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Recent Selected Publications
  • Ashton, R.S., A. Conway, C. Pangarkar, J. Bergen, K-I. Lim, P. Shah, M. Bissell, and D.V. Schaffer (2012) "Astrocytes Regulate Adult Hippocampal Neurogenesis Through Ephrin-B Signaling." Nature Neuroscience,15:1399-1406 (PMID: 22983209). View PDF
  • Dickinson, B.C., J. Peltier, D. Stone, D.V. Schaffer (co-corresponding author), and C.J Chang (2011) "Nox2 Redox Signaling Maintains Essential Cell Populations in the Brain." Nature Chemical Biology, 7:106-112 (PMID 21186346). View PDF
  • Lim, K-I., R.R. Klimczak, J.H. Yu, and D.V. Schaffer (2010) "Specific Insertions of Zinc Finger Domains into Gag-Pol Yields Engineered Retroviral Vectors with Selective Integration Properties." Proceedings of the National Academy of Sciences USA, 107:12475-12480 (PMID 20616052). View PDF
  • Excoffon, K.J., J.T. Koerber, D.D. Dickey, M. Murtha, S. Keshavjee, B.K. Kaspar, J. Zabner, and D.V. Schaffer (2009) "Directed Evolution of Adeno-Associated Virus to an Infectious Respiratory Virus." Proceedings of the National Academy of Sciences USA, 106:3865-3870 (PMID 19237554). View PDF
  • Koerber, J.T., N. Maheshri, B.K. Kaspar, and D.V. Schaffer (2006) "Construction of Diverse Adeno-Associated Viral Libraries for Directed Evolution of Enhanced Gene Delivery Vehicles." Nature Protocols, 1:701-706. View PDF
  • Maheshri, N., J.T. Koerber, B. Kaspar, and D.V. Schaffer (2006) "Directed Evolution of Adeno-Associated Virus Yields Enhanced Gene Delivery Vectors." Nature Biotechnology, 24:198-204. View PDF
  • Weinberger, L.S., J.C. Burnett, J.E. Toettcher, A.P. Arkin, and D.V. Schaffer (2005) "Stochastic Gene Expression in a Lentiviral Feedback Loop: HIV-1 Tat Expression Drives Phenotypic Diversity." Cell, 122:169-182. View PDF
  • Maheshri, N. and D.V. Schaffer (2003) "Computational and Experimental Analysis of DNA Shuffling." Proceedings of the National Academy of Sciences USA, 100:3071-3076. View PDF
  • Lai, K, B.K. Kaspar, F.H. Gage, and D.V. Schaffer (2003) "Sonic Hedgehog Regulates Adult Neural Progenitor Proliferation in Vitro and in Vivo." Nature Neuroscience, 6(1):21-27. View PDF

Recent Review Articles
  • Asokan, A., D.V. Schaffer, and R.J. Samulski (2012) "The AAV Vector Toolkit: Poised at the Clinical Crossroads." Molecular Therapy, 20:699-708 (PMID 22273577). View PDF
  • Bartel, M.A., J.R. Weinstein, and D.V. Schaffer (2012) "Directed Evolution of Novel Adeno-Associated Viruses for Therapeutic Gene Delivery." Gene Therapy, 19:694-700 (PMID 22402323). View PDF
  • Arkin, A.P. and D.V. Schaffer (2011) "Network News: Innovations in 21st Century Systems Biology." Cell, 144:844-849 (PMID 21414475). View PDF
  • Keung, A.J., S. Kumar, and D.V. Schaffer (2010) "Presentation Counts: Microenvironmental Regulation of Stem Cells by Biophysical and Material Cues." Annual Reviews in Cell and Developmental Biology, 26:533-556 (PMID 20590452). View PDF
  • Vazin, T. and D.V. Schaffer (2010) "Engineering Strategies to Emulate the Stem Cell Niche Trends in Biotechnology." Trends in Biotechnology, 28:117-124 (PMID 20042248). Selected as the Cover Article. View PDF

2012
  • Ashton, R.S., A. Conway, C. Pangarkar, J. Bergen, K-I. Lim, P. Shah, M. Bissell, and D.V. Schaffer (2012) "Astrocytes Regulate Adult Hippocampal Neurogenesis Through Ephrin-B Signaling." Nature Neuroscience,15:1399-1406 (PMID: 22983209). View PDF
  • Dalkara, D., L.C. Byrne, T. Lee, N.V. Hoffmann, D.V. Schaffer, and J.G. Flannery (2012) Enhanced Gene Delivery to the Neonatal Retina Through Systemic Administration of Tyrosine-Mutated AAV9." Gene Therapy, 19:176-181 (PMID: 22011645). View PDF
  • Bugaj, L.J. and D.V. Schaffer (2012) "Bringing Next-Generation Therapeutics to the Clinic Through Synthetic Biology." Current Opinion in Chemical Biology, 16(3-4):355-361 (PMID: 22609142). View PDF
  • Keung, A.J., P. Asuri, S. Kumar, and D.V. Schaffer (2012) "Soft Microenvironments Promote the Early Neurogenic Differentiation but not Self-renewal of Human Pluripotent Stem Cells." Integrative Biology, 4(9):1049-1058 (PMID: 22854634). View PDF
  • Pollock, J., R. Aston, N. Rode, D.V. Schaffer, K.E. Healy (2012) "Molecular Characterization of Multivalent Bioconjugates by Size-Exclusion Chromatography (SEC) with Multi-Angle Laser Light Scattering (MALS)." Bioconjugate Chemistry , 19;23(9):1794-801 (PMID: 22794081). View PDF
  • Ana, H.J, P. Gip, J. Kimc, S. Wua, C.T. McVaugh, D.V. Schaffer, C.R. Bertozzi, and C.B. Lebirlla (2012) "N-Glycan Profiling of Human Embryonic Stem Cell Surfaces Reveals an Unusual Abundance of High-Mannose Glycans." Molecular and Cellular Proteomics, 11:M111.010660 (PMID 22147732). View PDF
  • Jgamadze, J., J. Bergen, D. Stone, J-H. Jang, D.V. Schaffer, E.Y. Isacoff, and S. Pautot (2012) "Colloids as Mobile Substrates for the Implantation and Integration of Differentiated Neurons into the Mammalian Brain." PLoS ONE, 7:e30293 (PMID 22295079). View PDF
  • Shah, P.S., N.P. Phan, and D.V. Schaffer (2012) "HIV Develops Indirect Cross-resistance to Combinatorial RNAi Targeting Two Distinct and Spatially Distant Sites." Molecular Therapy, 20:840-848 (PMID 22294151). View PDF
  • Asokan, A., D.V. Schaffer, and R.J. Samulski (2012) "The AAV Vector Toolkit: Poised at the Clinical Crossroads." Molecular Therapy, 20:699-708 (PMID 22273577). View PDF
  • Dey, S.S., Y. Xue, M.P. Joachimiak, G.D. Friedland, J.C. Burnett, Q. Zhou, A.P. Arkin, and D.V. Schaffer (2012) "Mutual Information Analysis Reveals Coevolving Residues in Tat that Compensate for Two Distinct Functions in HIV-1 Gene Expression." Journal of Biological Chemistry, 287:7945-7955 (PMID 22253435). View PDF
  • Bartel, M.A., J.R. Weinstein, and D.V. Schaffer (2012) "Directed Evolution of Novel Adeno-Associated Viruses for Therapeutic Gene Delivery." Gene Therapy, 19:694-700 (PMID 22402323). View PDF
  • Miller-Jensen, K., S.S. Dey, N. Pham, J.E. Foley, A.P. Arkin, and D.V. Schaffer (2012) "Chromatin Accessibility at the HIV LTR Promoter Sets a Threshold for NF-κB Mediated Viral Gene Expression." Integrative Biology, 4:661-671 (PMID 22555315). View PDF
  • Asuri, P., M.A. Bartel, T. Vazin, J-H. Jang, T.B. Wong, and D.V. Schaffer "Directed Evolution of Adeno-Associated Virus for Enhanced Gene Delivery and Gene Targeting in Human Pluripotent Stem Cells." Molecular Therapy, 20(2):329-38 (PMID 22108859). View PDF
  • Perneta, V., S. Joly, D. Dalkara, O. Schwarz, Franziska Christ, D. Schaffer, J.G. Flannery, and M.E. Schwab "Neuronal NOGO-A Up-Regulation Does Not Contribute to ER Stress-Associated Apoptosis but Participates in the Regenerative Response in the Axotomized Adult Retina." Cell Death and Degeneration, Dec 23. doi: 10.1038/cdd.2011.191 (PMID 22193546). View PDF

2011
  • Little, L., K. Dane, P.S. Daugherty, K.E. Healy, and D.V Schaffer (2011) "Exploiting Bacterial Peptide Display Technology to Engineer Biomaterials for Neural Stem Cell Culture." Biomaterials, 32:1484-1494 (PMID 21129772). View PDF
  • Dickinson, B.C., J. Peltier, D. Stone, D.V. Schaffer (co-corresponding author), and C.J Chang (2011) "Nox2 Redox Signaling Maintains Essential Cell Populations in the Brain." Nature Chemical Biology, 7:106-112 (PMID 21186346). View PDF
  • Arkin, A.P. and D.V. Schaffer (2011) "Network News: Innovations in 21st Century Systems Biology." Cell, 144:844-849 (PMID 21414475). View PDF
  • Jang, J-H., J.T. Koerber, J-S. Kim, P. Asurim, T. Vazin, M. Bartel, A. Keung, I. Kwon, K.I. Park, and D.V. Schaffer (2011) "An Evolved Adeno-Associated Viral Variant Enhances Gene Delivery and Gene Targeting in Neural Stem Cells." Molecular Therapy, 19:667-675 (PMID 21224831).View PDF
  • Yin, Y., K. Greenberg, J.J. Hunter, D. Dalkara, K.D. Kolstad, B.D. Masella, R. Wolfe, M. Visel, D. Stone, R.T. Libby, D. DiLoreto, Jr., D. Schaffer, J. Flannery, D.R. Williams, W.H. Merigan (2011) "Intravitreal Injection of AAV2 Transduces Macaque Inner Retina." Investigative Ophthalmology and Visual Science, 52:2775-2783 (PMID 21310920). View PDF
  • Peltier, J., A. Conway, A. Keung, and D.V. Schaffer (2011) "Akt Increases Sox2 Expression in Adult Hippocampal Neural Progenitor Cells but Increased Sox2 does not Promote Proliferation." Stem Cells and Development, 20:1153-1161 (PMID 21028992).
  • Chen, S., N. Patel, D.V. Schaffer, and M.M. Maharbiz (2011) "Trap and Corral: A Two-step Approach for Constructing and Constraining Dynamic Cell Contact Events in Differentiating Progenitor Cell Populations." Journal of Micromechanics and Microengineering, 5:054027. View PDF
  • Dalkara, D., K.D. Kolstad, K.I. Guerin, N.V. Hoffmann, M. Visel, R.R. Klimczak, D.V. Schaffer, and J.G. Flannery (2011) "AAV-mediated GDNF Secretion from Retinal Glia Slows Down Retinal Degeneration in a Rat Model of Retinitis Pigmentosa." Molecular Therapy, 19:1602-1608 (PMID 21522134). View PDF
  • Ashton, R.A., A.J. Keung, J.L. Peltier, and D.V. Schaffer (2011) "Progress and Prospects for Stem Cell Engineering." Annual Reviews in Chemical and Biomolecular Engineering, 2:479-509. View PDF
  • Jang, J-H., D.V. Schaffer, and L. Shea (2011) "Engineering Biomaterial Systems to Enhance Viral Vector Gene Delivery." Molecular Therapy, 19:1407-1415 (PMID 21629221). View PDF
  • Miller-Jensen, K., S.S. Dey, D.V. Schaffer, and A.P. Arkin (2011) "Varying Virulence: Epigenetic Control of Expression Noise and Disease Processes." Trends in Biotechnology, 29:517-525 (PMID 21700350). View PDF
  • Dickey, D., K. Excoffon, J. Koerber, J. Bergen, B. Steines, J. Klesney-Tait, D.V. Schaffer, and J. Zabner (2011) "Enhanced Sialic Acid-dependent Endocytosis Explains the Increased Airway Epithelia Infection Efficiency of a Novel Adeno-associated Virus." Journal of Virology, 85:9023-9030 (PMID 21697483). View PDF
  • Hester, M.E., M.J. Murtha, S. Song, M. Rao, C.J. Miranda, K. Meyer, J. Tian, G. Boulting, D.V. Schaffer, M.X. Zhu, S.L. Pfaff, F.H. Gage, and B.K. Kaspar (2011) "Rapid and Efficient Generation of Functional Motor Neurons from Human Pluripotent Stem Cells Using Gene Delivered Transcription Factor Codes." Molecular Therapy, 19:1905-1912 (PMID 21772256). View PDF
  • Shah, P.S. and D.V. Schaffer (2011) "Antiviral RNAi: Translating Science Toward Therapeutic Success." Pharmaceutical Research, 28:2966-2982 (PMID 21826573). View PDF
  • Keung, A.J., E.M. de Juan-Pardo, D.V. Schaffer (co-corresponding author), and S. Kumar (2011) "Rho GTPases Mediate the Mechanosensitive Lineage Commitment of Neural Stem Cells." Stem Cells, 29: 1886-1897 (PMID 21956892). View PDF
  • Bartel, M.A., D.V. Schaffer (co-corresponding author), and H. Buening (2011). "Enhancing the Clinical Potential of AAV Vectors by Capsid Engineering to Evade Pre-Existing Immunity." Frontiers in Microbiology, 2:204 (PMID 22065962). View PDF

2010
  • Dickinson, B.C., J. Peltier, D. Stone, D.V. Schaffer (co-corresponding author), and C.J Chang "Nox2 Redox Signaling Maintains Essential Cell Populations in the Brain." Nature Chemical Biology, 7:106-112(PMID 21186346). View PDF
  • Little, L., K. Dane, P.S. Daugherty, K.E. Healy, and D.V Schaffer "Exploiting Bacterial Peptide Display Technology to Engineer Biomaterials for Neural Stem Cell Culture." Biomaterials (in press). View PDF
  • Saha, K., J. Kim, E. Irwin, J. Yoon, F. Momin, V. Trujillo, D.V. Schaffer, K.E. Healy, and R.C. Hayward "Surface Creasing Instability of Soft Polyacrylamide Cell Culture Substrates." Biophysical Journal (in press). View PDF
  • Peltier, J., A. Conway, A. Keung, and D.V. Schaffer (2010) "Akt Increases Sox2 Expression in Adult Hippocampal Neural Progenitor Cells but Increased Sox2 does not Promote Proliferation." Stem Cells and Development (PMID 21028992). View PDF
  • Willerth, S.M., H.A.M. Pedro, L. Pachter, L.M. Humeau, A.P. Arkin, and D.V. Schaffer (2010) "Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology." Public Library of Science (PLoS) ONE 5:e13564 (PMID 21042592). View PDF
  • Skupsky, R., J.C. Burnett, J.E. Foley, D.V. Schaffer (co-corresponding author), and A.P. Arkin (2010) "HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency." Public Library of Science (PLoS) Computational Biology, 6:e1000952 (PMID 20711350). View PDF
  • Keung, A.J., S. Kumar, and D.V. Schaffer (2010) "Presentation Counts: Microenvironmental Regulation of Stem Cells by Biophysical and Material Cues." Annual Reviews in Cell and Developmental Biology, 26:533-556 (PMID 20590452). View PDF
  • Ananthanarayanan, B., L. Little, D.V. Schaffer, K.E. Healy, and M. Tirrell (2010) "Neural Stem Cell Adhesion and Proliferation on Phospholipid Bilayers Functionalized with RGD Peptides." Biomaterials, 31:8706-15 (PMID 20728935).View PDF
  • Schaffer, D.V. (2010) "Microarraying for Mechanosensitivity." Cell Stem Cell, 7:273-4 (PMID 20804961). View PDF
  • Keung, A.J., K.E. Healy, S. Kumar, and D.V. Schaffer (2010) "Biophysics and Dynamics of Natural and Engineered Stem Cell Microenvironments." Wiley Interdisciplinary Reviews (WIRES): Systems Biology and Medicine, 2:49-64 (PMID 20836010). View PDF
  • Aviran, S., P.S. Shah, D.V. Schaffer, and A.P. Arkin (2010) "Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles." Public Library of Science (PLoS) Computational Biology, 6:e1000883 (PMID 20711350). View PDF
  • Lim, K-I., R.R. Klimczak, J.H. Yu, and D.V. Schaffer (2010) "Specific Insertions of Zinc Finger Domains into Gag-Pol Yields Engineered Retroviral Vectors with Selective Integration Properties." Proceedings of the National Academy of Sciences USA, 107:12475-12480 (PMID 20616052). View PDF
  • Jang, J-H., J.T. Koerber, K. Gujraty, S.R. Bethi, R.S. Kane, and D.V. Schaffer "Surface Immobilization of Hexa-histidine-tagged Adeno-associated Viral Vectors for Localized Gene Delivery." Gene Therapy (in press) (PMID 20508598). View PDF
  • Shah, P.S. and D.V. Schaffer (2010) "Gene Therapy Takes a Cue from HAART: Combinatorial Antiviral Therapeutics Reach the Clinic." Science Translational Medicine, 2:36ps30 (PMID 20555021). View PDF
  • Burnett, J.C., K.I. Lim, A. Calafi, J.J. Rossi, D.V. Schaffer (co-corresponding author), A.P. Arkin (2010) "Combinatorial Latency Reactivation for HIV-1 Subtypes and Variants." Journal of Virology, 84:5958-5974 (PMID 20357084). View PDF
  • Kurpinski, K., H. Lam, J. Chu, A. Kim, E. Tsay, S. Agrawal, D.V. Schaffer, A. Winoto, and S. Li (2010) "Transforming growth factor-beta and notch signaling mediate stem cell differentiation into smooth muscle cells." Stem Cells, 4:734-42 (PMID 20146266).
  • Kolstad, K.D., D. Dalkara, K. Guerin, M. Visel, N. Hoffmann, D.V. Schaffer, and J.G. Flannery (2010) "Changes to AAV Mediated Gene Delivery in Retinal Degeneration." Human Gene Therapy, 5:571-8 (PMID 20021232).
  • Peltier, J. and D.V. Schaffer (2010) "Viral Packaging and Transduction of Adult Hippocampal Neural Progenitors." Methods in Molecular Biology, 621:103-116 (PMID 20405362). View PDF
  • Robertson, M.J., J. Peltier, and D.V. Schaffer (2010) "In Vivo Analysis of Engrafted Adult Hippocampal Neural Progenitors." Methods in Molecular Biology, 621:89-102 (PMID 20405361). View PDF
  • Peltier, J., S. Agrawal, M.J. Robertson, and D.V. Schaffer (2010) "In Vitro Culture and Analysis of Adult Hippocampal Neural Progenitors." Methods in Molecular Biology, 621:65-87 (PMID 20405360). View PDF
  • Peltier, J., B.K. Ormerod, and D.V. Schaffer (2010) "Isolation of Adult Hippocampal Neural Progenitors." Methods in Molecular Biology, 621:57-63 (PMID 20405359). View PDF
  • Vazin, T. and D.V. Schaffer (2010) "Engineering Strategies to Emulate the Stem Cell Niche Trends in Biotechnology." Trends in Biotechnology, 28:117-124 (PMID 20042248). Selected as the Cover Article. View PDF
  • Peltier, J. and D.V. Schaffer (2010) "Systems Biology Approaches to Understanding Stem Cell Fate Choice."IET Systems Biology, 4:1-11 (PMID 20001088). View PDF

2009
  • Meng, Y., S. Eshghi, Y. Li, R. Schmidt, D.V. Schaffer, and K.E. Healy (2009) "Characterization of Integrin Engagement during Defined Human Embryonic Stem Cell Culture." FASEB Journal, 24:0 (PMID 19933311). View PDF
  • J.T. Koerber, R. Klimczak, J-H. Jang, D. Dalkara, J.G. Flannery, and D.V. Schaffer (2009) "Molecular Evolution of Adeno-Associated Virus for Enhanced Glial Gene Delivery." Molecular Therapy, 17: 2088-2095 (PMID 19672246). View PDF
  • Carlson, M.E., M.J. Conboy, M. Hsu, L. Barchas, J. Jeong, A. Agrawal, A.J. Mikels, S. Agrawal, D.V. Schaffer, and I.M. Conboy (2009) "Relative Roles of TGF-beta1 and Wnt in the Systemic Regulation and Aging of Satellite Cell Responses." Aging Cell, 8:676-689 (PMID 19732043).
  • R. Klimczak, J.T. Koerber, D. Dalkara, J.G. Flannery, and D.V. Schaffer (2009) "A Novel Adeno-Associated Viral Variant for Efficient and Selective Intravitreal Transduction of Rat MÜller Cells." Public Library of Science (PLoS) ONE, 4:e7467 (PMID 19826483). View PDF
  • Dalkara, D., K.D. Kolstad, N. Caporale, M. Visel, R.R. Klimczak, D.V. Schaffer, and J.G. Flannery (2009) "Inner Limiting Membrane Barriers to AAV Mediated Retinal Transduction from the Vitreous." Molecular Therapy, 17:2096-2102 (PMID 19672248). View PDF
  • Banerjeea, A., M. Arhaa, S. Choudhary, R.S. Ashton, S.R. Bhatia, D.V. Schaffer, and R.S. Kane (2009) "The Influence of Hydrogel Modulus on the Proliferation and Differentiation of Encapsulated Neural Stem Cells." Biomaterials, 30:4695-9 (PMID 19539367). View PDF
  • Agrawal, S., C. Archer, and D.V. Schaffer "Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling." Public Library of Science (PLoS) Computational Biology (in press). View PDF
  • Excoffon, K.J., J.T. Koerber, D.D. Dickey, M. Murtha, S. Keshavjee, B.K. Kaspar, J. Zabner, and D.V. Schaffer (2009) "Directed Evolution of Adeno-Associated Virus to an Infectious Respiratory Virus." Proceedings of the National Academy of Sciences USA, 106:3865-3870 (PMID 19237554). View PDF
  • Burnett, J.C., K. Miller-Jensen, P.S. Shah, A.P. Arkin, and D.V. Schaffer (2009) "Control of Stochastic Gene Expression by Host Factors at the HIV Promoter." Public Library of Science (PLoS) Pathogens, 5(1) (PMID 19132086). View PDF

2008
  • Leonard, J.N., P.S. Shah, J.C. Burnett, and D.V. Schaffer (2008) "HIV Evades RNA Interference Directed at TAR by an Indirect Compensatory Mechanism." Cell Host and Microbe, 4:484-94 (PMID 18996348).¬†Selected as the Featured Article. View PDF
  • Saha, K., A.J. Keung, E.F. Irwin, Y. Li, D.V. Schaffer (co-corresponding author), and K.E. Healy "Substrate Modulus Directs Neural Stem Cell Behavior." Biophysical Journal, 95:4426-38. (PMID 18658232). View PDF
  • Eshghi, S. and D.V. Schaffer "Engineering Microenvironments to Control Stem Cell Fate and Function." Stembook Stembook, D. Melton, ed. View PDF
  • Koerber, J.T., J-H. Jang, and D.V. Schaffer "DNA Shuffling of Adeno-Associated Virus Yields Functionally Diverse Viral Progeny." Molecular Therapy, 16:1703-9. (PMID 18728640). View PDF
  • Koerber, J.T. and D.V. Schaffer "Transposon-Based Mutagenesis Generates Diverse Adeno-Associated Viral Libraries with Novel Gene Delivery Properties." Methods in Molecular Biology, 434:161-170 (PMID 18470644). View PDF
  • Little, L., K.E. Healy, and D.V. Schaffer (2008) "Engineering Biomaterials for Synthetic Neural Stem Cell Microenvironments." Chemical Reviews, 108:1787-1796 (PMID 18476674). View PDF
  • Wall, S., K. Saha, R. Aston, K. Kam, D.V. Schaffer, and K.E. Healy "Multivalency of Sonic Hedgehog Conjugated to Linear Polymer Chains Modulates Protein Potency." Bioconjugate Chemistry, 19:806-812 (PMID 18380472). View PDF
  • Schaffer, D.V. (corresponding author), J.T. Koerber, and K.-I. Lim (2008) "Molecular Engineering of Viral Gene Delivery Vehicles." Annual Reviews in Biomedical Engineering, 10:169-94 (PMID 18647114). View PDF
  • Lim, K-I., and D.V. Schaffer (2008) "Library Selection Approaches to Engineering Enhanced Retroviral and Lentiviral Vectors." Combinatorial Chemistry and High Throughput Screening, 11:111-117 (PMID 18336204). View PDF
  • Ricci, C., V. Pastukh, J. Leonard, J. Turrens, G. Wilson, D. Schaffer, and S.W. Schaffer(2008) "Mitochondrial DNA Damage Triggers Mitochondrial Superoxide Generation and Apoptosis." American Journal of Physiology, 294:C413-22 PMID 18077603).
  • Kwon, I. and D.V. Schaffer (2008) "Designer Gene Delivery Vectors: Molecular Engineering and Evolution of Adeno-Associated Viral Vectors for Enhanced Gene Transfer." Pharmaceutical Research, 25:489-499. View PDF
  • Robertson, M.J., P. Gip, and D.V. Schaffer (2008) "Neural Stem Cell Engineering: Directed Differentiation of Adult and Embryonic Stem Cells into Neurons." Frontiers in Bioscience, 13:21-50 (PMID 17981526). View PDF

2007
  • Ashton, R.S., A. Banerjee, S. Punyani, D.V. Schaffer, and R.S Kane (2007) "Scaffolds Based on Degradable Alginate Hydrogels and Poly(lactide-co-glycolide) Microspheres for Stem Cell Culture Biomaterials." Biomaterials, 28:5518-5525. View PDF
  • Ashton, R.S., J. Peltier, C.A. Fasano, A. O'Neill, J. Leonard, S. Temple, D.V. Schaffer (co-corresponding author), and R.S. Kane (2007) "High-Throughput Screening of Gene Function in Stem Cells Using Clonal Microarrays." Stem Cells, 25:2928-2935. View PDF
  • Jang, J-H., K-I. Lim, and D.V. Schaffer (2007) "Library Selection and Directed Evolution Approaches to Engineering Targeted Viral Vectors." Biotechnology & Bioengineering, 98:515-524. View PDF
  • Saha, K., J. Pollock, D.V. Schaffer (co-corresponding author), and K.E. Healy (2007) "Designing Synthetic Materials to Control Stem Cell Phenotype." Current Opinion in Chemical Biology, 11:381-387. View PDF
  • Ho, J.E., E.H. Chung, S. Wall, D.V. Schaffer, and K.E. Healy (2007) "Immobilized Sonic Hedgehog N-Terminal Signaling Domain Enhances Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells." Journal of Biomedical Materials Research Part A, 83A:1200-1208. View PDF
  • Peltier, J., A. O'Neill, and D.V. Schaffer (2007) "PI3K/Akt and CREB Regulate Adult Neural Hippocampal Progenitor Proliferation and Differentiation." Developmental Neurobiology, 67:1348-1361. View PDF
  • Koerber, J.T., J-H. Jang, and D.V. Schaffer (2007) "Engineering Adeno-Associated Virus for One Step Purification via Immobilized Metal Affinity Chromatography." Human Gene Therapy, 18:367-378. View PDF
  • Leonard, J.N., P. Ferstl, A. Delgado, and D.V. Schaffer (2007) "Enhanced Preparation of Adeno-Associated Viral Vectors by Using High Hydrostatic Pressure to Selectively Inactivate Helper Adenovirus." Biotechnology & Bioengineering, 97:1170-1179. Selected as a Journal Spotlight Article. View PDF
  • Saha, K., E.F. Irwin, J. Kozhukh, D.V. Schaffer (corresponding author), and K.E. Healy (corresponding author) (2007) "Biomimetic Interfacial Interpenetrating Polymer Networks Control Neural Stem Cell Behavior." Journal of Biomedical Materials Research Part A, 81:240-249. View PDF

2006
  • Greenberg, K.P., S.F. Geller, D.V. Schaffer, and J.G. Flannery (2006) "Targeted Transgene Expression in Muller Glia of Normal and Diseased Retinas Using Lentiviral Vectors." Investigative Ophthalmology & Visual Science, 48:1844-1852. View PDF
  • Yu, J.H. and D.V. Schaffer (2006) "High-Throughput, Library-Based Selection of a Murine Leukemia Virus to Infect Nondividing Cells." Journal of Virology, 80:8981-8988.¬†Selected as a Journal of Virology Spotlight Article. View PDF
  • Jang, J-H. and D.V. Schaffer (2006) "Microarraying the Cellular Microenvironment" Molecular Systems Biology, 2:39. View PDF
  • Koerber, J.T., N. Maheshri, B.K. Kaspar, and D.V. Schaffer (2006) "Construction of Diverse Adeno-Associated Viral Libraries for Directed Evolution of Enhanced Gene Delivery Vehicles." Nature Protocols, 1:701-706. View PDF
  • Greenberg K.P., E.S. Lee, D.V. Schaffer, and J.G. Flannery (2006) "Gene Delivery to the Retina Using Lentiviral Vectors." Advances in Experimental Medicine and Biology, 572: 255-266. View PDF
  • Yu, J. and D.V. Schaffer (2006) "Selection of Novel Vesicular Stomatitis Virus Glycoprotein Variants from a Peptide Insertion Library for Enhanced Purification of Retroviral and Lentiviral Vectors." Journal of Virology, 80:3285-3292. View PDF
  • Saha, K. and D.V. Schaffer (2006) "Signaling Dynamics in Sonic Hedgehog Tissue Patterning." Development, 133:889-900. View PDF
  • Maheshri, N., J.T. Koerber, B. Kaspar, and D.V. Schaffer (2006) "Directed Evolution of Adeno-Associated Virus Yields Enhanced Gene Delivery Vectors." Nature Biotechnology, 24:198-204. View PDF
  • Abranches, E., O'Neill, A., Robertson, M.J., Schaffer, D.V. (corresponding author), and J. Cabral (2006) "Development of Quantitative PCR Methods to Analyze Adult Neural Progenitor Cell Culture State." Biotechnology & Applied Biochemistry, 44:1-8. View PDF
  • Leonard, J. and D.V. Schaffer (2006) "Antiviral RNAi Strategies: Emerging Approaches for Hitting a Moving Target." Gene Therapy, 13:532-540. View PDF

2005
  • Weinberger, L.S., J.C. Burnett, J.E. Toettcher, A.P. Arkin, and D.V. Schaffer (2005) "Stochastic Gene Expression in a Lentiviral Feedback Loop: HIV-1 Tat Expression Drives Phenotypic Diversity." Cell, 122:169-182. View PDF
  • Yu, J. and D.V. Schaffer (2005) "Advanced Targeting Strategies for Murine Retroviral and Adeno-Associated Viral Vectors." Advances in Biochemical Engineering & Biotechnology, 99:147-167. View PDF
  • Schaffer, D.V. and W.C. Zhou (2005) "Gene Therapy and Gene Delivery Systems as Future Human Therapeutics." Advances in Biochemical Engineering & Biotechnology, 99:1-5.
  • Lee, G., Maheshri, N., Kaspar, B.K., and D.V. Schaffer (2005) "PEG Conjugation Moderately Protects Adeno-Associated Viral Vectors Against Antibody Neutralization." Biotechnology & Bioengineering, 92:24-34. View PDF
  • Agrawal, S. and D.V. Schaffer (2005) "In Situ Stem Cell Therapy: Novel Targets, Familiar Challenges." Trends in Biotechnology, 23:78-83. View PDF
  • Leonard, J. and D.V. Schaffer (2005) "Computational Design of RNA Interference Strategies that Resist HIV Escape." Journal of Virology, 79:1645-1654. View PDF

2004
  • O'Neill, A. and D.V. Schaffer (2004) "The Biology and Engineering of Stem Cell Control." Biotechnology & Applied Biochemistry, 40:5-16. View PDF
  • Lai, K., M.J. Robertson, and D.V. Schaffer (2004) "The Sonic Hedgehog Signaling System as a Bistable Genetic Switch." Biophysical Journal, 86:2748-2757. View PDF
  • Ignowski, J. and D.V. Schaffer (2004) "Kinetic Analysis and Modeling of Firefly Luciferase as a Quantitative Reporter Gene in Live Mammalian Cells." Biotechnology & Bioengineering, 86(7):827-34. View PDF
  • Schaffer, D.V. and F.H. Gage (2004) "Neurogenesis and Neuroadaptation" Neuromolecular Medicine, 5:1-9. View PDF

2003
  • Weinberger, L., D.V. Schaffer (corresponding author), and A.P. Arkin (corresponding author) (2003) "Theoretical Design of a Gene Therapy to Prevent AIDS but Not HIV-1 Infection." Journal of Virology, 77:10028-10036. View PDF
  • Maheshri, N. and D.V. Schaffer (2003) "Computational and Experimental Analysis of DNA Shuffling." Proceedings of the National Academy of Sciences USA, 100:3071-3076. View PDF
  • Lai, K, B.K. Kaspar, F.H. Gage, and D.V. Schaffer (2003) "Sonic Hedgehog Regulates Adult Neural Progenitor Proliferation in Vitro and in Vivo." Nature Neuroscience, 6(1):21-27. View PDF

2002
  • Wiewrodt, W., A.P. Thomas, L. Cipelletti, D.A. Weitz, S.I. Feinstein, D.V. Schaffer, S.M. Albelda, M. Koval, and V.R. Muzykantov (2002) "Size-Dependent Intracellular Immunotargeting into Endothelial Cells via a Surface Adhesion Molecule, PECAM-1," Blood, 99:912-22. View PDF
  • Kaspar, B.K., Vissel, B., Bengoechea, T., Crone, S., Randolph-Moore, L., Muller, R., Brandon,E.P., Schaffer, D., Verma, I.M., Lee, K.F., Heinemann, S.F., and F.H. Gage (2002) "Adeno-associated Virus Effectively Mediates Conditional Gene Modification in the Brain." Proceedings of the National Academy of Sciences USA, 99:2320-5. View PDF
  • Kaspar, B.K., D. Erickson, D. Schaffer, L. Hinh, F.H. Gage, and D.A. Peterson (2002) "Targeted Retrograde Gene Delivery for Neuronal Protection." Molecular Therapy, 5:50-6. View PDF

2001
  • Mozaffari, M.S. and D.V. Schaffer (2001) "Taurine Modulates Arginine Vasopressin-Mediated Regulation of Renal Function." Journal of Cardiovascular Pharmacology, 37(6): 742-750.

2000
  • Schaffer, D.V. and D.A. Lauffenburger (2000) "Targeted Synthetic Gene Delivery Vectors." Current Opinions in Molecular Therapeutics, 2: 155-161.View PDF

1999
  • Schaffer, D.V., N. Fidelman, N. Dan, and D.A. Lauffenburger (1999) "Vector Unpackaging as a Potential Barrier for Receptor-Mediated Polyplex Gene Delivery." Biotechnology & Bioengineering, 67:598-606. View PDF
  • Lauffenburger, D.A. and D.V. Schaffer (1999) "The Matrix Delivers." Nature Medicine, 5: 733-734. View PDF

1998
  • Schaffer, D.V. and D.A. Lauffenburger (1998) "Optimization of Cell Surface Binding Enhances Efficiency and Specificity of Molecular Conjugate Gene Delivery." Journal of Biological Chemistry, 273:28004-28009.View PDF

1996
  • Schaffer, D.V., R.L. Neve, and D.A. Lauffenburger (1996) "Use of Green Fluorescent Protein as a Reporter of Epidermal Growth Factor Receptor-Mediated Gene Delivery." Tissue Engineering, 3:53-63.

1994
  • Gramer, M.J., D.V. Schaffer, M.B. Sliwkowski, and C.F. Goochee (1994) "Purification and Purification and Characterization of an a-L-Fucosidase from Chinese Hamster Ovary Cell Culture Supernatant." Glycobiology, 4:611-616.