Nicholas T Ingolia

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
  2. pmc Genome-wide annotation and quantitation of translation by ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
    Curr Protoc Mol Biol . 2013
  3. pmc The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
    Nat Protoc 7:1534-50. 2012
  4. doi request reprint Ribosome profiling: new views of translation, from single codons to genome scale
    Nicholas T Ingolia
    Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, Maryland 21218, USA Present address Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall 422, Berkeley, California 94720, USA
    Nat Rev Genet 15:205-13. 2014
  5. pmc High-resolution view of the yeast meiotic program revealed by ribosome profiling
    Gloria A Brar
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Science 335:552-7. 2012
  6. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
  7. pmc Decoding human cytomegalovirus
    Noam Stern-Ginossar
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisico, CA 94158, USA
    Science 338:1088-93. 2012
  8. pmc Rapid creation and quantitative monitoring of high coverage shRNA libraries
    Michael C Bassik
    Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California, USA
    Nat Methods 6:443-5. 2009
  9. pmc The translational landscape of mTOR signalling steers cancer initiation and metastasis
    Andrew C Hsieh
    School of Medicine and Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
    Nature 485:55-61. 2012
  10. pmc Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats
    Elena O Gracheva
    Department of Physiology, University of California, San Francisco, California 94158 2517, USA
    Nature 476:88-91. 2011

Research Grants

Collaborators

Detail Information

Publications11

  1. pmc Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA
    Science 324:218-23. 2009
    ..Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible...
  2. pmc Genome-wide annotation and quantitation of translation by ribosome profiling
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
    Curr Protoc Mol Biol . 2013
    ..The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 5 days...
  3. pmc The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
    Nat Protoc 7:1534-50. 2012
    ..The protocol we describe requires 5-7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4-5 days...
  4. doi request reprint Ribosome profiling: new views of translation, from single codons to genome scale
    Nicholas T Ingolia
    Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, Maryland 21218, USA Present address Department of Molecular and Cell Biology, University of California, Berkeley, Barker Hall 422, Berkeley, California 94720, USA
    Nat Rev Genet 15:205-13. 2014
    ..Studies using ribosome profiling have already provided new insights into the identity and the amount of proteins that are produced by cells, as well as detailed views into the mechanism of protein synthesis itself. ..
  5. pmc High-resolution view of the yeast meiotic program revealed by ribosome profiling
    Gloria A Brar
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Science 335:552-7. 2012
    ..This work reveals pervasive translational control in meiosis and helps to illuminate the molecular basis of the broad restructuring of meiotic cells...
  6. pmc Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    Nicholas T Ingolia
    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell 147:789-802. 2011
    ..We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes...
  7. pmc Decoding human cytomegalovirus
    Noam Stern-Ginossar
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisico, CA 94158, USA
    Science 338:1088-93. 2012
    ..Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity...
  8. pmc Rapid creation and quantitative monitoring of high coverage shRNA libraries
    Michael C Bassik
    Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, Howard Hughes Medical Institute, University of California, San Francisco, California, USA
    Nat Methods 6:443-5. 2009
    ..This approach enables identification of multiple effective target-specific shRNAs from a complex pool, allowing a rigorous statistical evaluation of true hits...
  9. pmc The translational landscape of mTOR signalling steers cancer initiation and metastasis
    Andrew C Hsieh
    School of Medicine and Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
    Nature 485:55-61. 2012
    ..Together, these findings extend our understanding of how the 'cancerous' translation machinery steers specific cancer cell behaviours, including metastasis, and may be therapeutically targeted...
  10. pmc Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats
    Elena O Gracheva
    Department of Physiology, University of California, San Francisco, California 94158 2517, USA
    Nature 476:88-91. 2011
    ..These findings reveal a novel molecular mechanism for physiological tuning of thermosensory nerve fibres...
  11. doi request reprint Genome-wide translational profiling by ribosome footprinting
    Nicholas T Ingolia
    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
    Methods Enzymol 470:119-42. 2010
    ..Finally, we discuss how deep sequencing data can be used to quantify gene expression at the level of translation...

Research Grants2

  1. Genome-wide Function and Substrate Recognition of the Chaperone Prefoldin
    Nicholas Ingolia; Fiscal Year: 2007
    ..Protein chaperones bind to newly-produced proteins and help them to fold while preventing them from aggregating. We want to know how the chaperone prefoldin binds specific target proteins and what role this has in normal cell function. ..