About the Schaffer Lab

The Schaffer research group applies molecular and cellular engineering approaches to investigate biomedical problems focused on engineering of stem cell and gene therapeutics. Our group is a part of the department of Chemical and Biological Engineering, the Helen Wills Neuroscience Institute, and the Bioengineering Graduate Group at UC Berkeley.
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Contact Us

The Schaffer Lab
University of California, Berkeley
278 Stanley Hall
Berkeley, CA 94720-3220

Lab Director and Chief Administrator:
Wanichaya Ramey
wramey@berkeley.edu

Lab Phone: (510) 642-4923
Fax: (510) 642-5198

Group News

  • Sabrina has been awarded AHA predoctoral Fellowship for 2017
  • Olivia has been selected as a Siebel Scholar for the 2017-18 school year.
  • Shakked has been selected as the Craven Scholar for the 2017-18 school year
  • Olivia has been selected for P.O.E Scholar Award for the 2017-2018 academic year.
  • Kira Mosher has been selected to be a 2017 Arnold O. Beckman Postdoctoral Fellow.
  • Schaffer lab won the Excellence in Laboratory Safety Award in the large life sciences category and the grand prize winner for 2016 Excellence in Laboratory Safety Award 
  • Prof. David Schaffer is the 2016 winner of the Biochemical Technology Division of the American Chemical Society Marvin Johnson Award (Marvin J. Johnson Award)

Links

David V. Schaffer

David Schaffer is a Professor of Chemical and Biomolecular Engineering, Bioengineering, and Neuroscience at University of California, Berkeley, where he also serves as the Director of the Berkeley Stem Cell Center. He graduated from Stanford University with a B.S. degree in Chemical Engineering in 1993. Afterward, he attended Massachusetts Institute of Technology and earned his Ph.D. also in Chemical Engineering in 1998 with Professor Doug Lauffenburger, while minoring in Molecular and Cell Biology. Finally, he conducted a postdoctoral fellowship in the laboratory of Fred Gage at the Salk Institute for Biological Studies in La Jolla, CA, before moving to UC Berkeley in 1999. At Berkeley, Dr. Schaffer applies engineering principles to enhance stem cell and gene therapy approaches for neuroregeneration. This work includes mechanistic investigation of stem cell control, as well as molecular evolution and engineering of viral gene delivery vehicles. David Schaffer has received an NSF CAREER Award, Office of Naval Research Young Investigator Award, Whitaker Foundation Young Investigator Award, and was named a Technology Review Top 100 Innovator. He was also awarded the American Chemical Society BIOT Division Young Investigator Award in 2006, the Biomedical Engineering Society Rita Shaffer Young Investigator Award in 2000, and was elected to the College of Fellows of the American Institute of Medical and Biological Engineering in 2010.

Awards and Honors

Positions and Employment

Additional Affiliations

Research Interests

Our research group employs molecular and cellular engineering approaches to investigate biomedical problems. We are interested in the related areas of stem cell bioengineering, gene delivery systems, and molecular virology, with applications in regenerative medicine and tissue engineering.

Stem Cells

Many of our efforts are dedicated to understanding the biology and exploring the therapeutic potential of stem cells. Stem cells are immature cells that exist in various locations of our bodies. Throughout our lifetimes, these cells divide and develop into the specialized cells that perform the functions necessary for organismal development and adult tissue function. Furthermore, if we contract a disease that kills those specialized cells, our stem cells are a potential source for replacing lost cells to counteract or even cure the disorder. However, there are several challenges that must be overcome in this field. In particular, efforts to engineer tissues rely upon the ability to control stem cells. That is, the signals that control stem cell function and fate must first be discovered, and then integrated into cellular microenvironments to control stem cell expansion and lineage-specific differentiation. We have efforts in novel signal discovery, computational and experimental analysis of the biological networks that cells use to interpret and implement these signals, and on the integration of these signals into biomaterial microenvironments for optimal stem cell control.

Scalable expansion and differentiation of pluripotent stem cells can greatly benefit many biological applications, including cell replacement therapy, disease modeling, in vitro organogenesis and drug screening, which typically require a large numbers of readily available cells. To this end, we are interested in engineering novel three-dimensional biomaterial platforms to facilitate large-scale compatible expansion and central nervous system (CNS) directed differentiation of pluripotent stem cells. Concurrently, our efforts shed new light on potential mechanistic effects of biomaterial properties on stem cell fate.

This blend of stem cell biology, systems biology analysis, and biomaterials engineering has led to significant advances in the application of stem cells for a variety of applications including tissue repair.

Researchers: Maroof, Nicole, Anusuya, Mike, Phillip, Olivia, Andrew, Brian, Alyssa, Riya, Chun, Kira, Yusuke and Christina

Gene Therapy

Our second major research thrust is dedicated to understanding the biology and exploring the therapeutic potential of gene delivery, which serves as an effective means to control stem cells. Gene therapy can be defined as the introduction of genetic material to the cells of an individual for therapeutic benefit. A variety of approaches are under development to use gene therapy for treating cancer, AIDS, and a number of inherited genetic disorders. For example, gene therapy could be used to replace the genes hemophilia patients are missing, to bolster the immune system to recognize and combat tumors, or to inhibit the replication of HIV virus. However, significant progress must still be made before these developing strategies become therapeutic realities. One of the most formidable obstacles to gene therapy is how to efficiently deliver genes to a sufficient number of cells to yield a therapeutic effect. A number of gene delivery vehicles, or vectors, are in development, and most exploit or emulate the abilities many viruses have evolved to deliver their genes to cells as part of their life cycles. However, while viruses have developed numerous strategies to deliver genes over millions of years of evolution, the efficiency and safety of vehicles based upon recombinant viruses must still be further improved. We have developed numerous high-throughput directed evolution approaches to engineer the properties of viral vehicles at the molecular level to enhance their abilities to deliver genes. These successful efforts are enhancing the abilities of several vectors to make them more effective at delivering gene "medicines."

Researchers: David, Maroof, Sabrina, Leah, Tim, Jonathan, Benjamin, Thom, Shakked and John

Our Research Group

David V. Schaffer, Ph.D.
Principal Investigator
schaffer@berkeley.edu

Wanichaya Ramey
Lab Director and Chief Administrator
wramey@berkeley.edu

Graduate Students

Postdocs

Visiting Scholars

Undergraduate Work-Study Students

Lab Alumni

Publications

Search for Publication

Recent Selected Publications

  • Tervo, D.G.R., B-Y. Hwang, S. Viswanathan, T. Gaj, M. Lavzin, K.D. Ritola, S. Lindo, S. Michael, E.P. Kuleshova, D. Ojala, C-C. Huang, C.R. Gerfen, J. Schiller, J.T. Dudman, A.W. Hantman, L.L. Looger, D.V. Schaffer (co-corresponding author), and A.Y. Karpova (2016) “A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons.” Neuron , 92:372-382 (PMID 27720486). View PDF
  • Chen, S. Y.S. Na, M.E. Todhunger, S. Hsiao, A.W. Bremer, O.J. Scheideler, P.R. Bomdica, M.M. Haharbiz, Z.J. Gartner, D.V. Schaffer (2016) “Interrogating Stem Cell Fate Decisions with High-throughput Arrays of Cellular Communities.” Nature Communications. Jan 12; 7:10309 (PMID 26754526). View PDF
  • Bugaj, L.J., D. P. Spelke, C.K. Mesuda, M. Varedi, R.S. Kane, and D.V. Schaffer (2015) “Regulation of Endogenous Transmembrane Receptors Through Optogenetic Cry2 Clustering.” Nature Communications, 6:6898 (PMID 25902152). View PDF
  • Kotterman, M.A. and D.V. Schaffer (2014) “Engineering Adeno-Associated Viruses for Clinical Gene Therapy.” Nature Reviews Genetics, 15:445-451 (PMID 24840552). View PDF
  • Hughes, A.J., D.P. Spelke, Z. Xu, C-C. Kang, D.V. Schaffer (co-corresponding author), and A.E. Herr (2014) “Single-cell Western Blotting.” Nature Methods, 11(7):749-55 (PMID 24880876). View PDF
  • Shapiro, M., P. Goodwill, A. Neogy, M. Yin, F. Foster, D.V. Schaffer, and S. Conolly (2014) “Biogenic Gas Nanostructures as Ultrasonic Molecular Reporters.” Nature Nanotechnology, 9(4):311-6 (PMID: 24633522). View PDF
  • Shapiro, M.G., R.M. Ramirez, L.J. Sperling, G. Sun, A. Pines, D.V. Schaffer, and V.S. Bajaj (2014) “Genetically Encoded Reporters for Hyperpolarized Xenon.” Nature Chemistry, 6:629-634 (PMID 24950334). View PDF
  • Lei, Y. and D.V. Schaffer (2013) “A Fully Defined and Scalable 3D Culture System for Human Pluripotent Stem Cell Expansion and Differentiation.” Proceedings of the National Academy of Sciences USA, 110:E5039-5048 (PMID 24248365). View PDF
  • Conway, A., T. Vazin, D.P. Spelke, N.A. Rode, K.E. Healy, R.S. Kane, and D.V. Schaffer (2013) “Multivalent Ligands to Control Stem Cell Behaviour in Vitro and in Vivo.” Nature Nanotechnology, 8:831-838 (PMID 24141540). View PDF
  • Downing, T.L., J. Soto, C. Morez, T. Houssin, A. Fritz, F. Yuan, J. Chu, S. Patel, D.V. Schaffer, and S. Li (2013) “Biophysical Regulation of Epigenetic State and Cell Reprogramming.” Nature Materials, 12:1154-1162 (PMID 24141451). View PDF
  • Dalkara, D., L.C. Byrne, R.R. Klimczak, M. Visel, L. Yin, W.H. Merigan, J.G. Flannery, and D.V. Schaffer (2013) "In Vivo–Directed Evolution of a New Adeno-Associated Virus for Therapeutic Outer-Retinal Gene Delivery from the Vitreous." Science Translational Medicine, 5:189ra76 (PMID 23761039). View PDF
  • Bugaj, L.J, A.T Choksi, C.K. Mesuda, R.S. Kane, and D.V. Schaffer (2013) "Optogenetic Protein Clustering and Signaling Activation in Mammalian Cells." Nature Methods, 10:249-252. View PDF
  • 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

  • Gaj T, Epstein BE, Schaffer DV (2016) “Genome Engineering Using Adeno-associated Virus: Basic and Clinical Research Applications.” Mol Ther.151. (PMID: 26373345). View PDF
  • Deng Y, Wang H, Hamamoto R, Schaffer D, Duan S (2015) “Functional genomics, genetics, and bioinformatics.” Biomed Res Int, 2015:184824 (PMID 25977917). View PDF
  • Kotterman, M.A. and D.V. Schaffer (2014)“Engineering Adeno-Associated Viruses for Clinical Gene Therapy.” Nature Reviews Genetics, 445-51 (PMID: 24840552). 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
  • 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

2017

  • Adil MM, Rodrigues GM, Kulkarni RU, Rao AT, Chernavsky NE, Miller EW, Schaffer DV (2017)”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 PDF

2016

  • Zheng. B., M.P. von See, E. Yu, B. Gunel, K. Lu, T. Vazin, D.V. Schaffer, P.W. Goodwill, and S.M. Conolly (2016) “Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells in Vivo.” Theranostics , 6:291-301 (PMID 26909106). View PDF
  • Rammensee, S., M.S. Kang, K. Georgiou, S. Kumar, and D.V. Schaffer (2016) “Dynamics of Mechanosensitive Neural Stem Cell Differentiation.” Stem Cells, 2016 Aug 30. doi: 10.1002/stem.2489 (PMID: 27573749). View PDF
  • Nierode, G.J., B.C. Perea, S.K. McFarland, J.F. Pascoal, D.S. Clark, D.V. Schaffer, and J.S. Dordick (2016) “High-Throughput Toxicity and Phenotypic Screening of 3D Human Neural Progenitor Cell Cultures on a Microarray Chip Platform.” Stem Cell Reports (in press). View PDF
  • Steines, B., D.D. Dickey, J. Bergen, K.J.D.A Excoffon, J.R. Weinstein, X. Li, Z. Yan, M.H. Abou Alaiwa, V.S. Shah, D.C. Bouzek, L.S. Powers, N.D. Gansemer, L.S. Ostedgaard, J.F. Engelhardt, D.A. Stoltz, M.J. Welsh, P.L. Sinn, D.V. Schaffer (co-corresponding author), and J. Zabner (2016) “CFTR Gene-transfer with AAV Improves Early Cystic Fibrosis Pig Phenotypes.” Journal of Clinical Investigation Insights, 1:e88728 (PMID 27699238).View PDF
  • Yao, K., S. Qiu, L. Tian, W.D. Snider, J.G. Flannery, D.V. Schaffer, and B. Chen (2016) “Wnt Regulates Proliferation and Neurogenic Potential of Müller Glial Cells via a Lin28/let-7 miRNA-Dependent Pathway in Adult Mammalian Retinas.” Cell Reports , 17:165-178 (PMID 27681429). View PDF
  • Zheng. B., M.P. von See, E. Yu, B. Gunel, K. Lu, T. Vazin, D.V. Schaffer, P.W. Goodwill, and S.M. Conolly (2016) “Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells in Vivo.” Theranostics , 6:291-301 (PMID 26909106). View PDF
  • Tervo, D.G.R., B-Y. Hwang, S. Viswanathan, T. Gaj, M. Lavzin, K.D. Ritola, S. Lindo, S. Michael, E.P. Kuleshova, D. Ojala, C-C. Huang, C.R. Gerfen, J. Schiller, J.T. Dudman, A.W. Hantman, L.L. Looger, D.V. Schaffer (co-corresponding author), and A.Y. Karpova (2016) “A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons.” Neuron, 92:372-382 (PMID 27720486). View PDF
  • Gaj., T., B.E. Epstein, and D.V. Schaffer (2016), “Genome Engineering Using Adeno-Associated Virus: Basic and Clinical Research Applications.” Molecular Therapy,1-7(PMID 26373345). View PDF
  • Santiago-Ortiz, J.L. and D.V. Schaffer (2016) “Adeno-associated Virus (AAV) Vectors in Cancer Gene Therapy” Journal of Controlled Release. Jan 12. pii: S0168-3659(16)30001-3 (PMID: 26796040). View PDF
  • Zheng. B., M.P. von See, E. Yu, B. Gunel, K. Lu, T. Vazin, D.V. Schaffer, P.W. Goodwill, and S.M. Conolly (2016) “Quantitative Magnetic Particle Imaging Monitors the Transplantation, Biodistribution, and Clearance of Stem Cells in Vivo.” Theranostics, 6:291-301 (PMID: 26909106). View PDF
  • Altiok, E.I., J.L. Santiago-Ortiz, F.L. Svedlund, A. Zbinden, A.K. Jha, D. Bhatnagar, P. Loskill, W.M. Jackson, D.V. Schaffer, and K.E. Healy (2016) “Multivalent Hyaluronic Acid Bioconjugates Improve sFlt-1 activity in Vitro.” Biomaterials, 93:95-105 (PMID: 27086270). View PDF
  • Luque, T., M.S. Kang, D.V. Schaffer, and S. Kumar (2016) “Microelastic Mapping of the Rat Dentate Gyrus.” Royal Society Open Sci, 3:150702 (PMID: 27152213). View PDF
  • Tsukamoto, A. S.E. Abbot, L.C. Kadyk, N.D. DeWitt, D.V. Schaffer, J.A. Wertheim, K.J. Whittlesey, M.J. Werner (2016) Regeneration to Transform Medicine.” Stem Cells Translational Medicine (PMID 26607174).
  • Limsirichai, P. T. Gaj, and D.V. Schaffer (2016) “CRISPR-Mediated Activation of Latent HIV-1 Expression.” Molecular Therapy (PMID 26607397). View PDF
  • Chen, S. Y.S. Na, M.E. Todhunger, S. Hsiao, A.W. Bremer, O.J. Scheideler, P.R. Bomdica, M.M. Haharbiz, Z.J. Gartner, D.V. Schaffer (2016) “Interrogating Stem Cell Fate Decisions with High-throughput Arrays of Cellular Communities.” Nature Communications View PDF

2015

  • Fritz, A.L., M.M. Adil, S.R. Mao, D.V. Schaffer (2015) “cAMP and EPAC Signaling Functionally Replace OCT4 During Induced Pluripotent Stem Cell Reprogramming.” Molecular Therapy , 23:952-963 (PMID 25666918). View PDF
  • Yousef, H., M.J. Conboy, A. Morgenthaler, C. Schlesinger, L. Bugaj, P. Paliwal, C. Greer, I.M. Conboy, and D.V. Schaffer (2015) “Systemic Attenuation of the TGF-β Pathway by a Single Drug Simultaneously Rejuvenates Hippocampal Neurogenesis and Myogenesis in the Same Old Mammal.” Oncotarget, 6:11959-11978 (PMID 26003168). View PDF
  • Santiago-Ortiz, J., D.S. Ojala, O. Westesson, J.R. Weinstein, S.Y. Wong, A. Steinsapir, S. Kumar, I. Holmes, and D.V. Schaffer (2015) “AAV Ancestral Reconstruction Library Enables Selection of Broadly Infectious Viral Variants.” Gene Therapy , 1-13 (PMID 26186661). View PDF
  • Han, B.W., H. Layman, N.A. Rode, A. Conway, D.V. Schaffer, N.J. Boudreau, W.M. Jackson, and K.E. Healy (2015) “Multivalent Conjugates of Sonic Hedgehog Accelerate Diabetic Wound Healing.” Tissue Engineering, 21:2366-2378 (PMID 26154888). View PDF
  • Zheng, V., T. Vazin, P.W. Goodwill, A. Conway, A. Verma, E. Ulku Saritas, D.V. Schaffer, and S.M. Conolly (2015) “Magnetic Particle Imaging Tracks the Long-term Fate of in Vivo Neural Cell Implants with High Image Contrast.” Scientific Reports, 5:14055 (PMID 26358296). View PDF
  • Ojala, D., D.P. Amara, and D.V. Schaffer (2015) “AAV Vectors and Neurological Gene Therapy.” Neuroscientist, 21(1): 84-98. View PDF
  • Fritz, A.L., S.R. Mao, M.G. West, and D.V. Schaffer (2015) “A Medium-Throughput Analysis of Signaling Pathways Involved in Early Stages of Stem Cell Reprogramming.” Biotechnology & Bioengineering, 112 (1): 209-19 (PMID 25065366). View PDF
  • Byrne, L.C., Y.J. Lin, T. Lee, D.V. Schaffer, and J.G. Flannery (2015) “The Expression Pattern of Systemically Injected AAV9 in the Developing Mouse Retina is Determined by Age.” Molecular Therapy, 23(2): 290-6 (PMID 25224467). View PDF
  • Kotterman, M.A., L. Yin, J.M. Strazzeri, J.G. Flannery, W.M. Merigan, and D.V. Schaffer (2015) “Antibody Neutralization Poses a Barrier to Intravitreal Adeno-Associated Viral Vector Gene Delivery to Non-Human Primates.” Gene Therapy, 22(2):116-26 (PMID 25503696). View PDF
  • Yousef, H., A. Morgenthaler, C. Schlesinger, L. Bugaj, I. Conboy, and D.V. Schaffer (2015) “Age-Associated Increase in BMP Signaling inhibits Hippocampal Neurogenesis.” Stem Cells (in press). View PDF
  • Jha, A.K., K.M. Tharp, J. Ye, J.L. Santiago-Ortiz, W.M. Jackson, A. Stahl, D.V. Schaffer, Y. Yeghiazarians, and K.E. Healy (2015)“Enhanced Survival and Engraftment of Transplanted Stem Cells Using Growth Factor Sequestering Hydrogels.” Biomaterials, 47:1-12 (PMID 25682155). View PDF
  • Schaffer, D.V. (corresponding author), M.A. Kotterman, and T.W. Chalberg (2015) “Viral Vectors for Gene Therapy: Translational and Clinical Outlook.” Annual Review of Biomedical Engineering View PDF
  • Bugaj, L.J., D. P. Spelke, C.K. Mesuda, M. Varedi, R.S. Kane, and D.V. Schaffer (2015)“Regulation of Endogenous Transmembrane Receptors Through Optogenetic Cry2 Clustering.” Nature Communications. View PDF
  • Kotterman, M.A., T. Vazin, and D.V. Schaffer (2015) “Adeno-Associated Viral Variant Enhances Selective Gene Delivery to Neural Stem Cells in Vivo.” Development. View PDF
  • Dey, S.S., J.E. Foley, P. Limsirichai, D.V. Schaffer (co-corresponding author), and A.P. Arkin (2015) “Orthogonal Control of Expression Mean and Variance by Epigenetic Features at Different Genomic Loci” Molecular Systems Biology. View PDF

2014

  • Conway A., D.P. Spelke, and D.V. Schaffer (2014) “Conjugation of Proteins to Polymer Chains to Create Multivalent Molecules.” Methods in Molecular Biology, 1202:95-102 (PMID 24014311). View PDF
  • Hughes, A.J., D.P. Spelke, Z. Xu, C-C. Kang, D.V. Schaffer (co-corresponding author), and A.E. Herr (2014) “Single-cell Western Blotting.” Nature Methods, 11:749-755 (PMID 24880876). View PDF
  • Kotterman, M.A. and D.V. Schaffer (2014) “Engineering Adeno-Associated Viruses for Clinical Gene Therapy.” Nature Reviews Genetics, 15:445-451 (PMID 24840552). View PDF
  • Shapiro, M.G., R.M. Ramirez, L.J. Sperling, G. Sun, A. Pines, D.V. Schaffer, and V.S. Bajaj (2014) “Genetically Encoded Reporters for Hyperpolarized Xenon.” Nature Chemistry, 6(7):629-34 (PMID: 24950334). View PDF
  • Shapiro, M., P. Goodwill, A. Neogy, M. Yin, F. Foster, D.V. Schaffer, and S. Conolly (2014) “Biogenic Gas Nanostructures as Ultrasonic Molecular Reporters.” Nature Nanotechnology, 9:311-316 (PMID 24633522). View PDF
  • Vazin, T., R.S. Ashton, A. Conway, N. Rode, S.M. Lee, V. Bravo, K.E. Healy, R.S. Kane, and D.V. Schaffer (2014) “The Effect of Multivalent Sonic Hedgehog on Differentiation of Human Embryonic Stem Cells into Dopaminergic and GABAergic Neurons.” Biomaterials, 35:941-948 (PMID 24172856). View PDF
  • Vacca, O., M. Darche, D.V. Schaffer, J.G. Flannery, J.A. Sahel, A. Rendon, and D. Dalkara (2014) “AAV-mediated Gene Delivery in Dp71-null Mouse Model with Compromised Barriers.” Glia, 62:468-476 (PMID 24382652). View PDF
  • Ojala, D., D.P. Amara, and D.V. Schaffer (2014) “AAV Vectors and Neurological Gene Therapy.” Neuroscientist (in press). View PDF
  • Conway, A. and D.V. Schaffer (2014) “Biomaterial Microenvironments to Support the Generation of New Neurons in the Adult Brain.” Stem Cells, 32:1220-1229 (PMID 24449485). View PDF
  • Bartel, M.A. and D.V. Schaffer (2014) “Enhanced Gene Targeting of Adult and Pluripotent Stem Cells Using Evolved Adeno-Associated Virus.” Methods in Molecular Biology, 1114: 169-179 (PMID 24557903). View PDF
  • Loring, J.F., T.C. McDevitt, S.P. Palecek, D.V. Schaffer, P.W. Zandstra, and R.M. Nerem (2014) “A Global Assessment of Stem Cell Engineering.” Tissue Engineering Part A, 20(19-20):2575-89 (PMID 24428577). View PDF
  • Schaffer, D.V. (2014) “AAV Shuffles to the Liver.” Molecular Therapy – Methods & Clinical Development, 14006. View PDF
  • Day, T.P., L.C. Byrne, D.V. Schaffer, and J.G. Flannery (2014) “Advances in AAV Vector Development for Gene Therapy in the Retina.” Advances in Experimental Medicine and Biology, 801:687-693 (PMID 24664759). View PDF
  • Yin, L., B. Masella, D. Dalkara, J. Zhang, J.G. Flannery, D.V. Schaffer, D.R. Williams, and W.H. Merigan (2014) “Imaging Light Responses of Foveal Ganglion Cells in the Living Macaque Eye.” Journal of Neuroscience, 7;34 (19) (PMID: 24806684). View PDF
  • Leo, Y., D. Jeong, J, Xiao, and D.V. Schaffer (2014) “Developing Defined and Scalable 3D Culture Systems for Culturing Human Pluripotent Stem Cells at High Densities.” Cell and Molecular Bioengineering, Volume 7, Issue 2, pp 172-183 View PDF
  • Byrne, L.C., B.E. Öztürk, T. Lee, C. Fortuny, M. Visel, D. Dalkara, D.V. Schaffer, and J.G. Flannery (2014) “Retinoschisin Gene Therapy in Photoreceptors Provides Long-term Rescue in the Rs1h-/- Mouse.” Gene Therapy, 21(6): 585-92 (PMID: 24694538). View PDF
  • Cao, J., M. Ahra, C. Sudrik, D.V. Schaffer, and R.S. Kane (2014) “Bidirectional Regulation of mRNA Translation in Mammalian Cells by Using PUF Domains.” Angewandte Chemie, 5;53 (19):4900-4 (PMID: 24677733). View PDF

2013

  • Lei, Y. and D.V. Schaffer (2013) “A Fully Defined and Scalable 3D Culture System for Human Pluripotent Stem Cell Expansion and Differentiation.” Proceedings of the National Academy of Sciences USA, 110:E5039-5048 (PMID 24248365). View PDF
  • Conway, A., T. Vazin, D.P. Spelke, N.A. Rode, K.E. Healy, R.S. Kane, and D.V. Schaffer (2013) “Multivalent Ligands to Control Stem Cell Behaviour in Vitro and in Vivo.” Nature Nanotechnology, 8:831-838 (PMID 24141540). View PDF
  • Downing, T.L., J. Soto, C. Morez, T. Houssin, A. Fritz, F. Yuan, J. Chu, S. Patel, D.V. Schaffer, and S. Li (2013) “Biophysical Regulation of Epigenetic State and Cell Reprogramming.” Nature Materials, 12:1154-1162 (PMID 24141451). View PDF
  • Dalkara, D., L.C. Byrne, R.R. Klimczak, M. Visel, L. Yin, W.H. Merigan, J.G. Flannery, and D.V. Schaffer (2013) "In Vivo–Directed Evolution of a New Adeno-Associated Virus for Therapeutic Outer-Retinal Gene Delivery from the Vitreous." Science Translational Medicine, 5:189ra76 (PMID 23761039). View PDF
  • Miller-Jensen, K., R. Skupsky, P.S. Shah, A.P. Arkin, and D.V. Schaffer (2013) “Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression.” Public Library of Science (PLoS) Computational Biology, 9:e1003135 (PMID 23874178). View PDF
  • Yousef, H., M.J. Conboy, J. Li, M. Zeiderman, T. Vazin, C. Schlesinger, D.V. Schaffer, and I.M. Conboy (2013) “hESC-Secreted Proteins can be Enriched for Multiple Regenerative Therapies by Heparin-Binding.” Aging, 5:357-372 (PMID 23793469). View PDF
  • Keung, A.J., M. Dong, D.V. Schaffer (co-corresponding author), and S. Kumar (2013) "Pan-neuronal Maturation But Not Neuronal Subtype Differentiation of Adult Neural Stem Cells is Mechanosensitive." Scientific Reports, 3:1817 (PMID 23660869). View PDF
  • Bugaj, L.J, A.T Choksi, C.K. Mesuda, R.S. Kane, and D.V. Schaffer (2013) "Optogenetic Protein Clustering and Signaling Activation in Mammalian Cells." Nature Methods, 10:249-252. View PDF
  • Hwang, B-Y. and D.V. Schaffer (2013) “Engineering a Serum-resistant and Thermostable Vesicular Stomatitis Virus G Glycoprotein for Pseudotyping Retroviral and Lentiviral Vectors." Gene Therapy, 20:807-815 (PMID 23364315). View PDF
  • Chen, S. and D.V. Schaffer (2013) “Newborn Neuroblasts Feel the Field in the Adult Brain.” EMBO Reports, 14:105-106 (PMID 23328741). View PDF
  • Pernet, V., S. Joly, D. Dalkara, N. Jordi, O. Schwarz, F. Christ, D.V. Schaffer, J.G. Flannery, and M.E. Schwab (2013) “Long-distance Axonal Regeneration Induced by CNTF Gene Transfer is Impaired by Axonal Misguidance in the Injured Adult Optic Nerve.” Neurobiology of Disease, 51:202-13 (PMID 23194670). View PDF
  • Sudrik C., M. Arha, J. Cao, D.V. Schaffer (co-corresponding author), and R.S. Kane (2013) “Translational Repression Using BIV Tat peptide-TAR RNA Interaction in Mammalian Cells.” Chemical Communications, 49(67):7457-7459 (PMID 23852014). View PDF
  • Cao, J., M. Arha, C. Sudrik, L.J. Bugaj, D.V. Schaffer (co-corresponding author), and R.S. Kane (2013) “Light-inducible Activation of Target mRNA Translation in Mammalian Cells” Chemical Communications, 49:8338-8340 (PMID 23925486). View PDF
  • Perry, S.J., S.G. Neumann, T. Neumann, K. Cheng, J. Ni, J.R. Weinstein, D.V. Schaffer, and M. Tirrell “Challenges in Nucleic Acid-Lipid Films for Transfection” AIChE Journal (in press).
  • Byrne, L.C., F. Khalid, T. Lee, E.A. Zin, K.P. Greenberg, M. Visel, D.V. Schaffer, and J.G. Flannery (2013) “AAV-mediated, Optogenetic Ablation of Müller Glia Leads to Structural and Functional Changes in the Mouse Retina.” Public Library of Science (PLoS) ONE, 8:e76075 (PMID 24086689). View PDF
  • Vazin, T., K.A. Ball, H. Lu, H. Park, Y. Ataeijannati, T. Head-Gordon, M-M Poo, and D. V. Schaffer (2013) “Efficient Derivation of Cortical Glutamatergic Neurons from Human Pluripotent Stem Cells: A Model System to Study Neurotoxicity in Alzheimer’s Disease.” Neurobiology of Disease, 62C:62-72 (PMID 24055772). View PDF
  • Ekerdt, B.L., R.A. Segalman, and D.V. Schaffer (2013) “Spatial Organization of Cell-Adhesive Ligands for Advanced Cell Culture.” Biotechnology Journal, 8:1411-1423 (PMID 24318636).

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
  • 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
  • Goodwill, P.W., E.U. Saritas, L.R. Croft, T.N. Kim, K.M. Krishnan, D.V. Schaffer, and S.M. Conolly (2012) “X-space MPI: Magnetic Nanoparticles for Safe Medical Imaging.” Advanced Materials, 24:3870-3877 (PMID 22988557). View PDF
  • Conway, A. and D.V. Schaffer (2012) “Biophysical Regulation of Stem Cell Behavior in the Niche.” Stem Cell Research and Therapy, 3:50 (PMID 23241436). 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
  • 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 (2012) "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, 19:1096-1108 (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 (2011) "Exploiting Bacterial Peptide Display Technology to Engineer Biomaterials for Neural Stem Cell Culture." Biomaterials, 32:1484-1494 (PMID 21129772). 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, 99:L94-96 (PMID 21156124). 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, 17:1384-1389 (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.

Meetings and Events

Group meetings are held on Mondays in 221 Stanley Hall from 2:30-4:30pm

Group Meeting Schedule 2019

Note: Research Format = Everyone will be presenting their current research

Lab Activities

Noem's 10th Anniversary | 2018 Lab Retreat | 2017 Lab Holiday Party | 2017 Lab Retreat | 2017 Stem Cell Retreat: Asiloma | 2016 Winner for Excellence in Lab Safety | 2016 Holiday Party | 2016 Russian River Retreat | 2015 Holiday Party | 2015 Tahoe Retreat | 2012 Winter Party | 2012 Sid's Farewell | 2012 Tubing Trip | 2012 Deniz&Albert's Farewell Party | 2010 Winter Party | 2009 Tahoe Ski Trip | 2008 Tahoe Ski Trip | 2007 Tahoe Ski Trip | 2011 Winter Party

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