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    22837 Publications
    3073 Total Profiles
    23 Edited Profiles

    Schaffer, David

    TitleChemist Faculty
    SchoolLawrence Berkeley National Lab
    DepartmentPhysical Biosciences
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/643-5963

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Zheng B, Vazin T, Goodwill PW, Conway A, Verma A, Ulku Saritas E, Schaffer D, Conolly SM. Magnetic Particle Imaging tracks the long-term fate of in vivo neural cell implants with high image contrast. Sci Rep. 2015; 5:14055.
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      2. Han BW, Layman H, Rode NA, Conway A, Schaffer DV, Boudreau NJ, Jackson WM, Healy KE. Multivalent Conjugates of Sonic Hedgehog Accelerate Diabetic Wound Healing. Tissue Eng Part A. 2015 Sep; 21(17-18):2366-78.
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      3. Yousef H, Conboy MJ, Morgenthaler A, Schlesinger C, Bugaj L, Paliwal P, Greer C, Conboy IM, Schaffer D. Systemic attenuation of the TGF-ß pathway by a single drug simultaneously rejuvenates hippocampal neurogenesis and myogenesis in the same old mammal. Oncotarget. 2015 May 20; 6(14):11959-78.
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      4. Kotterman MA, Vazin T, Schaffer DV. Enhanced selective gene delivery to neural stem cells in vivo by an adeno-associated viral variant. Development. 2015 May 15; 142(10):1885-92.
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      5. Dey SS, Foley JE, Limsirichai P, Schaffer DV, Arkin AP. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci. Mol Syst Biol. 2015; 11(5):806.
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      6. Yousef H, Morgenthaler A, Schlesinger C, Bugaj L, Conboy IM, Schaffer DV. Age-Associated Increase in BMP Signaling Inhibits Hippocampal Neurogenesis. Stem Cells. 2015 May; 33(5):1577-88.
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      7. Bugaj LJ, Spelke DP, Mesuda CK, Varedi M, Kane RS, Schaffer DV. Regulation of endogenous transmembrane receptors through optogenetic Cry2 clustering. Nat Commun. 2015; 6:6898.
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      8. Fritz AL, Adil MM, Mao SR, Schaffer DV. cAMP and EPAC Signaling Functionally Replace OCT4 During Induced Pluripotent Stem Cell Reprogramming. Mol Ther. 2015 May; 23(5):952-63.
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      9. Jha AK, Tharp KM, Ye J, Santiago-Ortiz JL, Jackson WM, Stahl A, Schaffer DV, Yeghiazarians Y, Healy KE. Enhanced survival and engraftment of transplanted stem cells using growth factor sequestering hydrogels. Biomaterials. 2015 Apr; 47:1-12.
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      10. Kotterman MA, Yin L, Strazzeri JM, Flannery JG, Merigan WH, Schaffer DV. Antibody neutralization poses a barrier to intravitreal adeno-associated viral vector gene delivery to non-human primates. Gene Ther. 2015 Feb; 22(2):116-26.
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      11. Byrne LC, Lin YJ, Lee T, Schaffer DV, Flannery JG. The Expression Pattern of Systemically Injected AAV9 in the Developing Mouse Retina Is Determined by Age. Mol Ther. 2015 Feb; 23(2):290-6.
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      12. Fritz AL, Mao SR, West MG, Schaffer DV. A medium-throughput analysis of signaling pathways involved in early stages of stem cell reprogramming. Biotechnol Bioeng. 2015 Jan; 112(1):209-19.
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      13. Yousef H, Conboy MJ, Mamiya H, Zeiderman M, Schlesinger C, Schaffer DV, Conboy IM. Mechanisms of action of hESC-secreted proteins that enhance human and mouse myogenesis. Aging (Albany NY). 2014 Aug; 6(8):602-20.
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      14. Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer DV, Herr AE. Single-cell western blotting. Nat Methods. 2014 Jul; 11(7):749-55.
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      15. Kotterman MA, Schaffer DV. Engineering adeno-associated viruses for clinical gene therapy. Nat Rev Genet. 2014 Jul; 15(7):445-51.
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      16. Yin L, Masella B, Dalkara D, Zhang J, Flannery JG, Schaffer DV, Williams DR, Merigan WH. Imaging light responses of foveal ganglion cells in the living macaque eye. J Neurosci. 2014 May 7; 34(19):6596-605.
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      17. Conway A, Schaffer DV. Biomaterial microenvironments to support the generation of new neurons in the adult brain. Stem Cells. 2014 May; 32(5):1220-9.
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      18. Shapiro MG, Ramirez RM, Sperling LJ, Sun G, Sun J, Pines A, Schaffer DV, Bajaj VS. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. Nat Chem. 2014 Jul; 6(7):629-34.
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      19. Byrne LC, Oztürk BE, Lee T, Fortuny C, Visel M, Dalkara D, Schaffer DV, Flannery JG. Retinoschisin gene therapy in photoreceptors, Müller glia or all retinal cells in the Rs1h-/- mouse. Gene Ther. 2014 Jun; 21(6):585-92.
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      20. Cao J, Arha M, Sudrik C, Schaffer DV, Kane RS. Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains. Angew Chem Int Ed Engl. 2014 May 5; 53(19):4900-4.
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      21. Shapiro MG, Goodwill PW, Neogy A, Yin M, Foster FS, Schaffer DV, Conolly SM. Biogenic gas nanostructures as ultrasonic molecular reporters. Nat Nanotechnol. 2014 Apr; 9(4):311-6.
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      22. Schaffer DV. AAV shuffles to the liver: commentary on Lisowski et al. Mol Ther Methods Clin Dev. 2014; 1:14006.
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      23. Loring JF, McDevitt TC, Palecek SP, Schaffer DV, Zandstra PW, Nerem RM. A global assessment of stem cell engineering. Tissue Eng Part A. 2014 Oct; 20(19-20):2575-89.
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      24. Ojala DS, Amara DP, Schaffer DV. Adeno-associated virus vectors and neurological gene therapy. Neuroscientist. 2015 Feb; 21(1):84-98.
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      25. Conway A, Spelke DP, Schaffer DV. Conjugation of proteins to polymer chains to create multivalent molecules. Methods Mol Biol. 2014; 1202:95-102.
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      26. Day TP, Byrne LC, Schaffer DV, Flannery JG. Advances in AAV Vector Development for Gene Therapy in the Retina. Adv Exp Med Biol. 2014; 801:687-93.
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      27. Bartel MA, Schaffer DV. Enhanced Gene Targeting of Adult and Pluripotent Stem Cells Using Evolved Adeno-associated Virus. Methods Mol Biol. 2014; 1114:169-79.
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      28. Vacca O, Darche M, Schaffer DV, Flannery JG, Sahel JA, Rendon A, Dalkara D. AAV-mediated gene delivery in Dp71-null mouse model with compromised barriers. Glia. 2014 Mar; 62(3):468-76.
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      29. Lei Y, Schaffer DV. A fully defined and scalable 3D culture system for human pluripotent stem cell expansion and differentiation. Proc Natl Acad Sci U S A. 2013 Dec 24; 110(52):E5039-48.
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      30. Ekerdt BL, Segalman RA, Schaffer DV. Spatial organization of cell-adhesive ligands for advanced cell culture. Biotechnol J. 2013 Dec; 8(12):1411-23.
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      31. Vazin T, Ashton RS, Conway A, Rode NA, Lee SM, Bravo V, Healy KE, Kane RS, Schaffer DV. The effect of multivalent Sonic hedgehog on differentiation of human embryonic stem cells into dopaminergic and GABAergic neurons. Biomaterials. 2014 Jan; 35(3):941-8.
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      32. Downing TL, Soto J, Morez C, Houssin T, Fritz A, Yuan F, Chu J, Patel S, Schaffer DV, Li S. Biophysical regulation of epigenetic state and cell reprogramming. Nat Mater. 2013 Dec; 12(12):1154-62.
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      33. Conway A, Vazin T, Spelke DP, Rode NA, Healy KE, Kane RS, Schaffer DV. Multivalent ligands control stem cell behaviour in vitro and in vivo. Nat Nanotechnol. 2013 Nov; 8(11):831-8.
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      34. Cao J, Arha M, Sudrik C, Bugaj LJ, Schaffer DV, Kane RS. Light-inducible activation of target mRNA translation in mammalian cells. Chem Commun (Camb). 2013 Sep 28; 49(75):8338-40.
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      35. Byrne LC, Khalid F, Lee T, Zin EA, Greenberg KP, Visel M, Schaffer DV, Flannery JG. AAV-Mediated, Optogenetic Ablation of Müller Glia Leads to Structural and Functional Changes in the Mouse Retina. PLoS One. 2013; 8(9):e76075.
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      36. Vazin T, Ball KA, Lu H, Park H, Ataeijannati Y, Head-Gordon T, Poo MM, Schaffer DV. Efficient derivation of cortical glutamatergic neurons from human pluripotent stem cells: A model system to study neurotoxicity in Alzheimer's disease. Neurobiol Dis. 2014 Feb; 62:62-72.
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      37. Sudrik C, Arha M, Cao J, Schaffer DV, Kane RS. Translational repression using BIV Tat peptide-TAR RNA interaction in mammalian cells. Chem Commun (Camb). 2013 Aug 28; 49(67):7457-9.
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      38. Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer DV. Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression. PLoS Comput Biol. 2013; 9(7):e1003135.
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      39. Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer DV. In vivo-directed evolution of a new adeno-associated virus for therapeutic outer retinal gene delivery from the vitreous. Sci Transl Med. 2013 Jun 12; 5(189):189ra76.
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      40. Yousef H, Conboy MJ, Li J, Zeiderman M, Vazin T, Schlesinger C, Schaffer DV, Conboy IM. hESC-secreted proteins can be enriched for multiple regenerative therapies by heparin-binding. Aging (Albany NY). 2013 May; 5(5):357-72.
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      41. Bugaj LJ, Choksi AT, Mesuda CK, Kane RS, Schaffer DV. Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods. 2013 Mar; 10(3):249-52.
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      42. Hwang BY, Schaffer DV. Engineering a serum-resistant and thermostable vesicular stomatitis virus G glycoprotein for pseudotyping retroviral and lentiviral vectors. Gene Ther. 2013 Aug; 20(8):807-15.
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      43. Chen S, Schaffer DV. Newborn neuroblasts feel the field in the adult brain. EMBO Rep. 2013 Feb; 14(2):105-6.
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      44. Keung AJ, Dong M, Schaffer DV, Kumar S. Pan-neuronal maturation but not neuronal subtype differentiation of adult neural stem cells is mechanosensitive. Sci Rep. 2013; 3:1817.
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      45. Conway A, Schaffer DV. Biophysical regulation of stem cell behavior within the niche. Stem Cell Res Ther. 2012; 3(6):50.
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      46. Pernet V, Joly S, Dalkara D, Jordi N, Schwarz O, Christ F, Schaffer DV, Flannery JG, Schwab ME. Long-distance axonal regeneration induced by CNTF gene transfer is impaired by axonal misguidance in the injured adult optic nerve. Neurobiol Dis. 2013 Mar; 51:202-13.
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      47. Ashton RS, Conway A, Pangarkar C, Bergen J, Lim KI, Shah P, Bissell M, Schaffer DV. Astrocytes regulate adult hippocampal neurogenesis through ephrin-B signaling. Nat Neurosci. 2012 Oct; 15(10):1399-406.
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      48. Pollock JF, Ashton RS, Rode NA, Schaffer DV, Healy KE. Molecular characterization of multivalent bioconjugates by size-exclusion chromatography with multiangle laser light scattering. Bioconjug Chem. 2012 Sep 19; 23(9):1794-801.
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      49. Keung AJ, Asuri P, Kumar S, Schaffer DV. Soft microenvironments promote the early neurogenic differentiation but not self-renewal of human pluripotent stem cells. Integr Biol (Camb). 2012 Sep; 4(9):1049-58.
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      50. Goodwill PW, Saritas EU, Croft LR, Kim TN, Krishnan KM, Schaffer DV, Conolly SM. X-space MPI: magnetic nanoparticles for safe medical imaging. Adv Mater. 2012 Jul 24; 24(28):3870-7.
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      51. Shah PS, Schaffer DV. Response to "HIV Escape From RNAi Antivirals: Yet Another Houdini Action?". Mol Ther Nucleic Acids. 2012; 1:e28.
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      52. Bugaj LJ, Schaffer DV. Bringing next-generation therapeutics to the clinic through synthetic biology. Curr Opin Chem Biol. 2012 Aug; 16(3-4):355-61.
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      53. Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer DV. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-?B mediated viral gene expression. Integr Biol (Camb). 2012 Jun; 4(6):661-71.
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      54. Bartel MA, Weinstein JR, Schaffer DV. Directed evolution of novel adeno-associated viruses for therapeutic gene delivery. Gene Ther. 2012 Jun; 19(6):694-700.
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      55. Shah PS, Pham NP, Schaffer DV. HIV develops indirect cross-resistance to combinatorial RNAi targeting two distinct and spatially distant sites. Mol Ther. 2012 Apr; 20(4):840-8.
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      56. Jgamadze D, Bergen J, Stone D, Jang JH, Schaffer DV, Isacoff EY, Pautot S. Colloids as mobile substrates for the implantation and integration of differentiated neurons into the mammalian brain. PLoS One. 2012; 7(1):e30293.
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      57. Asokan A, Schaffer DV, Samulski RJ. The AAV vector toolkit: poised at the clinical crossroads. Mol Ther. 2012 Apr; 20(4):699-708.
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      58. Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. J Biol Chem. 2012 Mar 9; 287(11):7945-55.
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      59. Pernet V, Joly S, Dalkara D, Schwarz O, Christ F, Schaffer D, Flannery JG, Schwab ME. Neuronal Nogo-A upregulation does not contribute to ER stress-associated apoptosis but participates in the regenerative response in the axotomized adult retina. Cell Death Differ. 2012 Jul; 19(7):1096-108.
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      60. An HJ, Gip P, Kim J, Wu S, Park KW, McVaugh CT, Schaffer DV, Bertozzi CR, Lebrilla CB. Extensive determination of glycan heterogeneity reveals an unusual abundance of high mannose glycans in enriched plasma membranes of human embryonic stem cells. Mol Cell Proteomics. 2012 Apr; 11(4):M111.010660.
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      61. Asuri P, Bartel MA, Vazin T, Jang JH, Wong TB, Schaffer DV. Directed evolution of adeno-associated virus for enhanced gene delivery and gene targeting in human pluripotent stem cells. Mol Ther. 2012 Feb; 20(2):329-38.
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      62. Keung AJ, de Juan-Pardo EM, Schaffer DV, Kumar S. Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells. Stem Cells. 2011 Nov; 29(11):1886-97.
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      63. Dalkara D, Byrne LC, Lee T, Hoffmann NV, Schaffer DV, Flannery JG. Enhanced gene delivery to the neonatal retina through systemic administration of tyrosine-mutated AAV9. Gene Ther. 2012 Feb; 19(2):176-81.
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      64. Bartel M, Schaffer D, Büning H. Enhancing the Clinical Potential of AAV Vectors by Capsid Engineering to Evade Pre-Existing Immunity. Front Microbiol. 2011; 2:204.
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      65. Shah PS, Schaffer DV. Antiviral RNAi: translating science towards therapeutic success. Pharm Res. 2011 Dec; 28(12):2966-82.
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      66. Hester ME, Murtha MJ, Song S, Rao M, Miranda CJ, Meyer K, Tian J, Boulting G, Schaffer DV, Zhu MX, Pfaff SL, Gage FH, Kaspar BK. Rapid and efficient generation of functional motor neurons from human pluripotent stem cells using gene delivered transcription factor codes. Mol Ther. 2011 Oct; 19(10):1905-12.
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      67. Dickey DD, Excoffon KJ, Koerber JT, Bergen J, Steines B, Klesney-Tait J, Schaffer DV, Zabner J. Enhanced sialic acid-dependent endocytosis explains the increased efficiency of infection of airway epithelia by a novel adeno-associated virus. J Virol. 2011 Sep; 85(17):9023-30.
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      68. Miller-Jensen K, Dey SS, Schaffer DV, Arkin AP. Varying virulence: epigenetic control of expression noise and disease processes. Trends Biotechnol. 2011 Oct; 29(10):517-25.
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      69. Jang JH, Schaffer DV, Shea LD. Engineering biomaterial systems to enhance viral vector gene delivery. Mol Ther. 2011 Aug; 19(8):1407-15.
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      70. Dalkara D, Kolstad KD, Guerin KI, Hoffmann NV, Visel M, Klimczak RR, Schaffer DV, Flannery JG. AAV mediated GDNF secretion from retinal glia slows down retinal degeneration in a rat model of retinitis pigmentosa. Mol Ther. 2011 Sep; 19(9):1602-8.
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      71. Yin L, Greenberg K, Hunter JJ, Dalkara D, Kolstad KD, Masella BD, Wolfe R, Visel M, Stone D, Libby RT, Diloreto D, Schaffer D, Flannery J, Williams DR, Merigan WH. Intravitreal injection of AAV2 transduces macaque inner retina. Invest Ophthalmol Vis Sci. 2011 Apr; 52(5):2775-83.
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      72. Arkin AP, Schaffer DV. Network news: innovations in 21st century systems biology. Cell. 2011 Mar 18; 144(6):844-9.
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      73. Jang JH, Koerber JT, Kim JS, Asuri P, Vazin T, Bartel M, Keung A, Kwon I, Park KI, Schaffer DV. An evolved adeno-associated viral variant enhances gene delivery and gene targeting in neural stem cells. Mol Ther. 2011 Apr; 19(4):667-75.
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      74. Ashton RS, Keung AJ, Peltier J, Schaffer DV. Progress and prospects for stem cell engineering. Annu Rev Chem Biomol Eng. 2011; 2:479-502.
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      75. Dickinson BC, Peltier J, Stone D, Schaffer DV, Chang CJ. Nox2 redox signaling maintains essential cell populations in the brain. Nat Chem Biol. 2011 Feb; 7(2):106-12.
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      76. Peltier J, Conway A, Keung AJ, Schaffer DV. Akt increases sox2 expression in adult hippocampal neural progenitor cells, but increased sox2 does not promote proliferation. Stem Cells Dev. 2011 Jul; 20(7):1153-61.
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      77. Saha K, Kim J, Irwin E, Yoon J, Momin F, Trujillo V, Schaffer DV, Healy KE, Hayward RC. Surface creasing instability of soft polyacrylamide cell culture substrates. Biophys J. 2010 Dec 15; 99(12):L94-6.
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      78. Little LE, Dane KY, Daugherty PS, Healy KE, Schaffer DV. Exploiting bacterial peptide display technology to engineer biomaterials for neural stem cell culture. Biomaterials. 2011 Feb; 32(6):1484-94.
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      79. Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One. 2010; 5(10):e13564.
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      80. Skupsky R, Burnett JC, Foley JE, Schaffer DV, Arkin AP. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol. 2010; 6(9).
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      81. Schaffer DV. Microarraying for mechanosensivitity. Cell Stem Cell. 2010 Sep 3; 7(3):273-4.
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      82. Ananthanarayanan B, Little L, Schaffer DV, Healy KE, Tirrell M. Neural stem cell adhesion and proliferation on phospholipid bilayers functionalized with RGD peptides. Biomaterials. 2010 Nov; 31(33):8706-15.
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      83. Aviran S, Shah PS, Schaffer DV, Arkin AP. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol. 2010; 6(8).
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      84. Lim KI, Klimczak R, Yu JH, Schaffer DV. Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12475-80.
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      85. Shah PS, Schaffer DV. Gene therapy takes a cue from HAART: combinatorial antiviral therapeutics reach the clinic. Sci Transl Med. 2010 Jun 16; 2(36):36ps30.
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      86. Jang JH, Koerber JT, Gujraty K, Bethi SR, Kane RS, Schaffer DV. Surface immobilization of hexa-histidine-tagged adeno-associated viral vectors for localized gene delivery. Gene Ther. 2010 Nov; 17(11):1384-9.
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      87. Kolstad KD, Dalkara D, Guerin K, Visel M, Hoffmann N, Schaffer DV, Flannery JG. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration. Hum Gene Ther. 2010 May; 21(5):571-8.
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      88. Kurpinski K, Lam H, Chu J, Wang A, Kim A, Tsay E, Agrawal S, Schaffer DV, Li S. Transforming growth factor-beta and notch signaling mediate stem cell differentiation into smooth muscle cells. Stem Cells. 2010 Apr; 28(4):734-42.
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      89. Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer DV, Arkin AP. Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol. 2010 Jun; 84(12):5958-74.
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      90. Peltier J, Agrawal S, Robertson MJ, Schaffer DV. In vitro culture and analysis of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:65-87.
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      91. Robertson MJ, Peltier J, Schaffer DV. In vivo analysis of engrafted adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:89-102.
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      92. Peltier J, Schaffer DV. Viral packaging and transduction of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:103-16.
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      93. Keung AJ, Healy KE, Kumar S, Schaffer DV. Biophysics and dynamics of natural and engineered stem cell microenvironments. Wiley Interdiscip Rev Syst Biol Med. 2010 Jan-Feb; 2(1):49-64.
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      94. Peltier J, Schaffer DV. Systems biology approaches to understanding stem cell fate choice. IET Syst Biol. 2010 Jan; 4(1):1-11.
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      95. Peltier J, Ormerod BK, Schaffer DV. Isolation of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:57-63.
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      96. Keung AJ, Kumar S, Schaffer DV. Presentation counts: microenvironmental regulation of stem cells by biophysical and material cues. Annu Rev Cell Dev Biol. 2010; 26:533-56.
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      97. Vazin T, Schaffer DV. Engineering strategies to emulate the stem cell niche. Trends Biotechnol. 2010 Mar; 28(3):117-24.
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      98. Meng Y, Eshghi S, Li YJ, Schmidt R, Schaffer DV, Healy KE. Characterization of integrin engagement during defined human embryonic stem cell culture. FASEB J. 2010 Apr; 24(4):1056-65.
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      99. Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer DV. A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Müller cells. PLoS One. 2009; 4(10):e7467.
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      100. Carlson ME, Conboy MJ, Hsu M, Barchas L, Jeong J, Agrawal A, Mikels AJ, Agrawal S, Schaffer DV, Conboy IM. Relative roles of TGF-beta1 and Wnt in the systemic regulation and aging of satellite cell responses. Aging Cell. 2009 Dec; 8(6):676-89.
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      101. Koerber JT, Klimczak R, Jang JH, Dalkara D, Flannery JG, Schaffer DV. Molecular evolution of adeno-associated virus for enhanced glial gene delivery. Mol Ther. 2009 Dec; 17(12):2088-95.
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      102. Dalkara D, Kolstad KD, Caporale N, Visel M, Klimczak RR, Schaffer DV, Flannery JG. Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous. Mol Ther. 2009 Dec; 17(12):2096-102.
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      103. Banerjee A, Arha M, Choudhary S, Ashton RS, Bhatia SR, Schaffer DV, Kane RS. The influence of hydrogel modulus on the proliferation and differentiation of encapsulated neural stem cells. Biomaterials. 2009 Sep; 30(27):4695-9.
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      104. Agrawal S, Archer C, Schaffer DV. Computational models of the Notch network elucidate mechanisms of context-dependent signaling. PLoS Comput Biol. 2009 May; 5(5):e1000390.
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      105. Excoffon KJ, Koerber JT, Dickey DD, Murtha M, Keshavjee S, Kaspar BK, Zabner J, Schaffer DV. Directed evolution of adeno-associated virus to an infectious respiratory virus. Proc Natl Acad Sci U S A. 2009 Mar 10; 106(10):3865-70.
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      106. Burnett JC, Miller-Jensen K, Shah PS, Arkin AP, Schaffer DV. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathog. 2009 Jan; 5(1):e1000260.
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      107. Leonard JN, Shah PS, Burnett JC, Schaffer DV. HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host Microbe. 2008 Nov 13; 4(5):484-94.
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      108. Koerber JT, Jang JH, Schaffer DV. DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. Mol Ther. 2008 Oct; 16(10):1703-9.
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      109. Saha K, Keung AJ, Irwin EF, Li Y, Little L, Schaffer DV, Healy KE. Substrate modulus directs neural stem cell behavior. Biophys J. 2008 Nov 1; 95(9):4426-38.
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      110. Little L, Healy KE, Schaffer D. Engineering biomaterials for synthetic neural stem cell microenvironments. Chem Rev. 2008 May; 108(5):1787-96.
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      111. Wall ST, Saha K, Ashton RS, Kam KR, Schaffer DV, Healy KE. Multivalency of Sonic hedgehog conjugated to linear polymer chains modulates protein potency. Bioconjug Chem. 2008 Apr; 19(4):806-12.
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      112. Lim KI, Schaffer DV. Library selection approaches to engineering enhanced retroviral and lentiviral vectors. Comb Chem High Throughput Screen. 2008 Feb; 11(2):111-7.
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      113. Koerber JT, Schaffer DV. Transposon-based mutagenesis generates diverse adeno-associated viral libraries with novel gene delivery properties. Methods Mol Biol. 2008; 434:161-70.
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      114. Robertson MJ, Gip P, Schaffer DV. Neural stem cell engineering: directed differentiation of adult and embryonic stem cells into neurons. Front Biosci. 2008; 13:21-50.
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      115. Schaffer DV, Koerber JT, Lim KI. Molecular engineering of viral gene delivery vehicles. Annu Rev Biomed Eng. 2008; 10:169-94.
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      116. Ho JE, Chung EH, Wall S, Schaffer DV, Healy KE. Immobilized sonic hedgehog N-terminal signaling domain enhances differentiation of bone marrow-derived mesenchymal stem cells. J Biomed Mater Res A. 2007 Dec 15; 83(4):1200-8.
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      117. Ricci C, Pastukh V, Leonard J, Turrens J, Wilson G, Schaffer D, Schaffer SW. Mitochondrial DNA damage triggers mitochondrial-superoxide generation and apoptosis. Am J Physiol Cell Physiol. 2008 Feb; 294(2):C413-22.
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      119. Ashton RS, Banerjee A, Punyani S, Schaffer DV, Kane RS. Scaffolds based on degradable alginate hydrogels and poly(lactide-co-glycolide) microspheres for stem cell culture. Biomaterials. 2007 Dec; 28(36):5518-25.
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      120. Kwon I, Schaffer DV. Designer gene delivery vectors: molecular engineering and evolution of adeno-associated viral vectors for enhanced gene transfer. Pharm Res. 2008 Mar; 25(3):489-99.
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      121. Peltier J, O'Neill A, Schaffer DV. PI3K/Akt and CREB regulate adult neural hippocampal progenitor proliferation and differentiation. Dev Neurobiol. 2007 Sep 1; 67(10):1348-61.
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      123. Leonard JN, Ferstl P, Delgado A, Schaffer DV. Enhanced preparation of adeno-associated viral vectors by using high hydrostatic pressure to selectively inactivate helper adenovirus. Biotechnol Bioeng. 2007 Aug 1; 97(5):1170-9.
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      124. Saha K, Pollock JF, Schaffer DV, Healy KE. Designing synthetic materials to control stem cell phenotype. Curr Opin Chem Biol. 2007 Aug; 11(4):381-7.
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      125. Koerber JT, Jang JH, Yu JH, Kane RS, Schaffer DV. Engineering adeno-associated virus for one-step purification via immobilized metal affinity chromatography. Hum Gene Ther. 2007 Apr; 18(4):367-78.
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      126. Greenberg KP, Geller SF, Schaffer DV, Flannery JG. Targeted transgene expression in muller glia of normal and diseased retinas using lentiviral vectors. Invest Ophthalmol Vis Sci. 2007 Apr; 48(4):1844-52.
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      127. Saha K, Irwin EF, Kozhukh J, Schaffer DV, Healy KE. Biomimetic interfacial interpenetrating polymer networks control neural stem cell behavior. J Biomed Mater Res A. 2007 Apr; 81(1):240-9.
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      128. Yu JH, Schaffer DV. High-throughput, library-based selection of a murine leukemia virus variant to infect nondividing cells. J Virol. 2006 Sep; 80(18):8981-8.
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      129. Jang JH, Schaffer DV. Microarraying the cellular microenvironment. Mol Syst Biol. 2006; 2:39.
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      130. Abranches E, O'Neill A, Robertson MJ, Schaffer DV, Cabral JM. Development of quantitative PCR methods to analyse neural progenitor cell culture state. Biotechnol Appl Biochem. 2006 Apr; 44(Pt 1):1-8.
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      131. Yu JH, Schaffer DV. Selection of novel vesicular stomatitis virus glycoprotein variants from a peptide insertion library for enhanced purification of retroviral and lentiviral vectors. J Virol. 2006 Apr; 80(7):3285-92.
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      132. Leonard JN, Schaffer DV. Antiviral RNAi therapy: emerging approaches for hitting a moving target. Gene Ther. 2006 Mar; 13(6):532-40.
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      133. Saha K, Schaffer DV. Signal dynamics in Sonic hedgehog tissue patterning. Development. 2006 Mar; 133(5):889-900.
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      134. Maheshri N, Koerber JT, Kaspar BK, Schaffer DV. Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat Biotechnol. 2006 Feb; 24(2):198-204.
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      135. Greenberg KP, Lee ES, Schaffer DV, Flannery JG. Gene delivery to the retina using lentiviral vectors. Adv Exp Med Biol. 2006; 572:255-66.
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      136. Koerber JT, Maheshri N, Kaspar BK, Schaffer DV. Construction of diverse adeno-associated viral libraries for directed evolution of enhanced gene delivery vehicles. Nat Protoc. 2006; 1(2):701-6.
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      137. Lee GK, Maheshri N, Kaspar B, Schaffer DV. PEG conjugation moderately protects adeno-associated viral vectors against antibody neutralization. Biotechnol Bioeng. 2005 Oct 5; 92(1):24-34.
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      138. Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul 29; 122(2):169-82.
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      139. Leonard JN, Schaffer DV. Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape. J Virol. 2005 Feb; 79(3):1645-54.
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      140. Agrawal S, Schaffer DV. In situ stem cell therapy: novel targets, familiar challenges. Trends Biotechnol. 2005 Feb; 23(2):78-83.
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      141. Yu JH, Schaffer DV. Advanced targeting strategies for murine retroviral and adeno-associated viral vectors. Adv Biochem Eng Biotechnol. 2005; 99:147-67.
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      142. Prokop A, Prokop Z, Schaffer D, Kozlov E, Wikswo J, Cliffel D, Baudenbacher F. NanoLiterBioReactor: long-term mammalian cell culture at nanofabricated scale. Biomed Microdevices. 2004 Dec; 6(4):325-39.
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      143. O'Neill A, Schaffer DV. The biology and engineering of stem-cell control. Biotechnol Appl Biochem. 2004 Aug; 40(Pt 1):5-16.
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      144. Ignowski JM, Schaffer DV. Kinetic analysis and modeling of firefly luciferase as a quantitative reporter gene in live mammalian cells. Biotechnol Bioeng. 2004 Jun 30; 86(7):827-34.
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      145. Lai K, Robertson MJ, Schaffer DV. The sonic hedgehog signaling system as a bistable genetic switch. Biophys J. 2004 May; 86(5):2748-57.
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      146. Schaffer DV, Gage FH. Neurogenesis and neuroadaptation. Neuromolecular Med. 2004; 5(1):1-9.
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      147. Schaffer DV, O'Neill A, Hochrein L, McGranahan T. Quantitative analysis of signaling mechanisms controlling adult neural progenitor cell proliferation. Conf Proc IEEE Eng Med Biol Soc. 2004; 7:4965.
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      148. Schaffer DV, Maheshri N. Directed evolution of AAV mutants for enhanced gene delivery. Conf Proc IEEE Eng Med Biol Soc. 2004; 5:3520-3.
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      149. Weinberger LS, Schaffer DV, Arkin AP. Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection. J Virol. 2003 Sep; 77(18):10028-36.
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      150. Maheshri N, Schaffer DV. Computational and experimental analysis of DNA shuffling. Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6):3071-6.
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      151. Lai K, Kaspar BK, Gage FH, Schaffer DV. Sonic hedgehog regulates adult neural progenitor proliferation in vitro and in vivo. Nat Neurosci. 2003 Jan; 6(1):21-7.
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      152. Lee G, Schaffer D. Engineering the surface properties of synthetic gene delivery vectors. Somat Cell Mol Genet. 2002 Nov; 27(1-6):17-25.
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      153. Schaffer DV. Genetic approaches to tissue repair. Ann N Y Acad Sci. 2002 Jun; 961:68-70.
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      154. Bonadio J, Woo SL, High K, Ghivizzani S, Schaffer D. Genetic approaches to tissue engineering: breakout session summary. Ann N Y Acad Sci. 2002 Jun; 961:71-2.
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      155. Kaspar BK, Vissel B, Bengoechea T, Crone S, Randolph-Moore L, Muller R, Brandon EP, Schaffer D, Verma IM, Lee KF, Heinemann SF, Gage FH. Adeno-associated virus effectively mediates conditional gene modification in the brain. Proc Natl Acad Sci U S A. 2002 Feb 19; 99(4):2320-5.
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      156. Kaspar BK, Erickson D, Schaffer D, Hinh L, Gage FH, Peterson DA. Targeted retrograde gene delivery for neuronal protection. Mol Ther. 2002 Jan; 5(1):50-6.
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      157. Slattery ML, Anderson K, Curtin K, Ma K, Schaffer D, Edwards S, Samowitz W. Lifestyle factors and Ki-ras mutations in colon cancer tumors. Mutat Res. 2001 Nov 1; 483(1-2):73-81.
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      158. Samowitz WS, Curtin K, Schaffer D, Robertson M, Leppert M, Slattery ML. Relationship of Ki-ras mutations in colon cancers to tumor location, stage, and survival: a population-based study. Cancer Epidemiol Biomarkers Prev. 2000 Nov; 9(11):1193-7.
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      159. Schaffer DV, Lauffenburger DA. Targeted synthetic gene delivery vectors. Curr Opin Mol Ther. 2000 Apr; 2(2):155-61.
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      160. Schaffer DV, Fidelman NA, Dan N, Lauffenburger DA. Vector unpacking as a potential barrier for receptor-mediated polyplex gene delivery. Biotechnol Bioeng. 2000 Mar 5; 67(5):598-606.
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      161. Lauffenburger DA, Schaffer DV. The matrix delivers. Nat Med. 1999 Jul; 5(7):733-4.
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      162. Schaffer DV, Lauffenburger DA. Optimization of cell surface binding enhances efficiency and specificity of molecular conjugate gene delivery. J Biol Chem. 1998 Oct 23; 273(43):28004-9.
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      163. Gramer MJ, Schaffer DV, Sliwkowski MB, Goochee CF. Purification and characterization of alpha-L-fucosidase from Chinese hamster ovary cell culture supernatant. Glycobiology. 1994 Oct; 4(5):611-6.
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      164. Johnson L, Schaffer D, Quinn G, Goldstein D, Mathis MJ, Otis C, Boggs TR. Vitamin E supplementation and the retinopathy of prematurity. Ann N Y Acad Sci. 1982; 393:473-95.
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