David E Root

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint Genome-scale loss-of-function screening with a lentiviral RNAi library
    David E Root
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Methods 3:715-9. 2006
  2. doi request reprint Genome-scale CRISPR-Cas9 knockout screening in human cells
    Ophir Shalem
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 343:84-7. 2014
  3. pmc ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens
    Diane D Shao
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 23:665-78. 2013
  4. doi request reprint A melanocyte lineage program confers resistance to MAP kinase pathway inhibition
    Cory M Johannessen
    1 The Broad Institute of Harvard University and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA 2 Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA 3 Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
    Nature 504:138-42. 2013
  5. pmc MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma
    Kris C Wood
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Sci Signal 5:rs4. 2012
  6. pmc A public genome-scale lentiviral expression library of human ORFs
    Xiaoping Yang
    RNA interference RNAi Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 8:659-61. 2011
  7. pmc Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4
    Yin Ren
    Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Sci Transl Med 4:147ra112. 2012
  8. pmc Systematic discovery of TLR signaling components delineates viral-sensing circuits
    Nicolas Chevrier
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Cell 147:853-67. 2011
  9. pmc The bromodomain protein Brd4 insulates chromatin from DNA damage signalling
    Scott R Floyd
    Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 498:246-50. 2013
  10. pmc lincRNAs act in the circuitry controlling pluripotency and differentiation
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 477:295-300. 2011

Collaborators

Detail Information

Publications20

  1. ncbi request reprint Genome-scale loss-of-function screening with a lentiviral RNAi library
    David E Root
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Methods 3:715-9. 2006
    ..Initial screening efforts have demonstrated that these libraries and methods are practical and powerful tools for high-throughput lentivirus RNAi screens...
  2. doi request reprint Genome-scale CRISPR-Cas9 knockout screening in human cells
    Ophir Shalem
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 343:84-7. 2014
    ..We observe a high level of consistency between independent guide RNAs targeting the same gene and a high rate of hit confirmation, demonstrating the promise of genome-scale screening with Cas9. ..
  3. pmc ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens
    Diane D Shao
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Genome Res 23:665-78. 2013
    ..ATARiS is publicly available at http://broadinstitute.org/ataris...
  4. doi request reprint A melanocyte lineage program confers resistance to MAP kinase pathway inhibition
    Cory M Johannessen
    1 The Broad Institute of Harvard University and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA 2 Department of Medical Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA 3 Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115, USA
    Nature 504:138-42. 2013
    ..Collectively, these data suggest that oncogenic dysregulation of a melanocyte lineage dependency can cause resistance to RAF-MEK-ERK inhibition, which may be overcome by combining signalling- and chromatin-directed therapeutics. ..
  5. pmc MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma
    Kris C Wood
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Sci Signal 5:rs4. 2012
    ....
  6. pmc A public genome-scale lentiviral expression library of human ORFs
    Xiaoping Yang
    RNA interference RNAi Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 8:659-61. 2011
    ..Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types...
  7. pmc Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4
    Yin Ren
    Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Sci Transl Med 4:147ra112. 2012
    ..These observations not only credential ID4 as an oncogene in 32% of high-grade ovarian cancers but also provide a framework for the identification, validation, and understanding of potential therapeutic cancer targets...
  8. pmc Systematic discovery of TLR signaling components delineates viral-sensing circuits
    Nicolas Chevrier
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Cell 147:853-67. 2011
    ..Our study illustrates the power of combining systematic measurements and perturbations to elucidate complex signaling circuits and discover potential therapeutic targets...
  9. pmc The bromodomain protein Brd4 insulates chromatin from DNA damage signalling
    Scott R Floyd
    Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 498:246-50. 2013
    ..These data implicate Brd4, previously known for its role in transcriptional control, as an insulator of chromatin that can modulate the signalling response to DNA damage...
  10. pmc lincRNAs act in the circuitry controlling pluripotency and differentiation
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 477:295-300. 2011
    ..Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state...
  11. ncbi request reprint A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
    Jason Moffat
    Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Cell 124:1283-98. 2006
    ..This work provides a widely applicable resource for loss-of-function screens, as well as a roadmap for its application to biological discovery...
  12. pmc A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection
    Sagi D Shapira
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Cell 139:1255-67. 2009
    ..This multilayered approach provides a comprehensive and unbiased physical and regulatory model of influenza-host interactions and demonstrates a general strategy for uncovering complex host-pathogen relationships...
  13. pmc Regulated ADAM17-dependent EGF family ligand release by substrate-selecting signaling pathways
    Michelle Dang
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 110:9776-81. 2013
    ..Thus, signaling-mediated substrate selection is clearly distinct from regulation of enzyme activity, an important mechanism that offers itself for application in disease...
  14. pmc COT drives resistance to RAF inhibition through MAP kinase pathway reactivation
    Cory M Johannessen
    Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 468:968-72. 2010
    ....
  15. pmc Functional genomics reveal that the serine synthesis pathway is essential in breast cancer
    Richard Possemato
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 476:346-50. 2011
    ....
  16. pmc Highly parallel identification of essential genes in cancer cells
    Biao Luo
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 105:20380-5. 2008
    ....
  17. doi request reprint Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks
    Joel P Wagner
    Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    Sci Signal 6:ra58. 2013
    ..Thus, classifying RTKs by their inferred networks and then therapeutically targeting multiple receptors within a class may delay or prevent the onset of resistance. ..
  18. pmc Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
    Ido Amit
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:257-63. 2009
    ..This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells...
  19. pmc Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
    Thouis R Jones
    The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:1826-31. 2009
    ..By using this approach, we successfully scored images in RNA interference screens in 2 organisms for the prevalence of 15 diverse cellular morphologies, some of which were previously intractable...
  20. ncbi request reprint Integrative genomic approaches identify IKBKE as a breast cancer oncogene
    Jesse S Boehm
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Cell 129:1065-79. 2007
    ..These observations suggest a mechanism for NF-kappaB activation in breast cancer, implicate the NF-kappaB pathway as a downstream mediator of PI3K, and provide a framework for integrated genomic approaches in oncogene discovery...