Chuanning Tang

Summary

Affiliation: University of Minnesota
Country: USA

Publications

  1. pmc Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
    Gloria M Sheynkman
    Chemistry Department, University of Wisconsin Madison, 1101 University Ave, Madison, WI 53706, USA
    BMC Genomics 15:703. 2014
  2. pmc Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis
    Sricharan Bandhakavi
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
    PLoS ONE 3:e1598. 2008
  3. pmc Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions
    Ebbing P de Jong
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
    PLoS ONE 5:e11148. 2010
  4. pmc Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery
    Joel A Kooren
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, 6 155 Jackson Hall, Minneapolis, Minnesota, 55455, USA
    Clin Proteomics 8:13. 2011
  5. pmc iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer
    Timothy J Griffin
    Department of Biochemistry, Molecular Biology, and Biophysics, Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Proteome Res 6:4200-9. 2007
  6. ncbi request reprint Advancing mammalian cell culture engineering using genome-scale technologies
    Timothy J Griffin
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
    Trends Biotechnol 25:401-8. 2007
  7. pmc Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection
    Ji Wan
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    Nucleic Acids Res 36:e22. 2008
  8. ncbi request reprint Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae
    Hongwei Xie
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, 6 155 Jackson Hall, Minneapolis, Minnesota 55455, USA
    Anal Chem 77:3198-207. 2005
  9. ncbi request reprint Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics
    Hongwei Xie
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 55455, USA
    J Proteome Res 5:1003-9. 2006
  10. pmc A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva
    Sricharan Bandhakavi
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6 155 Jackson Hall, 321 Church Street SE, Minneapolis, Minnesota 55455, USA
    J Proteome Res 8:5590-600. 2009

Research Grants

Collaborators

Detail Information

Publications34

  1. pmc Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
    Gloria M Sheynkman
    Chemistry Department, University of Wisconsin Madison, 1101 University Ave, Madison, WI 53706, USA
    BMC Genomics 15:703. 2014
    ..g. genomics, transcriptomics, proteomics) data...
  2. pmc Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis
    Sricharan Bandhakavi
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
    PLoS ONE 3:e1598. 2008
    ..cerevisiae. Additionally, these results highlight the value of comparative expression analyses between large-scale proteomic and transcriptomic datasets to reveal new regulatory connections...
  3. pmc Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions
    Ebbing P de Jong
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
    PLoS ONE 5:e11148. 2010
    ..A test for proteins, ones found in non-invasively-collected whole saliva and whose abundances distinguish these lesion types, would meet this critical need...
  4. pmc Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery
    Joel A Kooren
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church St SE, 6 155 Jackson Hall, Minneapolis, Minnesota, 55455, USA
    Clin Proteomics 8:13. 2011
    ..abstract:..
  5. pmc iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer
    Timothy J Griffin
    Department of Biochemistry, Molecular Biology, and Biophysics, Center for Mass Spectrometry and Proteomics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Proteome Res 6:4200-9. 2007
    ..Thus, we demonstrate the effectiveness of LTQ-PQD analyzing iTRAQ reagent-labeled peptides, and provide guidelines for successful quantitative proteomic studies...
  6. ncbi request reprint Advancing mammalian cell culture engineering using genome-scale technologies
    Timothy J Griffin
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
    Trends Biotechnol 25:401-8. 2007
    ..We also provide a focused review of relevant alternative and emerging technologies, which have seen limited use in cell culture engineering, but hold great potential for significant advancements in protein therapeutic production...
  7. pmc Meta-prediction of phosphorylation sites with weighted voting and restricted grid search parameter selection
    Ji Wan
    Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
    Nucleic Acids Res 36:e22. 2008
    ..An implementation of these meta-predictors is available on the web at: http://MetaPred.umn.edu/MetaPredPS/...
  8. ncbi request reprint Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae
    Hongwei Xie
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, 6 155 Jackson Hall, Minneapolis, Minnesota 55455, USA
    Anal Chem 77:3198-207. 2005
    ....
  9. ncbi request reprint Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics
    Hongwei Xie
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 55455, USA
    J Proteome Res 5:1003-9. 2006
    ....
  10. pmc A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva
    Sricharan Bandhakavi
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6 155 Jackson Hall, 321 Church Street SE, Minneapolis, Minnesota 55455, USA
    J Proteome Res 8:5590-600. 2009
    ..These results expand the potential for whole saliva in health monitoring/diagnostics and provide a general platform for improving proteomic coverage of complex biological samples...
  11. ncbi request reprint Proteomic mapping of 4-hydroxynonenal protein modification sites by solid-phase hydrazide chemistry and mass spectrometry
    Mikel R Roe
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 420 Washington Avenue SE, Minneapolis, Minnesota 55445, USA
    Anal Chem 79:3747-56. 2007
    ..These results demonstrate the effectiveness of this novel strategy as a general platform for proteome-scale identification of amino acid sites susceptible to HNE modification from within complex mixtures...
  12. pmc Cortical metabolites as biomarkers in the R6/2 model of Huntington's disease
    Lori Zacharoff
    Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Cereb Blood Flow Metab 32:502-14. 2012
    ..Thus, neurochemical changes precede volume shrinkage and become potential biomarkers for HD mouse models...
  13. pmc Meta-prediction of protein subcellular localization with reduced voting
    Jie Liu
    Department of Neuroscience, University of Minneapolis, MN 55455, USA
    Nucleic Acids Res 35:e96. 2007
    ..This and similar voting strategies, when properly applied, are expected to produce meta-predictors with outstanding performance in other life sciences problem domains...
  14. doi request reprint Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems
    Karthik P Jayapal
    Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
    J Proteome Res 9:2087-97. 2010
    ....
  15. pmc Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response
    Sricharan Bandhakavi
    Department of Biochemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Mol Cell Proteomics 9:403-14. 2010
    ..These findings reveal a novel functional link between mTOR and DDR pathways in the nucleus potentially operating as a survival mechanism against unfavorable growth conditions...
  16. pmc Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry
    Mikel R Roe
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
    J Am Soc Mass Spectrom 21:1190-203. 2010
    ..Collectively, our method and software should provide valuable new tools for investigators studying protein carbonylation via mass spectrometry-based proteomics...
  17. pmc Oxidative stress and covalent modification of protein with bioactive aldehydes
    Paul A Grimsrud
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Biol Chem 283:21837-41. 2008
    ..The use of mass spectrometric methods to identify the site and extent of protein carbonylation on a proteome-wide scale has expanded our view of how oxidative stress can regulate cellular processes...
  18. doi request reprint Global assessment of protein turnover in recombinant antibody producing myeloma cells
    Joon Chong Yee
    Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455 0132, USA
    J Biotechnol 148:182-93. 2010
    ..The label decay curve appears to show a second region with very slow kinetics, raising the possibility of two populations of IgG molecules with different secretion characteristics...
  19. ncbi request reprint Proteomics analysis of cells in whole saliva from oral cancer patients via value-added three-dimensional peptide fractionation and tandem mass spectrometry
    Hongwei Xie
    Department of Biochemistry, Molecular Biology, and Biophysics, School of Dentistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Mol Cell Proteomics 7:486-98. 2008
    ..Thus, for detecting salivary markers of oral cancer and possibly other conditions of the oral cavity, the results confirm both the potential of analyzing the cells in whole saliva and doing so with our proteomics method...
  20. ncbi request reprint A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry
    Hongwei Xie
    Department of Biochemistry, Molecular Biology, and Biophysics, School of Dentistry, University of Minnesota, Minneapolis 55455, USA
    Mol Cell Proteomics 4:1826-30. 2005
    ....
  21. ncbi request reprint Gel-free mass spectrometry-based high throughput proteomics: tools for studying biological response of proteins and proteomes
    Mikel R Roe
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
    Proteomics 6:4678-87. 2006
    ....
  22. ncbi request reprint Carbonylation of adipose proteins in obesity and insulin resistance: identification of adipocyte fatty acid-binding protein as a cellular target of 4-hydroxynonenal
    Paul A Grimsrud
    Department of Biochemistry, Molecular Biology and Biophysics, The University of Minnesota, Minneapolis, Minnesota 55455, USA
    Mol Cell Proteomics 6:624-37. 2007
    ....
  23. ncbi request reprint Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40
    Emilie Vander Haar
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6 155 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
    Nat Cell Biol 9:316-23. 2007
    ..These findings identify PRAS40 as an important regulator of insulin sensitivity of the Akt-mTOR pathway and a potential target for the treatment of cancers, insulin resistance and hamartoma syndromes...
  24. ncbi request reprint Identification of carbonylated proteins from enriched rat skeletal muscle mitochondria using affinity chromatography-stable isotope labeling and tandem mass spectrometry
    Danni L Meany
    Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
    Proteomics 7:1150-63. 2007
    ..The results also demonstrate the utility of PQD operation on the LTQ instrument for quantitative analysis of iTRAQ reagent-labeled peptide mixtures, as well as the quantitative reproducibility of the avidin-affinity enrichment method...
  25. ncbi request reprint Preparative peptide isoelectric focusing as a tool for improving the identification of lysine-acetylated peptides from complex mixtures
    Hongwei Xie
    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Proteome Res 6:2019-26. 2007
    ..These results demonstrate the potential utility of this general strategy for improving the identification of PTMs which cause a shift to the intrinsic isoelectric point of peptides...
  26. pmc Quantitative proteomic profiling of muscle type-dependent and age-dependent protein carbonylation in rat skeletal muscle mitochondria
    Juan Feng
    University of Minnesota, 321 Church St SE, 6 155 Jackson Hall, Minneapolis, MN 55455, USA
    J Gerontol A Biol Sci Med Sci 63:1137-52. 2008
    ....
  27. pmc Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor
    Karthik P Jayapal
    Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, United States of America
    PLoS ONE 3:e2097. 2008
    ....
  28. ncbi request reprint PRR5, a novel component of mTOR complex 2, regulates platelet-derived growth factor receptor beta expression and signaling
    So Yon Woo
    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota at the Twin Cities, Minneapolis, Minnesota 55455, USA
    J Biol Chem 282:25604-12. 2007
    ..These findings propose a potential role of mTORC2 in the cross-talk with the cellular machinery that regulates PDGFRbeta expression and signaling...
  29. ncbi request reprint Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis
    Hookeun Lee
    The Institute for Systems Biology, Seattle, Washington 98103 8904, USA
    Anal Chem 74:4353-60. 2002
    ..cerevisiae grown on two different carbon sources using the isotope-coded affinity tag (ICAT) reagent and matrix-assisted desorption/ionization quadrupole time-of-flight mass spectrometry...
  30. ncbi request reprint Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae
    Timothy J Griffin
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Mol Cell Proteomics 1:323-33. 2002
    ....
  31. ncbi request reprint Advances in quantitative proteomics using stable isotope tags
    Mark R Flory
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    Trends Biotechnol 20:S23-9. 2002
    ..This article summarizes recent technological advances in quantitative proteomics...
  32. 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...
  33. ncbi request reprint Proteome analysis of low-abundance proteins using multidimensional chromatography and isotope-coded affinity tags
    Steven P Gygi
    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA
    J Proteome Res 1:47-54. 2002
    ....

Research Grants1

  1. Characterizing Oral Cancer Progression via Saliva Proteomics
    Timothy J Griffin; Fiscal Year: 2010
    ..As such the findings from the proposed studies will have a direct impact on improving the diagnosis and treatment of oral cancer in the clinic, thereby leading to a decrease in the significant suffering and death caused by this cancer. ..