Qi Liu

Summary

Affiliation: Vanderbilt University
Country: USA

Publications

  1. pmc RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Mol Biosyst 9:3036-46. 2013
  2. pmc Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data
    Qi Liu
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Genomics 13:S8. 2012
  3. pmc Next generation sequencing in cancer research and clinical application
    Derek Shyr
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, 37232, Nashville, TN, USA
    Biol Proced Online 15:4. 2013
  4. pmc Proteogenomic characterization of human colon and rectal cancer
    Bing Zhang
    1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA 2 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Nature 513:382-7. 2014
  5. pmc Leveraging the complementary nature of RNA-Seq and shotgun proteomics data
    Xiaojing Wang
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN
    Proteomics 14:2676-87. 2014
  6. pmc Assessing Computational Steps for CLIP-Seq Data Analysis
    Qi Liu
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Biomed Res Int 2015:196082. 2015
  7. pmc Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
    J Proteome Res 15:766-76. 2016
  8. pmc p73 Is Required for Multiciliogenesis and Regulates the Foxj1-Associated Gene Network
    Clayton B Marshall
    Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
    Cell Rep 14:2289-300. 2016
  9. pmc Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Mol Cell Proteomics 12:1900-11. 2013

Collaborators

  • Yu Shyr
  • Lisa J Zimmerman
  • Henry Rodriguez
  • Yan Guo
  • Bing Zhang
  • Xiaojing Wang
  • Clayton B Marshall
  • Derek Shyr
  • Deborah J Mays
  • Bryan J Venters
  • Jennifer A Pietenpol
  • Kelli L Boyd
  • Jennifer M Rosenbluth
  • Mark A Magnuson
  • Lucy J Tang
  • Timothy M Shaver
  • J Scott Beeler
  • Gabriela L Santos Guasch
  • Matthew C Chambers
  • Sangtae Kim
  • Daniel C Liebler
  • Sean Wang
  • David L Tabb
  • Pei Wang
  • Jing Zhu
  • Jing Wang
  • Zhiao Shi
  • R Reid Townsend
  • Robert C Rivers
  • Steven A Carr
  • Sherri R Davies
  • Kent F Shaddox
  • Christopher R Kinsinger
  • Robert J Coffey
  • Matthew J C Ellis
  • Robbert J C Slebos

Detail Information

Publications9

  1. pmc RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Mol Biosyst 9:3036-46. 2013
    ....
  2. pmc Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data
    Qi Liu
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    BMC Genomics 13:S8. 2012
    ..In this study, we made a systematic assessment of the relative contribution of each step to the accuracy of variant calling from Illumina DNA sequencing data...
  3. pmc Next generation sequencing in cancer research and clinical application
    Derek Shyr
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, 37232, Nashville, TN, USA
    Biol Proced Online 15:4. 2013
    ....
  4. pmc Proteogenomic characterization of human colon and rectal cancer
    Bing Zhang
    1 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA 2 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Nature 513:382-7. 2014
    ..Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology. ..
  5. pmc Leveraging the complementary nature of RNA-Seq and shotgun proteomics data
    Xiaojing Wang
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN
    Proteomics 14:2676-87. 2014
    ..We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms. ..
  6. pmc Assessing Computational Steps for CLIP-Seq Data Analysis
    Qi Liu
    Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Biomed Res Int 2015:196082. 2015
    ..Our findings can serve as a general guideline for CLIP experiments design and the comprehensive analysis of CLIP-Seq data. ..
  7. pmc Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
    J Proteome Res 15:766-76. 2016
    ..With this method, we demonstrated that post-transcriptional regulation, coordinating protein expression with key players, initiates de novo and enhances protective host response in MSI cancers. ..
  8. pmc p73 Is Required for Multiciliogenesis and Regulates the Foxj1-Associated Gene Network
    Clayton B Marshall
    Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
    Cell Rep 14:2289-300. 2016
    ..In summary, p73 is essential for MCC differentiation, functions as a critical regulator of a transcriptome required for MCC differentiation, and, like p63, has an essential role in development of tissues. ..
  9. pmc Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation
    Qi Liu
    Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Mol Cell Proteomics 12:1900-11. 2013
    ..In addition, our study also provided interesting insights into colon cancer biology such as the possible contributions of miR-138 and miR-141/miR-200c in inducing specific phenotypes of SW480 and RKO cell lines, respectively. ..