Jeffry D Sander

Summary

Affiliation: Massachusetts General Hospital
Country: USA

Publications

  1. pmc ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms
    Deepak Reyon
    Department of Genetics, Iowa State University, Ames, IA 50011, USA
    BMC Genomics 12:83. 2011
  2. pmc ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Nucleic Acids Res 38:W462-8. 2010
  3. pmc Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
    BMC Bioinformatics 11:543. 2010
  4. pmc Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly
    Deepak Reyon
    Molecular Pathology Unit, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Curr Protoc Mol Biol . 2013
  5. pmc Efficient genome editing in zebrafish using a CRISPR-Cas system
    Woong Y Hwang
    Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Biotechnol 31:227-9. 2013
  6. pmc Heritable and precise zebrafish genome editing using a CRISPR-Cas system
    Woong Y Hwang
    Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 8:e68708. 2013
  7. pmc High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
    Yanfang Fu
    1 Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 4 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Biotechnol 31:822-6. 2013
  8. pmc Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs
    Lindsay Cade
    Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
    Nucleic Acids Res 40:8001-10. 2012
  9. pmc Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs)
    Finola E Moore
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 7:e37877. 2012
  10. pmc Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
    Morgan L Maeder
    1 Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA 4
    Nat Biotechnol 31:1137-42. 2013

Collaborators

Detail Information

Publications23

  1. pmc ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms
    Deepak Reyon
    Department of Genetics, Iowa State University, Ames, IA 50011, USA
    BMC Genomics 12:83. 2011
    ....
  2. pmc ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Nucleic Acids Res 38:W462-8. 2010
    ..ZiFiT is freely available on the web without registration at http://bindr.gdcb.iastate.edu/ZiFiT/...
  3. pmc Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA
    BMC Bioinformatics 11:543. 2010
    ..Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable...
  4. pmc Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly
    Deepak Reyon
    Molecular Pathology Unit, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Curr Protoc Mol Biol . 2013
    ..org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput...
  5. pmc Efficient genome editing in zebrafish using a CRISPR-Cas system
    Woong Y Hwang
    Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Biotechnol 31:227-9. 2013
    ....
  6. pmc Heritable and precise zebrafish genome editing using a CRISPR-Cas system
    Woong Y Hwang
    Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 8:e68708. 2013
    ..Together, these advances expand the utility of the CRISPR-Cas system in the zebrafish beyond somatic indel formation to heritable and precise genome modifications. ..
  7. pmc High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
    Yanfang Fu
    1 Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 4 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Biotechnol 31:822-6. 2013
    ..Our work demonstrates that RGNs can be highly active even with imperfectly matched RNA-DNA interfaces in human cells, a finding that might confound their use in research and therapeutic applications. ..
  8. pmc Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs
    Lindsay Cade
    Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA
    Nucleic Acids Res 40:8001-10. 2012
    ..Our results suggest that construction of one to two heterodimeric TALEN pairs for any given gene will, in most cases, enable researchers to rapidly generate knockout zebrafish...
  9. pmc Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs)
    Finola E Moore
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 7:e37877. 2012
    ....
  10. pmc Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
    Morgan L Maeder
    1 Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA 4
    Nat Biotechnol 31:1137-42. 2013
    ....
  11. pmc In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Pathology, Harvard Medical School, Boston, MA 02115, USA, Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 01238, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA and Howard Hughes Medical Institute, Chevy Chase, MD 02815, USA
    Nucleic Acids Res 41:e181. 2013
    ..Our improved method should enable more comprehensive profiling of ZFN specificities. ..
  12. pmc Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays
    Morgan L Maeder
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Protoc 4:1471-501. 2009
    ..Here we provide a detailed protocol for carrying out OPEN to engineer zinc-finger arrays that have a high probability of functioning as ZFNs. Using OPEN, researchers can generate multiple, customized ZFNs in approximately 8 weeks...
  13. pmc Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)
    Jeffry D Sander
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Methods 8:67-9. 2011
    ..The simplicity and efficacy of CoDA will enable broad adoption of ZFN technology and make possible large-scale projects focused on multigene pathways or genome-wide alterations...
  14. pmc Robust, synergistic regulation of human gene expression using TALE activators
    Morgan L Maeder
    Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Methods 10:243-5. 2013
    ..These findings will encourage applications of TALE activators for research and therapy, and guide design of monomeric TALE-based fusion proteins...
  15. pmc Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly
    Deepak Reyon
    Molecular Pathology Unit, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Curr Protoc Mol Biol . 2012
    ..With the described platform of reagents, protocols, and software, researchers can easily engineer multiple TALENs within 2 weeks using standard cloning techniques...
  16. pmc FLASH assembly of TALENs for high-throughput genome editing
    Deepak Reyon
    Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Nat Biotechnol 30:460-5. 2012
    ..Our results establish the robustness of TALEN technology and demonstrate that FLASH facilitates high-throughput genome editing at a scale not currently possible with other genome modification technologies...
  17. pmc Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN)
    Jonathan E Foley
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 4:e4348. 2009
    ..The Consortium has previously used this new method (known as OPEN for Oligomerized Pool ENgineering) to generate high quality ZFN pairs that function in human and plant cells...
  18. pmc TALENs: a widely applicable technology for targeted genome editing
    J Keith Joung
    Massachusetts General Hospital, Molecular Pathology Unit, The Center for Computational and Integrative Biology, and the Center for Cancer Research, Harvard Medical School, Department of Pathology, 149 13th Street, 6th Floor, Charlestown, Massachusetts 02129, USA
    Nat Rev Mol Cell Biol 14:49-55. 2013
    ..The capability to quickly and efficiently alter genes using TALENs promises to have profound impacts on biological research and to yield potential therapeutic strategies for genetic diseases...
  19. doi Engineering zinc finger nucleases for targeted mutagenesis of zebrafish
    Jeffry D Sander
    Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Methods Cell Biol 104:51-8. 2011
    ..We also provide a framework for choosing among the various publicly available platforms available to engineer ZFNs...
  20. pmc Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
    Yanfang Fu
    1 Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 4 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA 5
    Nat Biotechnol 32:279-84. 2014
    ..Our results delineate a simple, effective strategy to improve the specificities of Cas9 nucleases or paired nickases. ..
  21. pmc Engineering designer nucleases with customized cleavage specificities
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
    Curr Protoc Mol Biol . 2011
    ..Protocols for engineering ZFNs targeted to specific gene sequences of interest using the context-dependent assembly (CoDA) method are described in this unit...
  22. pmc Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification
    Morgan L Maeder
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Mol Cell 31:294-301. 2008
    ..In summary, OPEN provides an "open-source" method for rapidly engineering highly active zinc-finger arrays, thereby enabling broader practice, development, and application of ZFN technology for biological research and gene therapy...
  23. pmc CRISPR-Cas systems for editing, regulating and targeting genomes
    Jeffry D Sander
    1 Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Biotechnol 32:347-55. 2014
    ....