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Schaffer, David

TitleChemist Faculty
InstitutionLawrence Berkeley National Lab
DepartmentMolecular Biophys & Integ Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/643-5963
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    Collapse Research 
    Collapse Research Activities and Funding
    In Vivo Directed Evolution of Adeno-Associated Virus Vectors for Glioblastoma Multiforme Tumor-Initiating Cells
    NIH/NIBIB R21EB021572Sep 16, 2016 - Jul 31, 2018
    Role: Principal Investigator
    Multivalent Ligands to Control Stem Cell Fate
    NIH/NINDS R01NS083856Jul 1, 2014 - Jun 30, 2019
    Role: Principal Investigator
    Directed Evolution of Adeno-Associated Virus for Retinal Gene Therapy
    NIH/NEI R01EY022975May 1, 2014 - Apr 30, 2019
    Role: Principal Investigator
    Optogenetic Characterization and Control of Stem Cell Signaling
    NIH/NINDS R01NS087253Feb 15, 2014 - Jan 31, 2019
    Role: Principal Investigator
    Precise Surface Patterning to Investigate Cell-Cell Interactions that Regulate Ne
    NIH/NIBIB R21EB014610Aug 1, 2012 - Jul 31, 2014
    Role: Principal Investigator
    Mechanisms of Neural Stem Cell Mechanoregulation
    NIH/NINDS R01NS074831May 1, 2012 - Apr 30, 2022
    Role: Principal Investigator
    High-Throughput Platform for Identifying Stem Cell Toxicity
    NIH/NIEHS R01ES020903Dec 23, 2011 - Oct 31, 2015
    Role: Co-Principal Investigator
    Stem Cell Biological Engineering Training Program
    NIH/NIGMS T32GM098218Jul 1, 2011 - Jun 30, 2021
    Role: Principal Investigator
    Molecular Engineering of Bioactive Hydrogels
    NIH/NIDCR R21DE018044Apr 1, 2008 - Mar 31, 2011
    Role: Principal Investigator
    Engineering AAV Vectors to Evade Antibody Neutralization
    NIH/NHLBI R01HL081527Jun 8, 2007 - May 31, 2011
    Role: Principal Investigator
    Engineering Novel AAV Vectors for Retinal Gene Therapy
    NIH/NEI R21EY016994Aug 1, 2006 - Jul 31, 2009
    Role: Principal Investigator
    Investigation of Promoter Sequence-Function Relationships in a Model Retrovirus
    NIH/NIGMS R01GM073058Oct 1, 2004 - Mar 31, 2015
    Role: Principal Investigator
    Engineering Molecular Sensors for Stem Cell Function
    NIH/NINDS R21NS048248Apr 1, 2004 - Dec 31, 2006
    Role: Principal Investigator
    Molecular Engineering of AAV for Stealth and Targeting
    NIH/NIBIB R21EB003007Sep 1, 2003 - Aug 31, 2006
    Role: Principal Investigator
    GROWTH FACTOR SIGNALING AND NEURAL PROGENITOR CELL FATE
    NIH/NINDS F32NS010731Dec 1, 1998
    Role: Principal Investigator
    Applied Biology and Bioprocess Engineering Training
    NIH/NIGMS T32GM008352Sep 27, 1989 - Jun 30, 2009
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Mosher KI, Schaffer D. Proliferation versus Differentiation: Redefining Retinoic Acid's Role. Stem Cell Reports. 2018 Jun 05; 10(6):1673-1675. PMID: 29874625.
      View in: PubMed
    2. Ekerdt BL, Fuentes CM, Lei Y, Adil MM, Ramasubramanian A, Segalman RA, Schaffer D. Thermoreversible Hyaluronic Acid-PNIPAAm Hydrogel Systems for 3D Stem Cell Culture. Adv Healthc Mater. 2018 May 02; e1800225. PMID: 29717823.
      View in: PubMed
    3. Adil MM, Gaj T, Rao AT, Kulkarni RU, Fuentes CM, Ramadoss GN, Ekman FK, Miller EW, Schaffer D. hPSC-Derived Striatal Cells Generated Using a Scalable 3D Hydrogel Promote Recovery in a Huntington Disease Mouse Model. Stem Cell Reports. 2018 May 08; 10(5):1481-1491. PMID: 29628395.
      View in: PubMed
    4. Sun S, Schaffer D. Engineered viral vectors for functional interrogation, deconvolution, and manipulation of neural circuits. Curr Opin Neurobiol. 2018 Mar 31; 50:163-170. PMID: 29614429.
      View in: PubMed
    5. Adil MM, Schaffer D. hPSC-derived Midbrain Dopaminergic Neurons Generated in a Scalable 3-D Biomaterial. Curr Protoc Stem Cell Biol. 2018 Feb 28; 44:2D.21.1-2D.21.17. PMID: 29512105.
      View in: PubMed
    6. Chen KS, Xu M, Zhang Z, Chang WC, Gaj T, Schaffer D, Dan Y. A Hypothalamic Switch for REM and Non-REM Sleep. Neuron. 2018 Mar 07; 97(5):1168-1176.e4. PMID: 29478915.
      View in: PubMed
    7. Day TP, Byrne LC, Flannery JG, Schaffer D. Screening for Neutralizing Antibodies Against Natural and Engineered AAV Capsids in Nonhuman Primate Retinas. Methods Mol Biol. 2018; 1715:239-249. PMID: 29188518.
      View in: PubMed
    8. Gaj T, Ojala DS, Ekman FK, Byrne LC, Limsirichai P, Schaffer D. In vivo genome editing improves motor function and extends survival in a mouse model of ALS. Sci Adv. 2017 Dec; 3(12):eaar3952. PMID: 29279867.
      View in: PubMed
    9. Mukherjee A, Repina NA, Schaffer D, Kane RS. Optogenetic tools for cell biological applications. J Thorac Dis. 2017 Dec; 9(12):4867-4870. PMID: 29312679.
      View in: PubMed
    10. Kang PH, Kumar S, Schaffer D. Matrix degradation: Making way for neural stemness. Nat Mater. 2017 Nov 24; 16(12):1174-1176. PMID: 29170553.
      View in: PubMed
    11. Mosher KI, Schaffer D. Influence of hippocampal niche signals on neural stem cell functions during aging. Cell Tissue Res. 2018 01; 371(1):115-124. PMID: 29124394.
      View in: PubMed
    12. Kang P, Kumar S, Schaffer D. Novel biomaterials to study neural stem cell mechanobiology and improve cell-replacement therapies. Curr Opin Biomed Eng. 2017 Dec; 4:13-20. PMID: 29399646.
      View in: PubMed
    13. Wooley DP, Sharma P, Weinstein JR, Kotha Lakshmi Narayan P, Schaffer D, Excoffon KJDA. A directed evolution approach to select for novel Adeno-associated virus capsids on an HIV-1 producer T cell line. J Virol Methods. 2017 Dec; 250:47-54. PMID: 28918073.
      View in: PubMed
    14. Ojala DS, Sun S, Santiago-Ortiz JL, Shapiro MG, Romero PA, Schaffer D. In Vivo Selection of a Computationally Designed SCHEMA AAV Library Yields a Novel Variant for Infection of Adult Neural Stem Cells in the SVZ. Mol Ther. 2018 Jan 03; 26(1):304-319. PMID: 28988711.
      View in: PubMed
    15. Gaj T, Staahl BT, Rodrigues GMC, Limsirichai P, Ekman FK, Doudna JA, Schaffer D. Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res. 2017 Jun 20; 45(11):e98. PMID: 28334779.
      View in: PubMed
    16. Repina NA, Rosenbloom A, Mukherjee A, Schaffer D, Kane RS. At Light Speed: Advances in Optogenetic Systems for Regulating Cell Signaling and Behavior. Annu Rev Chem Biomol Eng. 2017 Jun 07; 8:13-39. PMID: 28592174.
      View in: PubMed
    17. Rodrigues GMC, Gaj T, Adil MM, Wahba J, Rao AT, Lorbeer FK, Kulkarni RU, Diogo MM, Cabral JMS, Miller EW, Hockemeyer D, Schaffer D. Defined and Scalable Differentiation of Human Oligodendrocyte Precursors from Pluripotent Stem Cells in a 3D Culture System. Stem Cell Reports. 2017 06 06; 8(6):1770-1783. PMID: 28552605.
      View in: PubMed
    18. Adil MM, Vazin T, Ananthanarayanan B, Rodrigues GMC, Rao AT, Kulkarni RU, Miller EW, Kumar S, Schaffer D. Engineered hydrogels increase the post-transplantation survival of encapsulated hESC-derived midbrain dopaminergic neurons. Biomaterials. 2017 Aug; 136:1-11. PMID: 28505596.
      View in: PubMed
    19. Adil MM, Rodrigues GM, Kulkarni RU, Rao AT, Chernavsky NE, Miller EW, Schaffer D. Efficient generation of hPSC-derived midbrain dopaminergic neurons in a fully defined, scalable, 3D biomaterial platform. Sci Rep. 2017 Jan 16; 7:40573. PMID: 28091566.
      View in: PubMed
    20. Zhang W, Schaffer D, Tso LS, Tang S, Tang W, Huang S, Yang B, Tucker JD. Innovation contests to promote sexual health in China: a qualitative evaluation. BMC Public Health. 2017 01 14; 17(1):78. PMID: 28088211.
      View in: PubMed
    21. Epstein BE, Schaffer D. Combining Engineered Nucleases with Adeno-associated Viral Vectors for Therapeutic Gene Editing. Adv Exp Med Biol. 2017; 1016:29-42. PMID: 29130152.
      View in: PubMed
    22. Kulkarni RU, Yin H, Pourmandi N, James F, Adil MM, Schaffer D, Wang Y, Miller EW. A Rationally Designed, General Strategy for Membrane Orientation of Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes. ACS Chem Biol. 2017 Feb 17; 12(2):407-413. PMID: 28004909.
      View in: PubMed
    23. Gaj T, Schaffer D. Adeno-Associated Virus-Mediated Delivery of CRISPR-Cas Systems for Genome Engineering in Mammalian Cells. Cold Spring Harb Protoc. 2016 11 01; 2016(11). PMID: 27803249.
      View in: PubMed
    24. Nierode GJ, Perea BC, McFarland SK, Pascoal JF, Clark DS, Schaffer D, Dordick JS. High-Throughput Toxicity and Phenotypic Screening of 3D Human Neural Progenitor Cell Cultures on a Microarray Chip Platform. Stem Cell Reports. 2016 11 08; 7(5):970-982. PMID: 28157485.
      View in: PubMed
    25. Tervo DG, Hwang BY, Viswanathan S, Gaj T, Lavzin M, Ritola KD, Lindo S, Michael S, Kuleshova E, Ojala D, Huang CC, Gerfen CR, Schiller J, Dudman JT, Hantman AW, Looger LL, Schaffer D, Karpova AY. A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons. Neuron. 2016 Oct 19; 92(2):372-382. PMID: 27720486.
      View in: PubMed
    26. Yao K, Qiu S, Tian L, Snider WD, Flannery JG, Schaffer D, Chen B. Wnt Regulates Proliferation and Neurogenic Potential of Müller Glial Cells via a Lin28/let-7 miRNA-Dependent Pathway in Adult Mammalian Retinas. Cell Rep. 2016 09 27; 17(1):165-178. PMID: 27681429.
      View in: PubMed
    27. Rammensee S, Kang MS, Georgiou K, Kumar S, Schaffer D. Dynamics of Mechanosensitive Neural Stem Cell Differentiation. Stem Cells. 2017 02; 35(2):497-506. PMID: 27573749.
      View in: PubMed
    28. Steines B, Dickey DD, Bergen J, Excoffon KJ, Weinstein JR, Li X, Yan Z, Abou Alaiwa MH, Shah VS, Bouzek DC, Powers LS, Gansemer ND, Ostedgaard LS, Engelhardt JF, Stoltz DA, Welsh MJ, Sinn PL, Schaffer D, Zabner J. CFTR gene transfer with AAV improves early cystic fibrosis pig phenotypes. JCI Insight. 2016 09 08; 1(14):e88728. PMID: 27699238.
      View in: PubMed
    29. Luque T, Kang MS, Schaffer D, Kumar S. Microelastic mapping of the rat dentate gyrus. R Soc Open Sci. 2016 Apr; 3(4):150702. PMID: 27152213; PMCID: PMC4852636.
    30. Altiok EI, Santiago-Ortiz JL, Svedlund FL, Zbinden A, Jha AK, Bhatnagar D, Loskill P, Jackson WM, Schaffer D, Healy KE. Multivalent hyaluronic acid bioconjugates improve sFlt-1 activity in vitro. Biomaterials. 2016 07; 93:95-105. PMID: 27086270.
      View in: PubMed
    31. Sun S, Schaffer D. Viral infection: A key host receptor for AAV. Nat Microbiol. 2016 Feb 01; 1:15027. PMID: 27572162.
      View in: PubMed
    32. Chen S, Bremer AW, Scheideler OJ, Na YS, Todhunter ME, Hsiao S, Bomdica PR, Maharbiz MM, Gartner ZJ, Schaffer D. Interrogating cellular fate decisions with high-throughput arrays of multiplexed cellular communities. Nat Commun. 2016 Jan 12; 7:10309. PMID: 26754526; PMCID: PMC4729920.
    33. Santiago-Ortiz JL, Schaffer D. Adeno-associated virus (AAV) vectors in cancer gene therapy. J Control Release. 2016 10 28; 240:287-301. PMID: 26796040.
      View in: PubMed
    34. Zheng B, von See MP, Yu E, Gunel B, Lu K, Vazin T, Schaffer D, Goodwill PW, Conolly SM. Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells In Vivo. Theranostics. 2016; 6(3):291-301. PMID: 26909106; PMCID: PMC4737718.
    35. A Kotterman M, Schaffer D. Engineered AAV vectors for improved central nervous system gene delivery. Neurogenesis (Austin). 2015; 2(1):e1122700. PMID: 27606332; PMCID: PMC4973602 [Available on 12/03/16].
    36. Limsirichai P, Gaj T, Schaffer D. CRISPR-mediated Activation of Latent HIV-1 Expression. Mol Ther. 2016 Mar; 24(3):499-507. PMID: 26607397; PMCID: PMC4786916 [Available on 03/01/17].
    37. Tsukamoto A, Abbot SE, Kadyk LC, DeWitt ND, Schaffer D, Wertheim JA, Whittlesey KJ, Werner MJ. Challenging Regeneration to Transform Medicine. Stem Cells Transl Med. 2016 Jan; 5(1):1-7. PMID: 26607174; PMCID: PMC4704880 [Available on 01/01/17].
    38. Gaj T, Epstein BE, Schaffer D. Genome Engineering Using Adeno-associated Virus: Basic and Clinical Research Applications. Mol Ther. 2016 Mar; 24(3):458-64. PMID: 26373345; PMCID: PMC4786909 [Available on 03/01/17].
    39. Zheng B, Vazin T, Goodwill PW, Conway A, Verma A, Saritas EU, 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 Sep 11; 5:14055. PMID: 26358296; PMCID: PMC4566119.
    40. Han BW, Layman H, Rode NA, Conway A, Schaffer D, 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. PMID: 26154888; PMCID: PMC4554933.
    41. 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. PMID: 26003168; PMCID: PMC4494916.
    42. Kotterman MA, Vazin T, Schaffer D. Enhanced selective gene delivery to neural stem cells in vivo by an adeno-associated viral variant. Development. 2015 May 15; 142(10):1885-92. PMID: 25968319; PMCID: PMC4440921.
    43. Dey SS, Foley JE, Limsirichai P, Schaffer D, Arkin AP. Orthogonal control of expression mean and variance by epigenetic features at different genomic loci. Mol Syst Biol. 2015 May 05; 11(5):806. PMID: 25943345; PMCID: PMC4461400.
    44. Yousef H, Morgenthaler A, Schlesinger C, Bugaj L, Conboy IM, Schaffer D. Age-Associated Increase in BMP Signaling Inhibits Hippocampal Neurogenesis. Stem Cells. 2015 May; 33(5):1577-88. PMID: 25538007; PMCID: PMC4818000.
    45. Fritz AL, Adil MM, Mao SR, Schaffer D. cAMP and EPAC Signaling Functionally Replace OCT4 During Induced Pluripotent Stem Cell Reprogramming. Mol Ther. 2015 May; 23(5):952-963. PMID: 25666918; PMCID: PMC4427878.
    46. Jha AK, Tharp KM, Ye J, Santiago-Ortiz JL, Jackson WM, Stahl A, Schaffer D, Yeghiazarians Y, Healy KE. Enhanced survival and engraftment of transplanted stem cells using growth factor sequestering hydrogels. Biomaterials. 2015 Apr; 47:1-12. PMID: 25682155; PMCID: PMC4457539.
    47. Kotterman MA, Chalberg TW, Schaffer D. Viral Vectors for Gene Therapy: Translational and Clinical Outlook. Annu Rev Biomed Eng. 2015; 17:63-89. PMID: 26643018.
      View in: PubMed
    48. Byrne LC, Lin YJ, Lee T, Schaffer D, 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. PMID: 25224467; PMCID: PMC4445607.
    49. Fritz AL, Mao SR, West MG, Schaffer D. A medium-throughput analysis of signaling pathways involved in early stages of stem cell reprogramming. Biotechnol Bioeng. 2015 Jan; 112(1):209-19. PMID: 25065366.
      View in: PubMed
    50. Reinhart-King CA, Mooney DJ, Schaffer D. The Young Innovators of Cellular and Molecular Bioengineering. Cell Mol Bioeng. 2014 Sep 01; 7(3):291-292. PMID: 25309632.
      View in: PubMed
    51. Yousef H, Conboy MJ, Mamiya H, Zeiderman M, Schlesinger C, Schaffer D, Conboy IM. Mechanisms of action of hESC-secreted proteins that enhance human and mouse myogenesis. Aging (Albany NY). 2014 Aug; 6(8):602-20. PMID: 25109702; PMCID: PMC4169857.
    52. Lei Y, Jeong D, Xiao J, Schaffer D. Developing Defined and Scalable 3D Culture Systems for Culturing Human Pluripotent Stem Cells at High Densities. Cell Mol Bioeng. 2014 Jun; 7(2):172-183. PMID: 25419247.
      View in: PubMed
    53. Hughes AJ, Spelke DP, Xu Z, Kang CC, Schaffer D, Herr AE. Single-cell western blotting. Nat Methods. 2014 Jul; 11(7):749-55. PMID: 24880876; PMCID: PMC4077215.
    54. Kotterman MA, Schaffer D. Engineering adeno-associated viruses for clinical gene therapy. Nat Rev Genet. 2014 Jul; 15(7):445-51. PMID: 24840552; PMCID: PMC4393649.
    55. Yin L, Masella B, Dalkara D, Zhang J, Flannery JG, Schaffer D, Williams DR, Merigan WH. Imaging light responses of foveal ganglion cells in the living macaque eye. J Neurosci. 2014 May 07; 34(19):6596-605. PMID: 24806684; PMCID: PMC4012315.
    56. Conway A, Schaffer D. Biomaterial microenvironments to support the generation of new neurons in the adult brain. Stem Cells. 2014 May; 32(5):1220-9. PMID: 24449485.
      View in: PubMed
    57. Shapiro MG, Ramirez RM, Sperling LJ, Sun G, Sun J, Pines A, Schaffer D, Bajaj VS. Genetically encoded reporters for hyperpolarized xenon magnetic resonance imaging. Nat Chem. 2014 Jul; 6(7):629-34. PMID: 24950334.
      View in: PubMed
    58. Cao J, Arha M, Sudrik C, Schaffer D, Kane RS. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chem Int Ed Engl. 2014 May 05; 53(19):4900-4. PMID: 24677733.
      View in: PubMed
    59. Shapiro MG, Goodwill PW, Neogy A, Yin M, Foster FS, Schaffer D, Conolly SM. Biogenic gas nanostructures as ultrasonic molecular reporters. Nat Nanotechnol. 2014 Apr; 9(4):311-6. PMID: 24633522; PMCID: PMC4023545.
    60. Schaffer D. AAV shuffles to the liver: commentary on Lisowski et al. Mol Ther Methods Clin Dev. 2014; 1:14006. PMID: 26015952; PMCID: PMC4441045.
    61. Loring JF, McDevitt TC, Palecek SP, Schaffer D, Zandstra PW, Nerem RM. A global assessment of stem cell engineering. Tissue Eng Part A. 2014 Oct; 20(19-20):2575-89. PMID: 24428577; PMCID: PMC4195431.
    62. Ojala DS, Amara DP, Schaffer D. Adeno-associated virus vectors and neurological gene therapy. Neuroscientist. 2015 Feb; 21(1):84-98. PMID: 24557878.
      View in: PubMed
    63. Day TP, Byrne LC, Schaffer D, Flannery JG. Advances in AAV vector development for gene therapy in the retina. Adv Exp Med Biol. 2014; 801:687-93. PMID: 24664759; PMCID: PMC4267879.
    64. Conway A, Spelke DP, Schaffer D. Conjugation of proteins to polymer chains to create multivalent molecules. Methods Mol Biol. 2014; 1202:95-102. PMID: 24014311.
      View in: PubMed
    65. Bartel MA, Schaffer D. Enhanced gene targeting of adult and pluripotent stem cells using evolved adeno-associated virus. Methods Mol Biol. 2014; 1114:169-79. PMID: 24557903.
      View in: PubMed
    66. Vacca O, Darche M, Schaffer D, 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. PMID: 24382652.
      View in: PubMed
    67. Lei Y, Schaffer D. 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. PMID: 24248365; PMCID: PMC3876251.
    68. Ekerdt BL, Segalman RA, Schaffer D. Spatial organization of cell-adhesive ligands for advanced cell culture. Biotechnol J. 2013 Dec; 8(12):1411-23. PMID: 24318636; PMCID: PMC4282480.
    69. Vazin T, Ashton RS, Conway A, Rode NA, Lee SM, Bravo V, Healy KE, Kane RS, Schaffer D. 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. PMID: 24172856.
      View in: PubMed
    70. Downing TL, Soto J, Morez C, Houssin T, Fritz A, Yuan F, Chu J, Patel S, Schaffer D, Li S. Biophysical regulation of epigenetic state and cell reprogramming. Nat Mater. 2013 Dec; 12(12):1154-62. PMID: 24141451.
      View in: PubMed
    71. Conway A, Vazin T, Spelke DP, Rode NA, Healy KE, Kane RS, Schaffer D. Multivalent ligands control stem cell behaviour in vitro and in vivo. Nat Nanotechnol. 2013 Nov; 8(11):831-8. PMID: 24141540; PMCID: PMC3830932.
    72. Cao J, Arha M, Sudrik C, Bugaj LJ, Schaffer D, Kane RS. Light-inducible activation of target mRNA translation in mammalian cells. Chem Commun (Camb). 2013 Sep 28; 49(75):8338-40. PMID: 23925486.
      View in: PubMed
    73. Byrne LC, Khalid F, Lee T, Zin EA, Greenberg KP, Visel M, Schaffer D, 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. PMID: 24086689; PMCID: PMC3785414.
    74. Vazin T, Ball KA, Lu H, Park H, Ataeijannati Y, Head-Gordon T, Poo MM, Schaffer D. 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. PMID: 24055772; PMCID: PMC4122237.
    75. Sudrik C, Arha M, Cao J, Schaffer D, Kane RS. Translational repression using BIV Tat peptide-TAR RNA interaction in mammalian cells. Chem Commun (Camb). 2013 Aug 28; 49(67):7457-9. PMID: 23852014.
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    76. Miller-Jensen K, Skupsky R, Shah PS, Arkin AP, Schaffer D. 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. PMID: 23874178; PMCID: PMC3708878.
    77. Dalkara D, Byrne LC, Klimczak RR, Visel M, Yin L, Merigan WH, Flannery JG, Schaffer D. 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. PMID: 23761039.
      View in: PubMed
    78. Yousef H, Conboy MJ, Li J, Zeiderman M, Vazin T, Schlesinger C, Schaffer D, Conboy IM. hESC-secreted proteins can be enriched for multiple regenerative therapies by heparin-binding. Aging (Albany NY). 2013 May; 5(5):357-72. PMID: 23793469; PMCID: PMC3701111.
    79. Bugaj LJ, Choksi AT, Mesuda CK, Kane RS, Schaffer D. Optogenetic protein clustering and signaling activation in mammalian cells. Nat Methods. 2013 Mar; 10(3):249-52. PMID: 23377377.
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    80. Chen S, Schaffer D. Newborn neuroblasts feel the field in the adult brain. EMBO Rep. 2013 Feb; 14(2):105-6. PMID: 23328741; PMCID: PMC3566847.
    81. Keung AJ, Dong M, Schaffer D, Kumar S. Pan-neuronal maturation but not neuronal subtype differentiation of adult neural stem cells is mechanosensitive. Sci Rep. 2013; 3:1817. PMID: 23660869; PMCID: PMC3650663.
    82. Conway A, Schaffer D. Biophysical regulation of stem cell behavior within the niche. Stem Cell Res Ther. 2012 Dec 14; 3(6):50. PMID: 23241436; PMCID: PMC3580480.
    83. Pernet V, Joly S, Dalkara D, Jordi N, Schwarz O, Christ F, Schaffer D, 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. PMID: 23194670.
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    84. Ashton RS, Conway A, Pangarkar C, Bergen J, Lim KI, Shah P, Bissell M, Schaffer D. Astrocytes regulate adult hippocampal neurogenesis through ephrin-B signaling. Nat Neurosci. 2012 Oct; 15(10):1399-406. PMID: 22983209; PMCID: PMC3458152.
    85. Pollock JF, Ashton RS, Rode NA, Schaffer D, 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. PMID: 22794081; PMCID: PMC3900495.
    86. Keung AJ, Asuri P, Kumar S, Schaffer D. 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. PMID: 22854634; PMCID: PMC3459311.
    87. Goodwill PW, Saritas EU, Croft LR, Kim TN, Krishnan KM, Schaffer D, Conolly SM. X-space MPI: magnetic nanoparticles for safe medical imaging. Adv Mater. 2012 Jul 24; 24(28):3870-7. PMID: 22988557.
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    88. Shah PS, Schaffer D. Response to "HIV Escape From RNAi Antivirals: Yet Another Houdini Action?". Mol Ther Nucleic Acids. 2012 Jun 12; 1:e28. PMID: 23344080; PMCID: PMC3390221.
    89. Bugaj LJ, Schaffer D. Bringing next-generation therapeutics to the clinic through synthetic biology. Curr Opin Chem Biol. 2012 Aug; 16(3-4):355-61. PMID: 22609142.
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    90. Miller-Jensen K, Dey SS, Pham N, Foley JE, Arkin AP, Schaffer D. 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. PMID: 22555315; PMCID: PMC3362694.
    91. Shah PS, Pham NP, Schaffer D. HIV develops indirect cross-resistance to combinatorial RNAi targeting two distinct and spatially distant sites. Mol Ther. 2012 Apr; 20(4):840-8. PMID: 22294151; PMCID: PMC3321590.
    92. Jgamadze D, Bergen J, Stone D, Jang JH, Schaffer D, 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. PMID: 22295079; PMCID: PMC3266246.
    93. Asokan A, Schaffer D, Samulski RJ. The AAV vector toolkit: poised at the clinical crossroads. Mol Ther. 2012 Apr; 20(4):699-708. PMID: 22273577; PMCID: PMC3321598.
    94. Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer D. Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression. J Biol Chem. 2012 Mar 09; 287(11):7945-55. PMID: 22253435; PMCID: PMC3318752.
    95. An HJ, Gip P, Kim J, Wu S, Park KW, McVaugh CT, Schaffer D, 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. PMID: 22147732; PMCID: PMC3322563.
    96. Asuri P, Bartel MA, Vazin T, Jang JH, Wong TB, Schaffer D. 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. PMID: 22108859; PMCID: PMC3277219.
    97. Keung AJ, de Juan-Pardo EM, Schaffer D, Kumar S. Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells. Stem Cells. 2011 Nov; 29(11):1886-97. PMID: 21956892.
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    98. 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. PMID: 22065962; PMCID: PMC3207363.
    99. Shah PS, Schaffer D. Antiviral RNAi: translating science towards therapeutic success. Pharm Res. 2011 Dec; 28(12):2966-82. PMID: 21826573; PMCID: PMC5012899.
    100. Hester ME, Murtha MJ, Song S, Rao M, Miranda CJ, Meyer K, Tian J, Boulting G, Schaffer D, 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. PMID: 21772256; PMCID: PMC3188742.
    101. Dickey DD, Excoffon KJ, Koerber JT, Bergen J, Steines B, Klesney-Tait J, Schaffer D, 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. PMID: 21697483; PMCID: PMC3165813.
    102. Miller-Jensen K, Dey SS, Schaffer D, Arkin AP. Varying virulence: epigenetic control of expression noise and disease processes. Trends Biotechnol. 2011 Oct; 29(10):517-25. PMID: 21700350.
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    103. Jang JH, Schaffer D, Shea LD. Engineering biomaterial systems to enhance viral vector gene delivery. Mol Ther. 2011 Aug; 19(8):1407-15. PMID: 21629221; PMCID: PMC3149164.
    104. Dalkara D, Kolstad KD, Guerin KI, Hoffmann NV, Visel M, Klimczak RR, Schaffer D, 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. PMID: 21522134; PMCID: PMC3182364.
    105. 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 25; 52(5):2775-83. PMID: 21310920; PMCID: PMC3088562.
    106. Arkin AP, Schaffer D. Network news: innovations in 21st century systems biology. Cell. 2011 Mar 18; 144(6):844-9. PMID: 21414475.
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    107. Jang JH, Koerber JT, Kim JS, Asuri P, Vazin T, Bartel M, Keung A, Kwon I, Park KI, Schaffer D. An evolved adeno-associated viral variant enhances gene delivery and gene targeting in neural stem cells. Mol Ther. 2011 Apr; 19(4):667-75. PMID: 21224831; PMCID: PMC3070092.
    108. Ashton RS, Keung AJ, Peltier J, Schaffer D. Progress and prospects for stem cell engineering. Annu Rev Chem Biomol Eng. 2011; 2:479-502. PMID: 22432628.
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    109. Dickinson BC, Peltier J, Stone D, Schaffer D, Chang CJ. Nox2 redox signaling maintains essential cell populations in the brain. Nat Chem Biol. 2011 Feb; 7(2):106-12. PMID: 21186346; PMCID: PMC3023843.
    110. Peltier J, Conway A, Keung AJ, Schaffer D. 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. PMID: 21028992; PMCID: PMC3121932.
    111. Saha K, Kim J, Irwin E, Yoon J, Momin F, Trujillo V, Schaffer D, Healy KE, Hayward RC. Surface creasing instability of soft polyacrylamide cell culture substrates. Biophys J. 2010 Dec 15; 99(12):L94-6. PMID: 21156124; PMCID: PMC3000484.
    112. Little LE, Dane KY, Daugherty PS, Healy KE, Schaffer D. Exploiting bacterial peptide display technology to engineer biomaterials for neural stem cell culture. Biomaterials. 2011 Feb; 32(6):1484-94. PMID: 21129772; PMCID: PMC3010314.
    113. Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer D. Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One. 2010 Oct 22; 5(10):e13564. PMID: 21042592; PMCID: PMC2962647.
    114. Skupsky R, Burnett JC, Foley JE, Schaffer D, Arkin AP. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLoS Comput Biol. 2010 Sep 30; 6(9). PMID: 20941390; PMCID: PMC2947985.
    115. Schaffer D. Microarraying for mechanosensivitity. Cell Stem Cell. 2010 Sep 03; 7(3):273-4. PMID: 20804961.
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    116. Ananthanarayanan B, Little L, Schaffer D, Healy KE, Tirrell M. Neural stem cell adhesion and proliferation on phospholipid bilayers functionalized with RGD peptides. Biomaterials. 2010 Nov; 31(33):8706-15. PMID: 20728935; PMCID: PMC2949453.
    117. Aviran S, Shah PS, Schaffer D, Arkin AP. Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles. PLoS Comput Biol. 2010 Aug 12; 6(8). PMID: 20711350; PMCID: PMC2920833.
    118. Lim KI, Klimczak R, Yu JH, Schaffer D. 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. PMID: 20616052; PMCID: PMC2906550.
    119. Shah PS, Schaffer D. Gene therapy takes a cue from HAART: combinatorial antiviral therapeutics reach the clinic. Sci Transl Med. 2010 Jun 16; 2(36):36ps30. PMID: 20555021.
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    120. Kolstad KD, Dalkara D, Guerin K, Visel M, Hoffmann N, Schaffer D, Flannery JG. Changes in adeno-associated virus-mediated gene delivery in retinal degeneration. Hum Gene Ther. 2010 May; 21(5):571-8. PMID: 20021232; PMCID: PMC3143418.
    121. Kurpinski K, Lam H, Chu J, Wang A, Kim A, Tsay E, Agrawal S, Schaffer D, 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. PMID: 20146266.
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    122. Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer D, Arkin AP. Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol. 2010 Jun; 84(12):5958-74. PMID: 20357084; PMCID: PMC2876650.
    123. Robertson MJ, Peltier J, Schaffer D. In vivo analysis of engrafted adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:89-102. PMID: 20405361.
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    124. Keung AJ, Healy KE, Kumar S, Schaffer D. Biophysics and dynamics of natural and engineered stem cell microenvironments. Wiley Interdiscip Rev Syst Biol Med. 2010 Jan-Feb; 2(1):49-64. PMID: 20836010.
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    125. Keung AJ, Kumar S, Schaffer D. Presentation counts: microenvironmental regulation of stem cells by biophysical and material cues. Annu Rev Cell Dev Biol. 2010; 26:533-56. PMID: 20590452.
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    126. Peltier J, Schaffer D. Viral packaging and transduction of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:103-16. PMID: 20405362.
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    127. Peltier J, Agrawal S, Robertson MJ, Schaffer D. In vitro culture and analysis of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:65-87. PMID: 20405360.
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    128. Peltier J, Ormerod BK, Schaffer D. Isolation of adult hippocampal neural progenitors. Methods Mol Biol. 2010; 621:57-63. PMID: 20405359.
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    129. Vazin T, Schaffer D. Engineering strategies to emulate the stem cell niche. Trends Biotechnol. 2010 Mar; 28(3):117-24. PMID: 20042248.
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    130. Meng Y, Eshghi S, Li YJ, Schmidt R, Schaffer D, Healy KE. Characterization of integrin engagement during defined human embryonic stem cell culture. FASEB J. 2010 Apr; 24(4):1056-65. PMID: 19933311; PMCID: PMC2845424.
    131. Klimczak RR, Koerber JT, Dalkara D, Flannery JG, Schaffer D. A novel adeno-associated viral variant for efficient and selective intravitreal transduction of rat Müller cells. PLoS One. 2009 Oct 14; 4(10):e7467. PMID: 19826483; PMCID: PMC2758586.
    132. Carlson ME, Conboy MJ, Hsu M, Barchas L, Jeong J, Agrawal A, Mikels AJ, Agrawal S, Schaffer D, 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. PMID: 19732043; PMCID: PMC2783265.
    133. Koerber JT, Klimczak R, Jang JH, Dalkara D, Flannery JG, Schaffer D. Molecular evolution of adeno-associated virus for enhanced glial gene delivery. Mol Ther. 2009 Dec; 17(12):2088-95. PMID: 19672246; PMCID: PMC2788045.
    134. Dalkara D, Kolstad KD, Caporale N, Visel M, Klimczak RR, Schaffer D, Flannery JG. Inner limiting membrane barriers to AAV-mediated retinal transduction from the vitreous. Mol Ther. 2009 Dec; 17(12):2096-102. PMID: 19672248; PMCID: PMC2814392.
    135. Banerjee A, Arha M, Choudhary S, Ashton RS, Bhatia SR, Schaffer D, Kane RS. The influence of hydrogel modulus on the proliferation and differentiation of encapsulated neural stem cells. Biomaterials. 2009 Sep; 30(27):4695-9. PMID: 19539367; PMCID: PMC2743317.
    136. Agrawal S, Archer C, Schaffer D. Computational models of the Notch network elucidate mechanisms of context-dependent signaling. PLoS Comput Biol. 2009 May; 5(5):e1000390. PMID: 19468305; PMCID: PMC2680760.
    137. Excoffon KJ, Koerber JT, Dickey DD, Murtha M, Keshavjee S, Kaspar BK, Zabner J, Schaffer D. 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. PMID: 19237554; PMCID: PMC2646629.
    138. Burnett JC, Miller-Jensen K, Shah PS, Arkin AP, Schaffer D. Control of stochastic gene expression by host factors at the HIV promoter. PLoS Pathog. 2009 Jan; 5(1):e1000260. PMID: 19132086; PMCID: PMC2607019.
    139. Leonard JN, Shah PS, Burnett JC, Schaffer D. HIV evades RNA interference directed at TAR by an indirect compensatory mechanism. Cell Host Microbe. 2008 Nov 13; 4(5):484-94. PMID: 18996348; PMCID: PMC2742160.
    140. Koerber JT, Jang JH, Schaffer D. DNA shuffling of adeno-associated virus yields functionally diverse viral progeny. Mol Ther. 2008 Oct; 16(10):1703-9. PMID: 18728640; PMCID: PMC2683895.
    141. Saha K, Keung AJ, Irwin EF, Li Y, Little L, Schaffer D, Healy KE. Substrate modulus directs neural stem cell behavior. Biophys J. 2008 Nov 01; 95(9):4426-38. PMID: 18658232; PMCID: PMC2567955.
    142. Little L, Healy KE, Schaffer D. Engineering biomaterials for synthetic neural stem cell microenvironments. Chem Rev. 2008 May; 108(5):1787-96. PMID: 18476674.
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    143. Wall ST, Saha K, Ashton RS, Kam KR, Schaffer D, Healy KE. Multivalency of Sonic hedgehog conjugated to linear polymer chains modulates protein potency. Bioconjug Chem. 2008 Apr; 19(4):806-12. PMID: 18380472.
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    144. Lim KI, Schaffer D. Library selection approaches to engineering enhanced retroviral and lentiviral vectors. Comb Chem High Throughput Screen. 2008 Feb; 11(2):111-7. PMID: 18336204.
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    145. Koerber JT, Schaffer D. Transposon-based mutagenesis generates diverse adeno-associated viral libraries with novel gene delivery properties. Methods Mol Biol. 2008; 434:161-70. PMID: 18470644.
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    146. Schaffer D, Koerber JT, Lim KI. Molecular engineering of viral gene delivery vehicles. Annu Rev Biomed Eng. 2008; 10:169-94. PMID: 18647114; PMCID: PMC2683887.
    147. Robertson MJ, Gip P, Schaffer D. Neural stem cell engineering: directed differentiation of adult and embryonic stem cells into neurons. Front Biosci. 2008 Jan 01; 13:21-50. PMID: 17981526.
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    148. Ho JE, Chung EH, Wall S, Schaffer D, 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. PMID: 17600327.
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    149. 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. PMID: 18077603.
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    150. Jang JH, Lim KI, Schaffer D. Library selection and directed evolution approaches to engineering targeted viral vectors. Biotechnol Bioeng. 2007 Oct 15; 98(3):515-24. PMID: 17614321.
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    151. Ashton RS, Banerjee A, Punyani S, Schaffer D, 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. PMID: 17881048.
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    152. Peltier J, O'Neill A, Schaffer D. PI3K/Akt and CREB regulate adult neural hippocampal progenitor proliferation and differentiation. Dev Neurobiol. 2007 Sep 01; 67(10):1348-61. PMID: 17638387.
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    153. Kwon I, Schaffer D. 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. PMID: 17763830; PMCID: PMC2265771.
    154. Ashton RS, Peltier J, Fasano CA, O'Neill A, Leonard J, Temple S, Schaffer D, Kane RS. High-throughput screening of gene function in stem cells using clonal microarrays. Stem Cells. 2007 Nov; 25(11):2928-35. PMID: 17673524.
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    155. Leonard JN, Ferstl P, Delgado A, Schaffer D. Enhanced preparation of adeno-associated viral vectors by using high hydrostatic pressure to selectively inactivate helper adenovirus. Biotechnol Bioeng. 2007 Aug 01; 97(5):1170-9. PMID: 17252611.
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    156. Schaffer D. Exploring and Engineering Stem Cells and their Niches. Curr Opin Chem Biol. 2007 Aug; 11(4):355-356. PMID: 18670582.
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    157. Saha K, Pollock JF, Schaffer D, Healy KE. Designing synthetic materials to control stem cell phenotype. Curr Opin Chem Biol. 2007 Aug; 11(4):381-7. PMID: 17669680; PMCID: PMC1993842.
    158. Koerber JT, Jang JH, Yu JH, Kane RS, Schaffer D. Engineering adeno-associated virus for one-step purification via immobilized metal affinity chromatography. Hum Gene Ther. 2007 Apr; 18(4):367-78. PMID: 17437357.
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    159. Saha K, Irwin EF, Kozhukh J, Schaffer D, Healy KE. Biomimetic interfacial interpenetrating polymer networks control neural stem cell behavior. J Biomed Mater Res A. 2007 Apr; 81(1):240-9. PMID: 17236216.
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    160. Greenberg KP, Geller SF, Schaffer D, 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. PMID: 17389520; PMCID: PMC1939809.
    161. Yu JH, Schaffer D. High-throughput, library-based selection of a murine leukemia virus variant to infect nondividing cells. J Virol. 2006 Sep; 80(18):8981-8. PMID: 16940510; PMCID: PMC1563944.
    162. Jang JH, Schaffer D. Microarraying the cellular microenvironment. Mol Syst Biol. 2006; 2:39. PMID: 16820780; PMCID: PMC1681511.
    163. Abranches E, O'Neill A, Robertson MJ, Schaffer D, Cabral JM. Development of quantitative PCR methods to analyse neural progenitor cell culture state. Biotechnol Appl Biochem. 2006 Apr; 44(Pt 1):1-8. PMID: 16336211.
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    164. Yu JH, Schaffer D. 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. PMID: 16537595; PMCID: PMC1440395.
    165. Saha K, Schaffer D. Signal dynamics in Sonic hedgehog tissue patterning. Development. 2006 Mar; 133(5):889-900. PMID: 16452094.
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    166. Maheshri N, Koerber JT, Kaspar BK, Schaffer D. Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat Biotechnol. 2006 Feb; 24(2):198-204. PMID: 16429148.
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    167. Greenberg KP, Lee ES, Schaffer D, Flannery JG. Gene delivery to the retina using lentiviral vectors. Adv Exp Med Biol. 2006; 572:255-66. PMID: 17249582.
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    168. Koerber JT, Maheshri N, Kaspar BK, Schaffer D. Construction of diverse adeno-associated viral libraries for directed evolution of enhanced gene delivery vehicles. Nat Protoc. 2006; 1(2):701-6. PMID: 17406299.
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    169. Lee GK, Maheshri N, Kaspar B, Schaffer D. PEG conjugation moderately protects adeno-associated viral vectors against antibody neutralization. Biotechnol Bioeng. 2005 Oct 05; 92(1):24-34. PMID: 15937953.
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    170. Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer D. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul 29; 122(2):169-82. PMID: 16051143.
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    171. Agrawal S, Schaffer D. In situ stem cell therapy: novel targets, familiar challenges. Trends Biotechnol. 2005 Feb; 23(2):78-83. PMID: 15661344.
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    172. Leonard JN, Schaffer D. Computational design of antiviral RNA interference strategies that resist human immunodeficiency virus escape. J Virol. 2005 Feb; 79(3):1645-54. PMID: 15650190; PMCID: PMC544124.
    173. Yu JH, Schaffer D. Advanced targeting strategies for murine retroviral and adeno-associated viral vectors. Adv Biochem Eng Biotechnol. 2005; 99:147-67. PMID: 16568891.
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    174. 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. PMID: 15548879.
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    175. O'Neill A, Schaffer D. The biology and engineering of stem-cell control. Biotechnol Appl Biochem. 2004 Aug; 40(Pt 1):5-16. PMID: 15270702.
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    176. Ignowski JM, Schaffer D. 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. PMID: 15162459.
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    177. Lai K, Robertson MJ, Schaffer D. The sonic hedgehog signaling system as a bistable genetic switch. Biophys J. 2004 May; 86(5):2748-57. PMID: 15111393; PMCID: PMC1304145.
    178. Schaffer D, 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. PMID: 17271428.
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    179. Schaffer D, Gage FH. Neurogenesis and neuroadaptation. Neuromolecular Med. 2004; 5(1):1-9. PMID: 15001808.
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    180. Weinberger LS, Schaffer D, 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. PMID: 12941913; PMCID: PMC224590.
    181. Maheshri N, Schaffer D. Computational and experimental analysis of DNA shuffling. Proc Natl Acad Sci U S A. 2003 Mar 18; 100(6):3071-6. PMID: 12626764; PMCID: PMC152248.
    182. Lai K, Kaspar BK, Gage FH, Schaffer D. Sonic hedgehog regulates adult neural progenitor proliferation in vitro and in vivo. Nat Neurosci. 2003 Jan; 6(1):21-7. PMID: 12469128.
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    183. Lee G, Schaffer D. Engineering the surface properties of synthetic gene delivery vectors. Somat Cell Mol Genet. 2002 Nov; 27(1-6):17-25. PMID: 12774938.
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    184. 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. PMID: 12081869.
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    185. Schaffer D. Genetic approaches to tissue repair. Ann N Y Acad Sci. 2002 Jun; 961:68-70. PMID: 12081868.
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    186. 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. PMID: 11842206; PMCID: PMC122363.
    187. 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. PMID: 11786045.
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