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Research Article

Exploiting Nucleotide Composition to Engineer Promoters

  • Manfred G. Grabherr equal contributor,

    equal contributor Contributed equally to this work with: Manfred G. Grabherr, Jens Pontiller

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Jens Pontiller equal contributor,

    equal contributor Contributed equally to this work with: Manfred G. Grabherr, Jens Pontiller

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Evan Mauceli mail,

    evan@broadinstitute.org

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Wolfgang Ernst,

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Martina Baumann,

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Tara Biagi,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Ross Swofford,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Pamela Russell,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Michael C. Zody,

    Affiliations: Broad Institute, Cambridge, Massachusetts, United States of America, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

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  • Federica Di Palma,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Kerstin Lindblad-Toh,

    Affiliations: Broad Institute, Cambridge, Massachusetts, United States of America, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    X
  • Reingard M. Grabherr

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Published: May 18, 2011
  • DOI: 10.1371/journal.pone.0020136
  • Published in PLOS ONE

About the Authors

Manfred G. Grabherr, Evan Mauceli, Tara Biagi, Ross Swofford, Pamela Russell, Michael C. Zody, Federica Di Palma, Kerstin Lindblad-Toh
Broad Institute, Cambridge, Massachusetts, United States of America
Jens Pontiller, Wolfgang Ernst, Martina Baumann, Reingard M. Grabherr
Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
Michael C. Zody, Kerstin Lindblad-Toh
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Corresponding Author

Email: evan@broadinstitute.org

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: MGG RMG WE JP EM PR MB MCZ KL-T FDP. Performed the experiments: JP MB TB RS. Analyzed the data: EM PR MCZ MGG. Contributed reagents/materials/analysis tools: EM PR MCZ MGG. Wrote the paper: MGG RMG JP EM WE MCZ FDP KL-T. Had the idea: MGG RMG. Designed laboratory experiments: JP WE RMG. Performed all in vitro experiments: JP. Designed and conducted the protein-DNA binding experiments: MB. Constructed the RNA library: TB RS. Conceived of and implemented the computational analyses: EM PR MCZ MGG. Advised on experimental design, computational analyses, and interpretation: KL-T FDP.