries. Artificial Cells, Blood Substitutes, Immobilization Biotechnology, 30: 157-188, 2002. [Abstract], [Full Text (pdf)]

D.M. Wootton, A.S. Popel, and B.R. Alevriadou. An experimental and theoretical study on the dissolution of mural fibrin clots by tissue-type plasminogen activator. Biotechnology and Bioengineering, 77: 405-419, 2002. [Abstract], [Full Text (pdf)]

M. Sharan and A.S. Popel. A two-phase model for blood flow in narrow tubes with increased viscosity near the wall. Biorheology, 38: 415-428, 2001. [Abstract], [Full Text (pdf)]

J.J. Bishop, A.S. Popel, M. Intaglietta, and P.C. Johnson. Rheological effects of red blood cell aggregation in the venous network: a review of recent studies. Biorheology, 38:263-274, 2001. [Abstract], [Full Text (pdf)]

W.E. Brownell, A.A. Spector, R.M. Raphael, and A.S. Popel. Micro- and nanomechanics of the cochlear outer hair cell. Annu. Rev. Biomed. Eng., 3: 169-194, 2001.[Abstract], [Full Text (pdf)]

J.J. Bishop, A.S. Popel, M. Intaglietta, and P.C. Johnson. Effects of erythrocyte aggregation and venous network geometry on red blood cell axial migration. Am. J. Physiol. (Heart Circ. Physiol.), 281: H939-950, 2001. [Abstract], [Full Text (pdf)]

J.J. Bishop, P.R. Nance, A.S. Popel, M. Intaglietta, and P.C. Johnson. Erythrocyte margination and sedimentation in skeletal muscle venules. Am. J. Physiol. (Heart Circ. Physiol.), 281: H951-958, 2001. [Abstract], [Full Text (pdf)]

D. Goldman and A.S. Popel. A computational study of the effect of vasomotion on oxygen transport from capillary networks. J. Theor. Biol. 209:189-199, 2001. [Abstract], [Full Text (pdf)]

A.A. Spector, M. Ameen, and A.S. Popel. Simulation of motor-driven outer hair cell electromotility. Biophys. J., 81:11-24, 2001. [Abstract], [Full Text (pdf)]

J.J. Bishop, P.R. Nance, A.S. Popel, M. Intaglietta, and P.C. Johnson. Effect of erythrocyte aggregation on velocity profiles in skeletal muscle venules. Am. J. Physiol. (Heart Circ. Physiol.) 280: H222-H236, 2001. [Abstract], [Full Text (pdf)]

D. Goldman and A.S. Popel. A computational study of the effect of capillary network anastomoses and tortuosity on oxygen transport. J. Theor. Biol., 206:181-194, 2000. [Abstract], [Full Text (pdf)]

C.D. Eggleton, A. Vadapalli, T.K. Roy, and A.S. Popel. Calculations of intracapillary oxygen tension distributions in muscle. Math. Biosci., 167:123-143, 2000. [Abstract], [Full Text (pdf)]

J.J. Bishop, P.R. Nance, A.S. Popel, M. Intaglietta, and P.C. Johnson. Diameter changes in skeletal muscle venules during arterial pressure reduction. Am. J. Physiol. (Heart Circ. Physiol.) 279: H47-H57, 2000. [Abstract], [Full Text (pdf)]

R.M. Raphael, A.S. Popel, and W.E. Brownell. A membrane bending model of outer hair cell electromotility. Biophys. J., 78: 2844-2862, 2000. [Abstract], [Full Text (pdf)]

A.R. Vadapalli, R.N. Pittman, and A.S. Popel. Estimating oxygen transport resistance of the microvascular wall. Am. J. Physiol. (Heart Circ. Physiol), 279: H657-H671, 2000. [Abstract], [Full Text (pdf)]

B. Das, P.C. Johnson, and A.S. Popel. Computational fluid dynamic studies of leukocyte adhesion effects on non-Newtonian blood flow through microvessels. Biorheology, 37: 239-258, 2000. [Abstract], [Full Text (pdf)]

A.S. Popel and R.N. Pittman. Mechanics and transport in the microcirculation. Handbook of Biomedical Engineering, Chapter 31, J. Bronzino, Ed., CRC Press, Boca Raton, 2nd edition, 2000, pp. 31.1-31.12.

J.T. Ratnanather, A.S. Popel, and W.E. Brownell. An analysis of the hydraulic conductivity of the extracisternal space of the cochlear outer hair cell. J. Math. Biol., 40: 372-382, 2000. [Abstract], [Full Text (pdf)]

A.S. Popel. Theory of Oxygen transport to tissue. Crit Rev Biomed Eng. 1989;17(3):257-321. [Abstract] [Full Text (pdf)]