Jeffry D Sander

Summary

Affiliation: Iowa State University
Country: USA

Publications

  1. doi request reprint Unexpected failure rates for modular assembly of engineered zinc fingers
    Cherie L Ramirez
    Nat Methods 5:374-5. 2008
  2. pmc Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool
    Jeffry D Sander
    Department of Genetics, Development and Cell Biology Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 35:W599-605. 2007
  3. pmc An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins
    Jeffry D Sander
    Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 37:506-15. 2009
  4. pmc Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays
    Fengli Fu
    Department of Genetics, Development and Cell Biology, 1043 Roy J Carver Co Laboratory, Iowa State University, Ames, Iowa 50011, USA
    Nucleic Acids Res 37:D279-83. 2009
  5. pmc RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
    Michael Terribilini
    Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
    Nucleic Acids Res 35:W578-84. 2007
  6. 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
  7. ncbi request reprint Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly
    David A Wright
    Department of Genetics, Development and Cell Biology, Iowa State University, 1035A Roy J Carver Co Lab, Ames, Iowa 50011, USA
    Nat Protoc 1:1637-52. 2006
  8. 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
  9. pmc Striking similarities in diverse telomerase proteins revealed by combining structure prediction and machine learning approaches
    Jae Hyung Lee
    Bioinformatics and Computational Biology Program, L H Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50010, USA
    Pac Symp Biocomput . 2008
  10. 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

Collaborators

Detail Information

Publications10

  1. doi request reprint Unexpected failure rates for modular assembly of engineered zinc fingers
    Cherie L Ramirez
    Nat Methods 5:374-5. 2008
  2. pmc Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool
    Jeffry D Sander
    Department of Genetics, Development and Cell Biology Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 35:W599-605. 2007
    ..In addition, ZiFiT output facilitates identification of specific zinc finger modules that are publicly available from the Zinc Finger Consortium. ZiFiT is freely available at http://bindr.gdcb.iastate.edu/ZiFiT/...
  3. pmc An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins
    Jeffry D Sander
    Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
    Nucleic Acids Res 37:506-15. 2009
    ..91). We propose that success rates for ZFP modular assembly can be significantly improved by exploiting the score-based strategy described here...
  4. pmc Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays
    Fengli Fu
    Department of Genetics, Development and Cell Biology, 1043 Roy J Carver Co Laboratory, Iowa State University, Ames, Iowa 50011, USA
    Nucleic Acids Res 37:D279-83. 2009
    ..ZiFDB will also be a valuable resource for those scientists interested in better understanding how zinc-finger proteins recognize target DNA...
  5. pmc RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
    Michael Terribilini
    Department of Genetics, Development and Cell Biology, Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa 50011, USA
    Nucleic Acids Res 35:W578-84. 2007
    ..RNABindR automatically displays 'high specificity' and 'high sensitivity' predictions of RNA-binding residues. RNABindR is freely available at http://bindr.gdcb.iastate.edu/RNABindR...
  6. 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
    ....
  7. ncbi request reprint Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly
    David A Wright
    Department of Genetics, Development and Cell Biology, Iowa State University, 1035A Roy J Carver Co Lab, Ames, Iowa 50011, USA
    Nat Protoc 1:1637-52. 2006
    ..We also describe a bacterial cell-based reporter assay for rapidly screening the DNA-binding activities of assembled multi-finger arrays. This protocol can be completed in approximately 24-26 d...
  8. 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. ..
  9. pmc Striking similarities in diverse telomerase proteins revealed by combining structure prediction and machine learning approaches
    Jae Hyung Lee
    Bioinformatics and Computational Biology Program, L H Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50010, USA
    Pac Symp Biocomput . 2008
    ..In addition, the combined evidence from machine learning and structural modeling identified several specific amino acids that are likely to play a role in binding DNA or RNA, but for which no experimental evidence is currently available...
  10. 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...