Jeffrey A Ranish

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. ncbi request reprint Identification of TFB5, a new component of general transcription and DNA repair factor IIH
    Jeffrey A Ranish
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nat Genet 36:707-13. 2004
  2. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
  3. pmc The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Genet 9:e1003216. 2013
  4. pmc Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes
    Charis L Himeda
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Mol Cell Biol 28:6521-35. 2008
  5. pmc Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genes Dev 23:2887-99. 2009
  6. pmc The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes
    Bong Kim
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:16068-73. 2007
  7. pmc RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation
    P Geetha Rani
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell Biol 24:1709-20. 2004
  8. pmc Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores
    Nitobe London
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Curr Biol 22:900-6. 2012
  9. pmc Tension directly stabilizes reconstituted kinetochore-microtubule attachments
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nature 468:576-9. 2010
  10. ncbi request reprint Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition
    Jeffrey A Ranish
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 359:17-35. 2007

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Identification of TFB5, a new component of general transcription and DNA repair factor IIH
    Jeffrey A Ranish
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nat Genet 36:707-13. 2004
    ..The identification of a new, evolutionarily conserved, core TFIIH subunit is essential for our understanding of TFIIH function in transcription, DNA repair and human disease...
  2. pmc Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
    Frank Desiere
    Nestle Research Center, 1000 Lausanne 26, Switzerland
    Genome Biol 6:R9. 2005
    ..This resource could serve as an expandable repository for MS-derived proteome information...
  3. pmc The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
    PLoS Genet 9:e1003216. 2013
    ..We propose that Mub1/Ubr2 are part of a quality control system that monitors kinetochore integrity, thus ensuring genomic stability...
  4. pmc Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes
    Charis L Himeda
    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
    Mol Cell Biol 28:6521-35. 2008
    ..Interestingly, MAZ occupies and is able to transactivate the Six4 promoter in skeletal but not cardiac myocytes. Taken together, these findings are consistent with a previously unrecognized role for MAZ in muscle gene regulation...
  5. pmc Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genes Dev 23:2887-99. 2009
    ..These data suggest that Fin1 is a PP1 regulatory subunit whose spatial and temporal activity must be precisely controlled to ensure genomic stability...
  6. pmc The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes
    Bong Kim
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:16068-73. 2007
    ..The results demonstrate that TFIIS is a PIC component that is required for efficient formation and/or stability of the complex...
  7. pmc RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation
    P Geetha Rani
    Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Mol Cell Biol 24:1709-20. 2004
    ..These results suggest that both the Pol II-Med and Pol II-TFIIF complexes can be recruited for transcription initiation but that only the Pol II-TFIIF complex is competent for transcription reinitiation...
  8. pmc Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores
    Nitobe London
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Curr Biol 22:900-6. 2012
    ..Together, these data identify Spc105 as a key target of the Mps1 kinase and show that the opposing activities of Mps1 and PP1 regulate the kinetochore localization of the Bub1 protein...
  9. pmc Tension directly stabilizes reconstituted kinetochore-microtubule attachments
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nature 468:576-9. 2010
    ..On the basis of these findings, we propose that tension selectively stabilizes proper kinetochore-microtubule attachments in vivo through a combination of direct mechanical stabilization and tension-dependent phosphoregulation...
  10. ncbi request reprint Using stable isotope tagging and mass spectrometry to characterize protein complexes and to detect changes in their composition
    Jeffrey A Ranish
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 359:17-35. 2007
    ..The use of software tools for statistical analysis of the data is also described...
  11. pmc KLF3 regulates muscle-specific gene expression and synergizes with serum response factor on KLF binding sites
    Charis L Himeda
    Department of Biochemistry, Box 357350, University of Washington, Seattle, WA 98195, USA
    Mol Cell Biol 30:3430-43. 2010
    ..Since both factors are expressed in all muscle lineages, SRF may regulate many striated- and smooth-muscle genes that lack known SRF control elements, thus further expanding the breadth of the emerging CArGome...
  12. pmc Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
    Nichole L King
    Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA
    Genome Biol 7:R106. 2006
    ..We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development...
  13. pmc Quantitative proteomic identification of six4 as the trex-binding factor in the muscle creatine kinase enhancer
    Charis L Himeda
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Mol Cell Biol 24:2132-43. 2004
    ..Our proteomics strategy will be useful for identifying transcription factors from complex mixtures using only defined DNA fragments for purification...
  14. pmc Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA
    Linda Warfield
    Fred Hutchinson Cancer Research Center, and Howard Hughes Medical Institute, Seattle, WA 98109, USA
    Genes Dev 18:1022-34. 2004
    ..Our results suggest a mechanism for the previously observed positive and negative effects of Spt8 on transcription observed in vivo...
  15. ncbi request reprint Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics
    Marjorie Brand
    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Nat Struct Mol Biol 11:73-80. 2004
    ....
  16. ncbi request reprint Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry
    Xiao Jun Li
    The Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Anal Chem 75:6648-57. 2003
    ....
  17. pmc Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae
    Bungo Akiyoshi
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genetics 183:1591-5. 2009
    ..We found that kinetochore-bound Ndc80 is phosphorylated on Ipl1 sites in vivo, but this phosphorylation is not essential. Instead, we show that additional Ipl1 targets contribute to segregation and the spindle checkpoint...
  18. ncbi request reprint Abundance ratio-dependent proteomic analysis by mass spectrometry
    Timothy J Griffin
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
    Anal Chem 75:867-74. 2003
    ..cerevisiae...
  19. ncbi request reprint The study of macromolecular complexes by quantitative proteomics
    Jeffrey A Ranish
    Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103 8904, USA
    Nat Genet 33:349-55. 2003
    ....
  20. ncbi request reprint Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics
    Bingyun Sun
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 6:141-9. 2007
    ..4) The approach is demonstrated here on the analysis of N-linked glycopeptides; however, it can be applied equally well to O-glycoprotein analysis...
  21. doi request reprint Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome
    Bingyun Sun
    Institute for Systems Biology, 401 N Terry Ave, Seattle, Washington 98109, USA
    J Proteome Res 12:2034-44. 2013
    ..The developed technique as well as the identified protein markers is translational to human studies. We hope our work can broaden the utility of blood proteomics in diagnosis and research of the whole-body response to pathogenic cues...
  22. ncbi request reprint Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry
    Huilin Zhou
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Nat Biotechnol 20:512-5. 2002
    ..A side-by-side comparison with the isotope-coded affinity tag (ICAT) method demonstrated that the solid-phase method for stable isotope tagging of peptides is comparatively simpler, more efficient, and more sensitive...