Aleksander Popel

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc Module-based multiscale simulation of angiogenesis in skeletal muscle
    Gang Liu
    Systems Biology Laboratory, Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Theor Biol Med Model 8:6. 2011
  2. pmc Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies
    Stacey D Finley
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205, USA
    BMC Syst Biol 5:193. 2011
  3. pmc Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis
    Prakash Vempati
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    BMC Syst Biol 5:59. 2011
  4. pmc A compartment model of VEGF distribution in blood, healthy and diseased tissues
    Marianne O Stefanini
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
    BMC Syst Biol 2:77. 2008
  5. pmc Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
    Amina A Qutub
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
    BMC Syst Biol 3:13. 2009
  6. pmc Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model
    Jacob E Koskimaki
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    BMC Cancer 10:29. 2010
  7. ncbi request reprint The Microcirculation Physiome Project
    A S Popel
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Ann Biomed Eng 26:911-3. 1998
  8. ncbi request reprint Skeletal muscle VEGF gradients in peripheral arterial disease: simulations of rest and exercise
    James W Ji
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore MD 21205, USA
    Am J Physiol Heart Circ Physiol 293:H3740-9. 2007
  9. pmc Modeling of growth factor-receptor systems from molecular-level protein interaction networks to whole-body compartment models
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Methods Enzymol 467:461-97. 2009
  10. ncbi request reprint 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
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
    J Biol Chem 279:39105-14. 2004

Collaborators

Detail Information

Publications85

  1. pmc Module-based multiscale simulation of angiogenesis in skeletal muscle
    Gang Liu
    Systems Biology Laboratory, Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Theor Biol Med Model 8:6. 2011
    ..Integration of models at different scales is a challenging and currently unsolved problem...
  2. pmc Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies
    Stacey D Finley
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205, USA
    BMC Syst Biol 5:193. 2011
    ..The model is applied to investigate the action of VEGF-neutralizing agents (called "anti-VEGF") in the treatment of cancer...
  3. pmc Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis
    Prakash Vempati
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    BMC Syst Biol 5:59. 2011
    ..However, computational models have predicted that HSPG binding alone does not affect VEGF localization or gradients at steady state...
  4. pmc A compartment model of VEGF distribution in blood, healthy and diseased tissues
    Marianne O Stefanini
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
    BMC Syst Biol 2:77. 2008
    ..We analyze the sensitivity of this distribution to the secretion rate, clearance rate and vascular permeability of VEGF...
  5. pmc Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting
    Amina A Qutub
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
    BMC Syst Biol 3:13. 2009
    ..model that bridges the gap between these two perspectives, and addresses a remaining question in angiogenic sprouting: how do the processes of endothelial cell elongation, migration and proliferation contribute to vessel formation?..
  6. pmc Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model
    Jacob E Koskimaki
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    BMC Cancer 10:29. 2010
    ....
  7. ncbi request reprint The Microcirculation Physiome Project
    A S Popel
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Ann Biomed Eng 26:911-3. 1998
    ..The discussion includes issues of database utility, organization, data deposition, and linkage to other databases. The database will span levels from gene to tissue and will serve both research and educational purposes...
  8. ncbi request reprint Skeletal muscle VEGF gradients in peripheral arterial disease: simulations of rest and exercise
    James W Ji
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore MD 21205, USA
    Am J Physiol Heart Circ Physiol 293:H3740-9. 2007
    ....
  9. pmc Modeling of growth factor-receptor systems from molecular-level protein interaction networks to whole-body compartment models
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Methods Enzymol 467:461-97. 2009
    ..g., vascular permeability and lymphatic drainage). The given examples will demonstrate the utility of computational models in aiding both basic science and clinical research on VEGF systems biology...
  10. ncbi request reprint 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
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA
    J Biol Chem 279:39105-14. 2004
    ....
  11. pmc A computational model of oxygen delivery by hemoglobin-based oxygen carriers in three-dimensional microvascular networks
    Nikolaos M Tsoukias
    Department of Biomedical Engineering, Florida International University, 10555 W Flagler Street, Miami, FL 33174, USA
    J Theor Biol 248:657-74. 2007
    ..O(2) transport simulations in realistic representations of microvascular networks should provide a theoretical framework for choosing optimal parameter values in the development of hemoglobin-based blood substitutes...
  12. ncbi request reprint Erythrocyte consumption of nitric oxide in presence and absence of plasma-based hemoglobin
    Nikolaos M Tsoukias
    Department of Biomedical Engineering and Center for Computational Medicine and Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
    Am J Physiol Heart Circ Physiol 282:H2265-77. 2002
    ..1 and 40 cm/s. Our results suggest that the difference in NO uptake by RBCs and free hemoglobin is smaller than previously reported and it is hematocrit dependent...
  13. pmc Systems biology of vascular endothelial growth factors
    Feilim Mac Gabhann
    Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, USA
    Microcirculation 15:715-38. 2008
    ....
  14. ncbi request reprint Interactions of VEGF isoforms with VEGFR-1, VEGFR-2, and neuropilin in vivo: a computational model of human skeletal muscle
    Feilim Mac Gabhann
    Dept of Biomedical Engineering, Johns Hopkins Univ School of Medicine, 720 Rutland Ave, 613 Traylor Bldg, Baltimore, MD 21205, USA
    Am J Physiol Heart Circ Physiol 292:H459-74. 2007
    ..This model is the first to study VEGF tissue distribution and receptor activation in human muscle, and it provides a platform for the design and evaluation of therapeutic approaches...
  15. ncbi request reprint A reaction-diffusion model of basic fibroblast growth factor interactions with cell surface receptors
    Renee J Filion
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Ann Biomed Eng 32:645-63. 2004
    ..Moreover, ligand dimerization is shown to potentially regulate FGF-2 activity by shifting the distribution of signaling complexes from the less stable triads to the more stable double triads...
  16. ncbi request reprint Calculations of oxygen transport by red blood cells and hemoglobin solutions in capillaries
    Arjun Vadapalli
    Department of Biomedical Engineering, School of Medicine, John Hopkins University, Baltimore, MD 21205, USA
    Artif Cells Blood Substit Immobil Biotechnol 30:157-88. 2002
    ..The mass transfer coefficients obtained will be used in simulations of O2 transport in complex capillary networks...
  17. pmc A systems biology perspective on sVEGFR1: its biological function, pathogenic role and therapeutic use
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Cell Mol Med 14:528-52. 2010
    ..Finally, we present the need for a systems biology perspective in interpreting circulating VEGF and sVEGFR1 concentrations as surrogate markers of angiogenic status in angiogenesis-dependent diseases...
  18. pmc Reactive oxygen species regulate hypoxia-inducible factor 1alpha differentially in cancer and ischemia
    Amina A Qutub
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 613 Traylor Bldg, 720 Rutland Ave, Baltimore, MD 21205, USA
    Mol Cell Biol 28:5106-19. 2008
    ....
  19. doi request reprint Trans-scleral delivery of antiangiogenic proteins
    Anna M Demetriades
    Department of Ophthalmology, The Johns Hopkins University, School of Medicine, Baltimore, MD, USA
    J Ocul Pharmacol Ther 24:70-9. 2008
    ..In this study, we investigated the penetration of various proteins into the mouse eye after a periocular injection of the protein or an adenoviral vector (Ad) expressing the protein...
  20. pmc Nitric oxide in the vasculature: where does it come from and where does it go? A quantitative perspective
    Kejing Chen
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Antioxid Redox Signal 10:1185-98. 2008
    ..Resolving these issues is highly relevant to improving our understanding of vascular biology and to developing pharmaceutical agents that target NO pathways, such as vasodilating drugs...
  21. pmc Nitric oxide from nitrite reduction by hemoglobin in the plasma and erythrocytes
    Kejing Chen
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 613 Traylor Building, 720 Rutland Avenue, Baltimore, MD 21205, USA
    Nitric Oxide 18:47-60. 2008
    ..mM in erythrocyte); (3) intraerythrocytic hemoglobin encapsulated by a NO-resistant membrane is the major source of NO from nitrite reduction, and cell-free hemoglobin is a significant scavenger of both paracrine and endocrine NO...
  22. ncbi request reprint Outer hair cell active force generation in the cochlear environment
    Zhijie Liao
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Acoust Soc Am 122:2215-25. 2007
    ..Our findings can provide a better understanding of the outer hair cell's role in the cochlear amplifier...
  23. ncbi request reprint Vascular smooth muscle NO exposure from intraerythrocytic SNOHb: a mathematical model
    Kejing Chen
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Antioxid Redox Signal 9:1097-110. 2007
    ..In conclusion, our mathematical model predicts that picomolar amounts of NO can be delivered to the vascular smooth muscle by intraerythrocytic SNOHb; this amount of NO alone appears not sufficient to induce the hypoxic vasodilation...
  24. pmc Three autocrine feedback loops determine HIF1 alpha expression in chronic hypoxia
    Amina A Qutub
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 613 Traylor Building, 720 Rutland Avenue, Baltimore, MD 21205, USA
    Biochim Biophys Acta 1773:1511-25. 2007
    ..The model provides quantitative insight critical for characterizing molecular mechanisms underlying a cell's response to long-term hypoxia...
  25. pmc Dimerization of VEGF receptors and implications for signal transduction: a computational study
    Feilim Mac Gabhann
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Biophys Chem 128:125-39. 2007
    ..These results have significant implications for VEGF signal transduction and interpretation of experimental studies. These results may be applicable to other ligand-receptor pairs, in particular PDGF...
  26. ncbi request reprint A biochemical model of matrix metalloproteinase 9 activation and inhibition
    Prakash Vempati
    Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, MD 21205, USA
    J Biol Chem 282:37585-96. 2007
    ..In all, our analysis serves as a summary of existing kinetic data for MMP9 and a foundation for future models utilizing MMP9 or other MMPs under physiologically well defined microenvironments...
  27. pmc A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 105:13775-80. 2008
    ..In some cases, this combinatorial screening identified strong synergism between peptides. The current work provides a guideline for a computational-based peptidomics approach for the discovery of endogenous bioactive peptides...
  28. pmc Quantification and cell-to-cell variation of vascular endothelial growth factor receptors
    P I Imoukhuede
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
    Exp Cell Res 317:955-65. 2011
    ..Altogether, we determine inherent differences in the surface expression levels of these receptors and the role of VEGF in regulating the balance of anti-angiogenic or modulatory (VEGFR1) and pro-angiogenic (VEGFR2) receptors...
  29. pmc Quantifying the proteolytic release of extracellular matrix-sequestered VEGF with a computational model
    Prakash Vempati
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 5:e11860. 2010
    ..To address these uncertainties, we develop a molecular-detailed quantitative model of VEGF proteolysis, used here in the context of an endothelial sprout...
  30. pmc VEGF and soluble VEGF receptor-1 (sFlt-1) distributions in peripheral arterial disease: an in silico model
    Florence T H Wu
    Dept of Biomedical Engineering, Johns Hopkins Univ School of Medicine, 720 Rutland Ave, 613 Traylor Research Bldg, Baltimore, MD 21205, USA
    Am J Physiol Heart Circ Physiol 298:H2174-91. 2010
    ....
  31. pmc The presence of VEGF receptors on the luminal surface of endothelial cells affects VEGF distribution and VEGF signaling
    Marianne O Stefanini
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    PLoS Comput Biol 5:e1000622. 2009
    ....
  32. ncbi request reprint Wall shear stress differentially affects NO level in arterioles for volume expanders and Hb-based O2 carriers
    Mahendra Kavdia
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Microvasc Res 66:49-58. 2003
    ..These predictions are consistent with the results of animal studies of vascular tone following administration of HBOCs and volume expanders...
  33. pmc Computational fluid dynamics of aggregating red blood cells in postcapillary venules
    Bong Chung
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, USA
    Comput Methods Biomech Biomed Engin 12:385-97. 2009
    ..Aggregate formation also depends on the angle and location of the cells before they enter the bifurcation region. Comparisons with experimental data are discussed...
  34. pmc Nitric oxide production pathways in erythrocytes and plasma
    Kejing Chen
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Biorheology 46:107-19. 2009
    ..Here we review the hypotheses that have been put forward concerning blood-borne NO and its contribution to hemorheological properties and the regulation of vascular tone, with an emphasis on the quantitative aspects of these processes...
  35. pmc A compartment model of VEGF distribution in humans in the presence of soluble VEGF receptor-1 acting as a ligand trap
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 4:e5108. 2009
    ....
  36. pmc Computational kinetic model of VEGF trapping by soluble VEGF receptor-1: effects of transendothelial and lymphatic macromolecular transport
    Florence T H Wu
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Physiol Genomics 38:29-41. 2009
    ..sVEGFR1's interactions with cell surface receptors such as NRP1 are also expected to affect its molecular interplay with VEGF...
  37. pmc Multiscale models of angiogenesis
    Amina A Qutub
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
    IEEE Eng Med Biol Mag 28:14-31. 2009
    ..As bioengineers, we approach angiogenesis as a complex, interconnected system of events occurring in sequence and in parallel, on multiple levels, triggered by a main stimulus, e.g., hypoxia...
  38. pmc Hemorrhagic shock and nitric oxide release from erythrocytic nitric oxide synthase: a quantitative analysis
    Kejing Chen
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 613 Traylor Building, 720 Rutland Avenue, Baltimore, MD 21205, USA
    Microvasc Res 78:107-18. 2009
    ..This study provides a basis for detailed studies to characterize the impairment of NO release pathways during hemorrhage and yield important insights for the development of resuscitation methods...
  39. doi request reprint A peptide derived from type 1 thrombospondin repeat-containing protein WISP-1 inhibits corneal and choroidal neovascularization
    Marisol del Valle Cano
    Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, School of Medicine, Baltimore, MD 21231, USA
    Invest Ophthalmol Vis Sci 50:3840-5. 2009
    ..The peptide was also tested in vivo in the corneal micropocket and the laser-induced choroidal neovascularization (CNV) mouse models...
  40. ncbi request reprint Multi-scale computational models of pro-angiogenic treatments in peripheral arterial disease
    Feilim Mac Gabhann
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Ann Biomed Eng 35:982-94. 2007
    ....
  41. ncbi request reprint Model of nitric oxide diffusion in an arteriole: impact of hemoglobin-based blood substitutes
    Mahendra Kavdia
    Department of Biomedical Engineering and Center for Computational Medicine and Biology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland 21205, USA
    Am J Physiol Heart Circ Physiol 282:H2245-53. 2002
    ..The SM NO concentration was significantly reduced when the extravasation of HBOC molecules was considered. The myoglobin present in the parenchymal cells scavenges NO, which reduces the SM NO concentration...
  42. ncbi request reprint Mechanosensitive channels in the lateral wall can enhance the cochlear outer hair cell frequency response
    Alexander A Spector
    Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Traylor 411, Baltimore, MD 21205, USA
    Ann Biomed Eng 33:991-1002. 2005
    ..The effect of the channels is especially significant in an intermediate range of sound frequencies, and the channel-related gain is up to 3-4 times between 3 and 15 kHz...
  43. ncbi request reprint Effect of voltage-dependent membrane properties on active force generation in cochlear outer hair cell
    Zhijie Liao
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Acoust Soc Am 118:3737-46. 2005
    ..The obtained results can be important for a better understanding of the OHC active force production and the contribution of cell electromotility to the cochlear amplification, sensitivity, and nonlinearity...
  44. ncbi request reprint A computational model of oxygen transport in skeletal muscle for sprouting and splitting modes of angiogenesis
    James W Ji
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, 613 Traylor Bldg, Baltimore, MD 21205, USA
    J Theor Biol 241:94-108. 2006
    ..This study also shows that under the steady-state conditions the effect of myoglobin (Mb) on oxygen transport was small...
  45. ncbi request reprint Monte Carlo simulations of VEGF binding to cell surface receptors in vitro
    Feilim Mac Gabhann
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 720 Rutland Ave, 613 Traylor, Baltimore, MD 21205, USA
    Biochim Biophys Acta 1746:95-107. 2005
    ..The variability is expected to be more prominent in in vivo situations where the number of ligand molecules available for binding is less...
  46. pmc High-frequency force generation in the constrained cochlear outer hair cell: a model study
    Zhijie Liao
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Assoc Res Otolaryngol 6:378-89. 2005
    ....
  47. ncbi request reprint 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
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
    J Theor Biol 238:124-45. 2006
    ..It also identifies critical parameters whose values are not presently available and which should be determined in future experiments...
  48. ncbi request reprint Modeling high-frequency electromotility of cochlear outer hair cell in microchamber experiment
    Zhijie Liao
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Acoust Soc Am 117:2147-57. 2005
    ..The distribution of the viscous losses inside the fluids was also estimated. The proposed approach can help in a better understanding of the high-frequency OHC electromotility under experimental and physiological conditions...
  49. ncbi request reprint Differential binding of VEGF isoforms to VEGF receptor 2 in the presence of neuropilin-1: a computational model
    Feilim Mac Gabhann
    Dept of Biomedical Engineering, Johns Hopkins Univ School of Medicine, 720 Rutland Ave, 611 Traylor, Baltimore, MD 21205, USA
    Am J Physiol Heart Circ Physiol 288:H2851-60. 2005
    ..The model has applications for both proangiogenic and antiangiogenic therapies, such as for heart disease and cancer, as well as in tissue engineering...
  50. ncbi request reprint A model of nitric oxide capillary exchange
    Nikolaos M Tsoukias
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Microcirculation 10:479-95. 2003
    ....
  51. ncbi request reprint A theoretical model of nitric oxide transport in arterioles: frequency- vs. amplitude-dependent control of cGMP formation
    Nikolaos M Tsoukias
    Dept of Biomedical Engineering, Johns Hopkins Univ School of Medicine, 613 Traylor Bldg, 720 Rutland Ave, Baltimore, MD 21205, USA
    Am J Physiol Heart Circ Physiol 286:H1043-56. 2004
    ..The proposed hypothesis suggests a new functional role for Ca(2+) oscillations in endothelial cells. Further experimentation is needed to test whether and under what conditions in silico predictions occur in vivo...
  52. ncbi request reprint Model of competitive binding of vascular endothelial growth factor and placental growth factor to VEGF receptors on endothelial cells
    Feilim Mac Gabhann
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Traylor 613, 720 Rutland Ave, Baltimore, MD 21205, USA
    Am J Physiol Heart Circ Physiol 286:H153-64. 2004
    ..These results suggest that VEGFR1 signaling can be functional in adult-derived endothelial cells...
  53. ncbi request reprint Effect of outer hair cell piezoelectricity on high-frequency receptor potentials
    Alexander A Spector
    Department of Biomedical Engineering and Center for Computational Medicine and Biology, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Acoust Soc Am 113:453-61. 2003
    ..4 mV throughout the whole frequency range. In long cells, we have found that the effect of the piezoelectric properties is much weaker. These results are consistent with major features of the cochlear amplifier...
  54. ncbi request reprint Theoretical analysis of biochemical pathways of nitric oxide release from vascular endothelial cells
    Kejing Chen
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 720 Rutland Avenue, 613 Traylor Building, Baltimore, MD 21205, USA
    Free Radic Biol Med 41:668-80. 2006
    ..The results indicated that the predicted low level of NO production can be attributed primarily to a low expression of eNOS in the microvascular endothelial cells...
  55. pmc A computational model of intracellular oxygen sensing by hypoxia-inducible factor HIF1 alpha
    Amina A Qutub
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, 613 Traylor Bldg, 720 Rutland Avenue, Baltimore, MD 21205, USA
    J Cell Sci 119:3467-80. 2006
    ..The model advances quantitative molecular level understanding of HIF1 pathways--an endeavor that will help elucidate the diverse responses to hypoxia found in cancer, ischemia and exercise...
  56. ncbi request reprint Theoretical analysis of effects of blood substitute affinity and cooperativity on organ oxygen transport
    Mahendra Kavdia
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
    J Appl Physiol 93:2122-8. 2002
    ....
  57. pmc Targeting neuropilin-1 to inhibit VEGF signaling in cancer: Comparison of therapeutic approaches
    Feilim Mac Gabhann
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS Comput Biol 2:e180. 2006
    ..The tumor type and the microenvironment of the target tissue are also significant in determining therapeutic efficacy of each of the treatments studied...
  58. ncbi request reprint Protein transport to choroid and retina following periocular injection: theoretical and experimental study
    Feilim Mac Gabhann
    Department of Biomedical Engineering, The Wilmer Eye Institute, Johns Hopkins University School of Medicine, 720 Rutland Ave, 613 Traylor, Baltimore, MD 21205, USA
    Ann Biomed Eng 35:615-30. 2007
    ..This is the first model of ocular drug delivery to explicitly account for transport properties of each eye layer...
  59. pmc Identification of novel short peptides derived from the alpha 4, alpha 5, and alpha 6 fibrils of type IV collagen with anti-angiogenic properties
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biochem Biophys Res Commun 354:434-9. 2007
    ..These peptides may have potential as anti-angiogenic therapeutic agents...
  60. pmc Vascular and perivascular nitric oxide release and transport: biochemical pathways of neuronal nitric oxide synthase (NOS1) and endothelial nitric oxide synthase (NOS3)
    Kejing Chen
    Department of Biomedical Engineering, 613 Traylor Building, 720 Rutland Avenue, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Free Radic Biol Med 42:811-22. 2007
    ....
  61. pmc Computational model of vascular endothelial growth factor spatial distribution in muscle and pro-angiogenic cell therapy
    Feilim Mac Gabhann
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS Comput Biol 2:e127. 2006
    ..The VEGF gradients also result in heterogeneity in the activation of blood vessel VEGF receptors. This first model of VEGF tissue transport and heterogeneity provides a platform for the design and evaluation of therapeutic approaches...
  62. ncbi request reprint VEGF gradients, receptor activation, and sprout guidance in resting and exercising skeletal muscle
    Feilim Mac Gabhann
    Dept of Biomedical Engineering, Johns Hopkins Univ School of Medicine, 720 Rutland Ave, Baltimore, MD 2120, USA
    J Appl Physiol 102:722-34. 2007
    ..e., perpendicular to the muscle fibers) than in the longitudinal direction. This may explain observed perpendicular anastomoses in skeletal muscle...
  63. pmc Anti-angiogenic peptides identified in thrombospondin type I domains
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University, School of Medicine, 613 Traylor Building, 720 Rultland Avenue, Baltimore, MD 21205, USA
    Biochem Biophys Res Commun 359:63-9. 2007
    ....
  64. ncbi request reprint Nanostructure, effective properties, and deformation pattern of the cochlear outer hair cell cytoskeleton
    Alexander A Spector
    Department of Biomedical Engineering and Center for Computational Medicine and Biology, Johns Hopkins University, Baltimore, MD 21205, USA
    J Biomech Eng 124:180-7. 2002
    ..We discovered a pattern of highly inhomogeneous deformation of the cytoskeleton where the circumferential strain is primarily determined by the deformation of the intermediate material...
  65. ncbi request reprint Modeling of oxygen diffusion from the blood vessels to intracellular organelles
    Aleksander S Popel
    Department of Biomedical Engineering, Center for Computational Medicine and Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Adv Exp Med Biol 530:485-95. 2003
    ..Mathematical and computational models provide a powerful set of tools for studies of these complex phenomena...
  66. pmc Peptides derived from type I thrombospondin repeat-containing proteins of the CCN family inhibit proliferation and migration of endothelial cells
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Int J Biochem Cell Biol 39:2314-23. 2007
    ....
  67. doi request reprint Novel anti-angiogenic peptides derived from ELR-containing CXC chemokines
    Emmanouil D Karagiannis
    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Cell Biochem 104:1356-63. 2008
    ....
  68. pmc Anti-angiogenic peptides for cancer therapeutics
    Elena V Rosca
    Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
    Curr Pharm Biotechnol 12:1101-16. 2011
    ..g., through L-to-D and non-natural amino acid substitutions. We highlight technological advances in peptide discovery and optimization including computational and bioinformatics tools and novel experimental techniques...
  69. ncbi request reprint Impaired angiogenesis after hindlimb ischemia in type 2 diabetes mellitus: differential regulation of vascular endothelial growth factor receptor 1 and soluble vascular endothelial growth factor receptor 1
    Surovi Hazarika
    Division of Cardiology, Duke University and Durham VA Medical Center, Durham, NC 27710, USA
    Circ Res 101:948-56. 2007
    ..After ischemia, maladaptive upregulation of these receptors further reduces the capacity of VEGF to induce an angiogenic response, which may provide a novel target for therapy...
  70. pmc Hypotonic swelling of salicylate-treated cochlear outer hair cells
    Man Zhi
    Bobby R Alford Department of Otolaryngology Head and Neck Surgery, Baylor College of Medicine, Houston, TX 77030, United States
    Hear Res 228:95-104. 2007
    ....
  71. ncbi request reprint Effect of erythrocyte aggregation at normal human levels on functional capillary density in rat spinotrapezius muscle
    Sangho Kim
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
    Am J Physiol Heart Circ Physiol 290:H941-7. 2006
    ..We conclude that the level of aggregability seen in healthy humans is an important determinant of FCD only at reduced arterial pressure...
  72. ncbi request reprint Effect of aggregation and shear rate on the dispersion of red blood cells flowing in venules
    Jeffrey J Bishop
    Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
    Am J Physiol Heart Circ Physiol 283:H1985-96. 2002
    ..The shear-induced random movements observed in this study may increase the radial transport of particles and solutes within the bloodstream by orders of magnitude...
  73. ncbi request reprint A compartmental model for oxygen transport in brain microcirculation in the presence of blood substitutes
    Maithili Sharan
    Centre for Atmospheric Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
    J Theor Biol 216:479-500. 2002
    ....
  74. ncbi request reprint Computational fluid dynamic simulation of aggregation of deformable cells in a shear flow
    Prosenjit Bagchi
    Department of Mechanical and Aerospace Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854, USA
    J Biomech Eng 127:1070-80. 2005
    ..The cyclic behavior is related to the rolling orientation of the aggregate. The frequency and amplitude of oscillation in the number of bonds also depend on the rheological properties...
  75. ncbi request reprint Relationship between erythrocyte aggregate size and flow rate in skeletal muscle venules
    Jeffrey J Bishop
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Am J Physiol Heart Circ Physiol 286:H113-20. 2004
    ..This study provides direct confirmation of aggregate formation at low shear in venules with high-molecular-weight dextran as well as an estimate of aggregate size and range...
  76. ncbi request reprint Red blood cell velocity profiles in skeletal muscle venules at low flow rates are described by the Casson model
    Bigyani Das
    Center for Scientific Computation and Mathematical Modeling, University of Maryland, College Park, MD 20742, USA
    Clin Hemorheol Microcirc 36:217-33. 2007
    ..These results have implications for pathological low-flow conditions, such as hemorrhage and sepsis, and they quantitatively describe blunted velocity profiles and elevated flow resistance in postcapillary venules...
  77. pmc Experimental and theoretical studies of oxygen gradients in rat pial microvessels
    Maithili Sharan
    Centre for Atmospheric Sciences, Indian Institute of Technology, Delhi, India
    J Cereb Blood Flow Metab 28:1597-604. 2008
    ....
  78. ncbi request reprint Temporal and spatial variations of cell-free layer width in arterioles
    Sangho Kim
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Am J Physiol Heart Circ Physiol 293:H1526-35. 2007
    ..The temporal variations increase as diameter increases and are inversely related on opposite sides of the vessel...
  79. ncbi request reprint Contribution of nNOS- and eNOS-derived NO to microvascular smooth muscle NO exposure
    Mahendra Kavdia
    Biomedical Engineering, University of Arkansas, Fayetteville, AR 72701, USA
    J Appl Physiol 97:293-301. 2004
    ..Further experimental and theoretical studies are required to account for distribution of NOS isoforms and determine NO availability in vasculatures of different tissues...
  80. ncbi request reprint Aggregate formation of erythrocytes in postcapillary venules
    Sangho Kim
    Department of Bioengineering, University of California, San Diego, La Jolla, California 92093 0412, USA
    Am J Physiol Heart Circ Physiol 288:H584-90. 2005
    ..Approximately 90% of aggregate formation occurred in a short time period (0.15-0.30 s after entering the venule) in a region 15 to 30 microm from the entrance. The time delay may reflect rheological entrance conditions in the venule...
  81. pmc Effects of chlorpromazine on mechanical properties of the outer hair cell plasma membrane
    David R Murdock
    Department of Bioengineering, Rice University, Houston, Texas 77251 1892, USA
    Biophys J 89:4090-5. 2005
    ..The CPZ-induced changes in tether viscoelastic behavior suggest that alterations in the mechanical properties of the OHC lateral wall could play a role in the modulation of OHC electromotility by CPZ...
  82. ncbi request reprint Contributions of collision rate and collision efficiency to erythrocyte aggregation in postcapillary venules at low flow rates
    Sangho Kim
    Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093 0412, USA
    Am J Physiol Heart Circ Physiol 293:H1947-54. 2007
    ..We conclude that while collision frequency influences red blood cell aggregate formation in postcapillary venules, collision efficiency is more important...
  83. doi request reprint An immersed boundary lattice Boltzmann approach to simulate deformable liquid capsules and its application to microscopic blood flows
    Junfeng Zhang
    School of Engineering, Laurentian University, Sudbury, ON P3E 2C6, Canada
    Phys Biol 4:285-95. 2007
    ..However, extension of this algorithm to three-dimensional situations is necessary for more realistic simulations...
  84. ncbi request reprint Venular endothelium-derived NO can affect paired arteriole: a computational model
    Mahendra Kavdia
    Biomedical Engineering Program, College of Engineering, 203 Engineering Hall, Univ of Arkansas, Fayetteville, AR 72701, USA
    Am J Physiol Heart Circ Physiol 290:H716-23. 2006
    ..These results will have significant implications for our understanding of tissue NO levels in both physiological and pathophysiological conditions...
  85. pmc Red blood cell aggregation and dissociation in shear flows simulated by lattice Boltzmann method
    Junfeng Zhang
    School of Engineering, Laurentian University, Sudbury, Ont, Canada P3E 2C6
    J Biomech 41:47-55. 2008
    ..These behaviors are qualitatively similar to experimental observations and show the potential of this numerical scheme for future studies of blood flow in microvessels...

Research Grants12

  1. Systems Biology of Angiogenesis in Peripheral Arterial Disease
    Aleksander S Popel; Fiscal Year: 2010
    ..The project will combine computational and experimental approaches to allow a better understanding of how the body responds to blockages in the leg arteries as well as better ways to design new therapies. ..
  2. Predictive experiment-based multiscale models of angiogenesis in breast cancer
    Aleksander S Popel; Fiscal Year: 2010
    ..The synergistic combination of computational and experimental studies should provide significant insights into the nature of the disease. ..
  3. Predictive experiment-based multiscale models of angiogenesis in breast cancer
    Aleksander Popel; Fiscal Year: 2009
    ....
  4. Quantitative Analysis of Angiogenesis in Skeletal Muscle
    Aleksander Popel; Fiscal Year: 2009
    ..It will have an impact on understanding both basic mechanisms of angiogenesis and therapeutic applications in peripheral vascular disease. ..
  5. Systems Biology of Angiogenesis: from Molecules to Therapy
    Aleksander Popel; Fiscal Year: 2007
    ....
  6. Systems Biology of Angiogenesis in Peripheral Arterial Disease
    Aleksander S Popel; Fiscal Year: 2010
    ..The project will combine computational and experimental approaches to allow a better understanding of how the body responds to blockages in the leg arteries as well as better ways to design new therapies. ..