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Journal Publications

  1. A. Agrawal, R. Deo, G. D. Wang, M. D. Wang, and S. M. Nie, “Nanometer-scale mapping and single molecule detection with color-coded nanoparticle probes,” Proc. Natl. Acad. Sci. USA, 2008, 105, 3298-3303.  PMCID: PMC2265145.
  2. A. M. Smith and S. M. Nie, “Nanocrystal synthesis in an amphibious bath: spontaneous generation of hydrophilic and hydrophobic surface coatings,” Agnew. Chem. Int. Ed. Engl. 2008, 47, 9916-9921.  PMCID: PMC2702705.
  3. A. M. Smith, A. M. Mohs, and S. M. Nie, “Tuning the optical and electronic properties of colloidal nanocrystals by lattice strain,” Nature Nanotechnology 2009, 4, 56-63.  PMCID: PMC2711767.
  4. A. M. Smith, G. Ruan, M. V. Rhyner, and S. M. Nie, “Engineering luminescent quantum dots for in-vivo molecular and cellular imaging,” Annals of Biomedical Engineering, published online on February 1, 2006.
  5. A. Smith, H. Duan, A. Mohs, and S. M. Nie, “Bioconjugated quantum dots for in-vivo molecular and cellular imaging,” Adv. Drug Delivery Rev. 2008, 60, 1126-1140.  PMCID: PMC2649798.
  6. Agrawal A, Zhang C, Byassee T and Nie S. (2006) Counting Single Native Biomolecules and Intact Viruses with Color Coded Nanoparticles. Anal. Chem. 78, 1061-1070.
  7. Andrew M. Smith and Shuming Nie, “Minimizing the Hydrodynamic Size of Quantum Dots with Multifunctional Multidentate Polymer Ligands.” J. Am. Chem. Soc., 2008, 130, 11278–11279. PMCID: PMC2703485.[My p
  8. B. A. Kairdolf, A. M. Smith, and S. M. Nie, “One-Pot Synthesis, Encapsulation, and Solubilization of Size-Tuned Quantum Dots with Amphiphilic Multidentate Ligands," J. Am. Chem. Soc., 2008, 130, 12866-12867. PMCID: PMC2711769.
  9. B. Kairdolf, M. Mancini, A. Smith, and S. M. Nie, “Minimizing nonspecific cellular binding of quantum dots with hydroxyl-derivatized surface coatings,” Anal. Chem. 2008, 80, 3029-3034.  PMID: 18324840.
  10. Bao G and Bao XR. (2005) Shedding light on the dynamics of endocytosis and viral budding. Proc Natl Acad Sci USA. 120, 9997-9998.
  11. Bao G. Protein Mechanics, Experimental Mechanics, 2009; 49:153-164.
  12. Bao G, Rhee WJ, Tsourkas A, Fluorescent Probes for Live-Cell RNA Detection, Annu Rev Biomed Eng. 11, 25-47 (2009).
  13. Chang K, Weiss D, Suo J, Vega JD, Giddens D, Taylor WR, and Jo H. (2007) Bone morphogenic protein (BMP) antagonists are co-expressed with BMP4 in endothelial cells exposed to unstable flow in vitro, in mouse aortas and in human coronary arteries- Role of BMP antagonists in inflammation and atherosclerosis.  Circulation. 116, 1258-1266.  *Accompanied by an Editorial.  Circulation 116, 1221 (2007).
  14. Dennis AM and Bao G. (2008) Quantum dot-fluorescent protein pairs as novel fluorescence resonance energy transfer probes. Nano Letters, 8, 1439-1445. PMID: 18412403.
  15. Duan H, Kuang M, Wang X, Wang YA, Mao H and Nie SM. (2008) Reexamining the effects of particle size and surface chemistry on magnetic properties of iron oxide nanocrystals: new insights into spin disorder and proton relaxivity. J Phys Chem C, 112, 8127-8131.
  16. Ferrara DE, Romay-Penabad Z, Liu XW, Taylor WR, Pierangeli S. (2008) Antiphospholipid antibodies induce expression of VCAM-1 in the aorta of mice detected using quantum dot nano crystals and two-photon excitation laser scanning microscopy.  J of Throm Haemost, in press.
  17. Ferrara DE, Weiss D, Carnell PH, Vito RP, Vega D, Gao X, Nie S, Taylor WR. (2006) Quantitative 3D fluorescence technique for the analysis of en face preparations of arterial walls using quantum dot nanocrystals and two-photon excitation laser scanning microscopy. Am J Physiol Regul Integr Comp Physiol. 290, R114-123.
  18. Gongora MC, Lob HE, Landmesser U, Guzik TJ, Martin WD, Ozumi K, Wall SM, Wilson DS, Murthy N, Gravanis M, Fukai T, Harrison DG, “Loss of extracellular superoxide dismutase leads to acute lung damage in the presence of ambient air: a potential mechanism underlying adult respiratory distress syndrome,” American Journal of Pathology, 2009=8 Oct; 173(4):915-26. Epub 2008 Sep 11.  PMCID: PMC2543061.
  19. H. Duan and S. M. Nie, “Cell-Penetrating Quantum Dots Based on Multivalent and Endosome-Disrupting Surface Coatings,” J. Am. Chem. Soc. 2007, 129, 3333-3338 PMCID: 17319667.
  20. H. Duan and S. M. Nie, “Etching Colloidal Gold Nanocrystals with Hyper-branched and Multivalent Polymers: A New Route to Fluorescent and Water-Soluble Atomic Clusters,” J. Am. Chem. Soc. 2007, 129, 2412-2413.  PMCID: 17295485.
  21. Haghighat A, Weiss D, Whalin MK, Cowan DP, Taylor WR. (2007) Granulocyte colony-stimulating factor and granulocyte macrophage colony-stimulating factor exacerbate atherosclerosis in apolipoprotein E-deficient mice.  Circulation 115, 2049-54.
  22. Hao J, Kwissa M, Pulendran B, Murthy N. “Peptide crosslinked micelles: A new strategy for the design and synthesis of peptide vaccines”.  International Journal of Nanomedicine. (2006), (1),  97-103.  PMCID: PMC2426769.
  23. He JH, Lin YH, McConney ME, Tsukruk VV, Wang ZL and Bao G. (2007) Enhancing UV photoconductivity of ZnO nanobelt by polyacrylonitrile functionalization. J. Appl. Phys., 102, 084303.
  24. Heffernan M, Murthy N. “Polyketal nanoparticles: A new pH sensitive, biodegradable drug delivery vehicle”.  Bioconj. Chem. (2005), 16(6), 1340-1342.  PMID: 16287226.
  25. Heffernan MJ, Kasturi SP, Yang S, Pulendran B, Murthy N. “The stimulation of CD8+ T cells by dendritic cells pulsed with polyketal microparticles containing ion-paired protein antigen and poly(inosinic acid)-poly(cytidylic acid)”.  Biomaterials (2009), 30 (5) 910-918.  PMID: 19036430.  NIHMSID: 88731.
  26. Hu CG, Li Y, Liu JP, Zhang YY, Bao G, Buchine B and Wang ZL. (2006) Sonochemical synthesis of ferromagnetic core-shell Fe3O4-FeP nanoparticles and FeP nanoshells. Chem. Phys. Lett., 428, 343-347.
  27. Hu CG, Liu H, Dong WT, Zhang YY, Bao G, Lao CS and Wang ZL. (2007)   La(OH)3 and La2O3 Nanobelts-Synthesis and Physical Properties.  Adv. Mater., 19,  470-474
  28. Jin Suo, Dardo Ferrara, Robert Taylor, Robert Gulberg and Don Giddens, “Wall Deformation, Wall shear Stress and atherosclerosis Around the Intercostal Ostia of C57 Mice,” ASME Summer Bioengineering Conference, 2007.
  29. Jin Suo, Dardo Ferrara, Robert Taylor, Robert Gulberg, Dan Sorescu, John Oshinski and Don Giddens, “Atherogenesis and Wall Shear Stress in The Mouse Aorta Using Quantum Dots, Micro-CT and Numerical Simulation,” In Proceedings of ASME BIO2006.
  30. Jin Suo, Michael McDaniel, Habib Samady and Don Giddens, “Relation between Wall Shear Stress and Plaque Necrotic Core in the Left coronary Arteries of Patients using Intravascular Ultrasound and Computational Fluid Dynamics,” ASME SBC2008.
  31. Jin Suo, Michael McDaniel, Saurabh Dhawan, Habib Samady and Don Giddens, “Investigation of Wall Shear Stress Over an Early Atherosclerotic Plaque in the Left Coronary Artery of a Patient by Intravascular Ultrasound and Computational Fluid Dynamics,” ASME SBC2009.
  32. Jin Suo, Smbat Amirbekian, Robert C. Long Jr., John Oshinski, Robert W. Taylor and Don P. Giddens, “Effect of Aortic Compliance on Blood Flow Patterns and Atherogenesis,” BMES2007.
  33. Jones R, Baker MB, Weber M, Harrison DG, Bao G, Searles CD (2009) Molecular Beacons Can Assess Changes in Expression and 3’Polyadenylation of Human eNOS mRNA, American Journal of Physiology-Cell Physiology, 296(3):C498-504. PMCID: PMC2660266.
  34. Khaja S, Lee S, and Murthy, N. “Acid degradable protein delivery vehicles based on metathesis chemistry”.  Biomacromolecules.  (2007), 8(5), 1391-1395.  PMID: 17461546.
  35. Kousik Kundu, Sarah F. Knight, Seungjun Lee, W. Robert Taylor, Niren Murthy, "The Kinetic Isotope Effect Improves the Efficacy of Radical Oxidant Probes in Vitro in Cell Culture and in Vivo".  Submitted to JACs 2009.
  36. Kundu K, Knight S, Willett N, Lee S, Taylor W, Murthy N. “Hydrocyanines: A new class of fluorescent sensors that can image reactive oxygen species in cell culture, tissue and in vivo”.  Angewandte Chemie International (2009), 48 (2), 299-303.  PMID: 19065548.
  37. LaConte LEW, Nitin N, Zurkiya O, Caruntu D, O’Connor CJ, Hu and G. Bao G. (2007) Coating thickness of magnetic iron oxide nanoparticles affects R2 relaxivity. J Magn Reson Imaging, 26, 1634-1641.
  38. Lee D, Erigala VR, Dasari M, Yu J, Dickson RM, Murthy N. “Detection of hydrogen peroxide with chemiluminescent micelles”.  International Journal of Nanomedicine. (2008), 3 (4) 471-476.  PMCID: PMC2636589.
  39. Lee D, Khaja S, Velasquez CJ, Dasari M, Sun C, Petros J, Taylor W, Murthy N. “In vivo imaging of hydrogen peroxide with chemiluminescent nanoparticles”.  Nature Materials.  (2007), 6(10), 765-769.  PMID:  17704780.
  40. Lee S, Murthy N. “Targeted delivery of catalase and superoxide dismutase to macrophages using folate”.  Biochemical and Biophysical Research Communications.  (2007), 360(1), 275-279.  PMID: 17586472.
  41. Lee S, Yang SC, Heffernan MJ, Taylor WR, Murthy N. “Polyketal microparticles: a new delivery vehicle for superoxide dismutase”.  Bioconj. Chem. (2007), 18(1) 4-7.  PMID: 17226951.
  42. M. C. Mancini, B. A. Kairdolf, A. M. Smith, S. M. Nie, “Oxidative Quenching and Degradation of Polymer-Encapsulated Quantum Dots: New Insights into the Long-Term Fate and Toxicity of Nanocrystals in Vivo.” J. Am. Chem. Soc. 2008; 130, 10836-10837.  PMID: 18652463.
  43. Moo Yeol Lee, Alejandra San Martin, Puja K. Mehta, Anna E. Dikalova, Abel Martin Garrido, S. Raju Datla, Erin Lyons, Karl-Heinz Krause, Botond Banfi, J. David Lambeth, Bernard Lasse` gue, Kathy K. Griendling. Mechanisms of Vascular Smooth Muscle NADPH Oxidase 1 (Nox1) Contribution to Injury-Induced Neointimal Formation, Arterioscler Thromb Vasc Biol. 2009 Apr;29(4):480-7. 2009.  PMID: 19150879; NIHMSID: 126036.
  44. Nam D*, Ni C-W*, Rezvan A, Suo J, Budzyn K, Llanos A, Harrison D, Giddens D, and Jo H. Partial carotid ligation is a model of acutely induced disturbed flow which results in rapid endothelial dysfunction and atherosclerosis. Am J Physiol Heart Circ Physiol. 2009 in press.  PMID: 19684185.
  45. Nazarewicz RR, Patrushev NA, Hilenski L, Ushio-Fukai M, Alexander RW. Novel Role of Early Endosome Antigen 1 in Reactive Oxygen Species-Depenent AT1 Receptor-mediated Signaling Linked to Hypertrophy in Vascular Smooth Muscle Cells. Circulation 2008. American Heart Association, Scientific Sessions 2008. New Orleans.
  46. Nazarewicz RR, Salazar G, Patrushev N, Hilenski L, San Martin A, Xiong S, Ushio-Fukai M, Alexander RW. Central role of Early Endosomal Antigen 1 (EEA1) in organization of Angiotensin II signaling leading to Akt activation in early endosome. Circulation 2009. American Heart Association, Scientific Sessions 2009. Orland FL.
  47. Nitin N, Rhee WJ and Bao G. Translation Inhibition Reveals Interaction of 2'-deoxy and 2'-O-methyl Molecular Beacons with mRNA Targets in Living Cells, submitted to Nucleic Acids Res, 2008; in revision.
  48. Phan JH, Young AN, and Wang MD, Translational Feedback in Biomarker Identification using Clinically-Derived Prior Knowledge and Bayesian Algorithm Selection", Journal of Biomedical Informatics, Submitted.
  49. Rhee WJ and Bao G. Simultaneous Detection of mRNA and Protein Stem Cell Markers in Live Cells, submitted to BMC Biotechnology, 2008; in revision.
  50. Rhee WJ, Santangelo P, Jo, H, and Bao, G. Target Accessibility and Signal Specificity in Live-cell Detection of BMP-4 mRNA Using Molecular Beacons.  Nucleic Acid Research 2008 36(5):e30.  PMCID: PMC2275124.
  51. Rhyner M, Smith AM, Gao X, Yang J, Mao H, and Nie SM. (2006) Quantum Dots and Multifunctional Nanoparticles as Contrast Agents for In-Vivo Tumor Imaging. Nanomedicine, 2006, 1, 209-217. 
  52. Ruan G, Agrawal A, Marcus AI, and Nie SM. (2007) Imaging and Tracking Tat-Peptide Conjugated Quantum Dots in Living Cells: New Insights into Nanoparticle Uptake, Intracellular Transport, and Vesicle Shedding. J. Am. Chem. Soc, 129, 14759-14766.
  53. Santangelo PJ, Nitin N and Bao G. (2006) Nanostructured probes for RNA detection in living cells, Ann Biomed Eng. 34: 39-50.
  54. Sesahdri G, Sy JC, Brown ME, Dikalov S, Yang SC, Murthy N, and Davis ME.  Delivery of SOD with polyketal particles protects rats from myocardial ischemia-reperfusion injury.
  55. Shiqin Xiong, Gloria Salazar, Alejandra San Martin, Mushtaq Ahmad, Nikolay Patrushev, Lula Hilenski, Rafal Robert Nazarewicz, Masuko Ushio-Fukai, R Wayne Alexander. PGC-1a Ser570 phosphorylation and GCN5-mediated acetylation by angiotensin II induces catalase downregulation and vascular hypertrophy. PNAS submitted in 2009
  56. Smith AM, Rhyner MV, Ruan G, Duan H, and Nie SM. (2006)  A Systematic Examination of Surface Coatings on the Optical and Chemical Properties of Semiconductor Quantum Dots. Phys. Chem. Chem. Phys. 8, 3895-3903.
  57. Smith AM, Ruan G, Rhyner MV and Nie S. (2006) Engineering luminescent quantum dots for in-vivo molecular and cellular imaging. Ann Biomed Eng. 34: 3-14.
  58. Sungmun Lee, Stephen C. Yang, Chen-Yu Kao, Robert H. Pierce, and Niren Murthy, "Solid polymeric microparticles enhance the delivery of siRNA to macrophages in vivo" Submitted to Nucleic Acid Research 2009.
  59. Suo J, Ferrara DE, Sorescu D, Guldberg RE, Taylor RW and Giddens DP. (2007) Hemodynamic shear stresses in mouse aortas: Implications for atherogenesis; Arterioscler Thromb Vasc Biol., 27, 346-351.
  60. Suo J, Oshinski JN and Giddens DP, Blood Flow Patterns in the Proximal Human Coronary Arteries: Relationship to Atherosclerotic Plaque Occurrence, Molecular and Cellular Biomechanics, 2008; 5:9-18.
  61. Suo Jin, John Oshinski and Don Giddens, “Flow Patterns and Wall Shear Stress in the Proximal Segments of Human Coronary Arteries With and Without Aorta,” 2005 Summer Bioengineering Conference (ASME), 2005.
  62. Sy J, Iyer G, Yang S, Brown M, Oh T, Dikalov S, Murthy N, Davis ME. “Sustained release of a p38-inhibitor from non-inflammatory microspheres inhibits cardiac dysfunction”.  Nature Materials. (2008), 7 (11), 863-868.  PMCID: PMC2705946.
  63. Tressel SL, Huang RP, Tomsen N, Jo H.  Laminar shear inhibits tubule formation and migration of endothelial cells by an angiopoietin-2-dependent mechanism.  Arterioscler Thromb Vasc Biol. 2007; 27:2150-6.  PMCID: PMC2699463.
  64. Tressel SL, Kim H, Ni C-W, Chang K, Velasquez-Castano JC, Taylor WR, Yoon Y-S, Jo H. Angiopoietin-2 Stimulates Blood Flow Recovery after Femoral Artery Occlusion by Inducing Inflammation and Arteriogenesis.  Arterioscler Thromb Vasc Biol. 2008; 28:1989-95.  PMCID: PMC2613177.
  65. Vega-Ostertag ME, Ferrara DE, Romay-Penabad Z, Liu X, Taylor WR. (2007) Colden-Stanfield M, Pierangeli SS.  Role of p38 mitogen-activated protein kinase in antiphospholipid antibody-mediated thrombosis and endothelial cell activation.  J Thromb Haemost, 5, 1828-1834.
  66. X. Gao, M. V. Yezhelyev, L. Qi, R. M. O’Regan, and S. M. Nie, “Proton-sponge-coated quantum dots for siRNA delivery and intracellular imaging,” J. Am. Chem. Soc., 2008, 130, 9006-1012. PMCID: PMC2621273.
  67. X. M. Qian, X. Zhou, and S. M. Nie, “Surface-Enhanced Raman Nanoparticle Beacons Based on Bioconjugated Gold Nanocrystals and Long Range Plasmonic Coupling,” J. Am. Chem. Soc. 2008, 130, 14934-14935. PMID: 18937463.
  68. Xiong S, Ahmad M, Patrushev NA, Hilenski L, San Martin A, Ushio-Fukai M, Alexander, RW. PGC-1a as a Novel Regulator for Angiotensin II-induced Reactive Oxygen Species Production and Hypertrophy in Vascular Smooth Muscle Cells. Circulation 2008. American Heart Association, Scientific Sessions 2008. New Orleans.
  69. Yang SC, Bhide M, Crispe IN, Pierce RH, Murthy N.   “Polyketal Copolymers: A New Acid-Sensitive Delivery Vehicle for Treating Acute Inflammatory Diseases”.  Bioconj Chem.  (2008), 19 (6), 1164-1169.  PMID: 18691251.
  70. Zhang S, Li J, Lykotrafitis G, Bao G, and Suresh S, Size-Dependent Endocytosis of Nanoparticles, Adv. Mater., 2009; 21:419-424. PMCID: PMC2709876.
  71. Zuo L, Ushio-Fukai M, Ikeda S, Patrushev N, Alexander RW. Reactive Oxygen Species-dependent Transactivation of EGF receptor in Signaling Endosomes Following AT1 Receptor Stimulation in Vascular Smooth Muscle Cells.  Circulation 2005. American Heart Association, Scientific Sessions 2005. Dallas TX
  72. Zuo L, Ushio-Fukai M, Schafer-Hales K, Marcus AI, Hilenski L, Alexander RW. Direct Evidence for Role of Caveolin1 and Microtubules/Actin Cytoskeleton in AT1 Receptor Trafficking and Signaling in Living Cells: Real-time Imaging Analysis. American Heart Association, Scientific Sessions 2006. Chicago, IL.
  73. Zurkiya O, Chan AWS and Hu X. (2008) MagA is sufficient for producing magnetic nanoparticles in mammalian cells, making it an MRI reporter, Magn Reson Med. 59, 1225-31. PMID: 18506784.
  74. Zurkiya O, Hu X. (2006) Off-resonance saturation as a means of generating contrast with superparamagnetic nanoparticles.  Magn Reson Med. 56, 726-32.
  75. Boeneman K, Mei BC, Dennis AM, Bao G, Deschamps, JR Mattoussi H, Medintz IL, “Sensing caspase 3 activity with quantum dot-fluorescent protein assemblies”, J. Am. Chem. Soc. 131, 3828-3829 (2009).
  76. Glaus CR, Rossin R, Welch MJ, Bao G, “In Vivo Evaluation of 64Cu-labeled Magnetic Nanoparticles as Dual-Modality PET/MR Imaging Agent”, submitted to Bioconj. Chem (2009).
  77. Rhee WJ, C-W. Ni, Z. Zheng, K. Chang, H. Jo, and G. Bao, “HuR regulates the expression of stress-sensitive genes and mediates inflammatory response in human umbilical vein endothelial cells”, submitted to PNAS (2009).
  78. Dennis AM, Sotto D, Mei BC, Medintz IL, Mattoussi H and Bao G.. Surface Ligand Effects on Metal-Affinity Coordination to Quantum Dots: Implications for Nanoprobe Self-Assembly.  Submitted to Bioconj. Chem (2009) 
  79. Medintz IL, Pons T, Susumu K, Boeneman K, Dennis AM, Farrell D, Deschamps JR, Melinger JS, Bao G and Mattoussi H. Resonance Energy Transfer Between Luminescent Quantum Dots and Diverse Fluorescent Protein Acceptors. Submitted to Journal of Physical Chemistry (2009) 
  80. Tong S, Hou S, Zheng Z, Zhou J and Bao G. Tunable superparamagnetic iron oxide nanoparticles as an MR contract agent for molecular imaging. Submitted to Nat. Nanotech (2009). 
  81. Rhee WJ and Bao G. Slow non-specific accumulation of 2'-deoxy and 2'-O-methyl oligonucleotide probes at mitochondria in live cells. Submitted to Nucleic Acid Res. (2009).
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