Xing Qiu

Summary

Publications

  1. doi request reprint Gene selection with the δ-sequence method
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
    Methods Mol Biol 972:57-71. 2013
  2. doi request reprint Are endoscopic therapies appropriate for superficial submucosal esophageal adenocarcinoma? An analysis of esophagectomy specimens
    Boris Sepesi
    Division of Thoracic and Foregut Surgery, Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA
    J Am Coll Surg 210:418-27. 2010
  3. ncbi request reprint Some comments on instability of false discovery rate estimation
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    J Bioinform Comput Biol 4:1057-68. 2006
  4. pmc A new gene selection procedure based on the covariance distance
    Rui Hu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bioinformatics 26:348-54. 2010
  5. pmc Genomic responses from the estrogen-responsive element-dependent signaling pathway mediated by estrogen receptor alpha are required to elicit cellular alterations
    Stephanie L Nott
    Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
    J Biol Chem 284:15277-88. 2009
  6. pmc Detecting intergene correlation changes in microarray analysis: a new approach to gene selection
    Rui Hu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    BMC Bioinformatics 10:20. 2009
  7. ncbi request reprint Comments on probabilistic models behind the concept of false discovery rate
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    J Bioinform Comput Biol 5:963-75. 2007
  8. pmc Assessing stability of gene selection in microarray data analysis
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Rochester, New York 14642, USA
    BMC Bioinformatics 7:50. 2006
  9. pmc Utility of correlation measures in analysis of gene expression
    Anthony Almudevar
    Department of Biostatistics and Computational Biology, University of Rochester, New York 14642, USA
    NeuroRx 3:384-95. 2006
  10. ncbi request reprint SPatial REgression Analysis of Diffusion tensor imaging (SPREAD) for longitudinal progression of neurodegenerative disease in individual subjects
    Tong Zhu
    Department Imaging Sciences, University of Rochester, Rochester, NY, USA
    Magn Reson Imaging 31:1657-67. 2013

Collaborators

Detail Information

Publications21

  1. doi request reprint Gene selection with the δ-sequence method
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, USA
    Methods Mol Biol 972:57-71. 2013
    ..Furthermore, its outcomes are entirely free from the log-additive array-specific technical noise. The new paradigm offers considerable scope for future developments in this area of methodological research...
  2. doi request reprint Are endoscopic therapies appropriate for superficial submucosal esophageal adenocarcinoma? An analysis of esophagectomy specimens
    Boris Sepesi
    Division of Thoracic and Foregut Surgery, Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA
    J Am Coll Surg 210:418-27. 2010
    ..Controversy exists regarding the prevalence of nodal metastases at various depths of mucosal and submucosal invasion. Our aim was to clarify this prevalence and identify predictors of nodal spread...
  3. ncbi request reprint Some comments on instability of false discovery rate estimation
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    J Bioinform Comput Biol 4:1057-68. 2006
    ..The present communication shows that the variance of the proposed estimators may be intolerably high, the correlation structure of microarray data being the main cause of their instability...
  4. pmc A new gene selection procedure based on the covariance distance
    Rui Hu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, NY 14642, USA
    Bioinformatics 26:348-54. 2010
    ..We propose a statistical procedure to select genes that have different associations with others across different phenotypes. This procedure is based on a new gene association score, called the covariance distance...
  5. pmc Genomic responses from the estrogen-responsive element-dependent signaling pathway mediated by estrogen receptor alpha are required to elicit cellular alterations
    Stephanie L Nott
    Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
    J Biol Chem 284:15277-88. 2009
    ..E2-ERalpha, on the other hand, effectively repressed growth in this cell line. Our findings suggest that genomic responses from the ERE-dependent signaling pathway are required for E2-ERalpha to induce alterations in cellular responses...
  6. pmc Detecting intergene correlation changes in microarray analysis: a new approach to gene selection
    Rui Hu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    BMC Bioinformatics 10:20. 2009
    ..We intend to enrich the above procedure by proposing a nonparametric selection procedure that selects differentially correlated genes...
  7. ncbi request reprint Comments on probabilistic models behind the concept of false discovery rate
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    J Bioinform Comput Biol 5:963-75. 2007
    ..We also present a simulation study designed to assess the effects of inter-gene correlations on some theoretical results based on such models...
  8. pmc Assessing stability of gene selection in microarray data analysis
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Rochester, New York 14642, USA
    BMC Bioinformatics 7:50. 2006
    ..We have conducted studies to assess stability and some other properties of several gene selection procedures with biological and simulated data...
  9. pmc Utility of correlation measures in analysis of gene expression
    Anthony Almudevar
    Department of Biostatistics and Computational Biology, University of Rochester, New York 14642, USA
    NeuroRx 3:384-95. 2006
    ..These issues have broad applicability to all genomic studies examining the biology, diagnosis, and treatment of neurological disorders...
  10. ncbi request reprint SPatial REgression Analysis of Diffusion tensor imaging (SPREAD) for longitudinal progression of neurodegenerative disease in individual subjects
    Tong Zhu
    Department Imaging Sciences, University of Rochester, Rochester, NY, USA
    Magn Reson Imaging 31:1657-67. 2013
    ..To develop a novel statistical method for analysis of longitudinal DTI data in individual subjects...
  11. pmc The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    BMC Bioinformatics 14:124. 2013
    ..In this study, we find that these normalization procedures can have a profound impact on differential expression analysis, especially in terms of testing power...
  12. pmc Ribosomal protein L17, RpL17, is an inhibitor of vascular smooth muscle growth and carotid intima formation
    Elaine M Smolock
    Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Circulation 126:2418-27. 2012
    ..The purpose of this study was to identify candidate genes contributing to intima formation...
  13. pmc HER2 amplification, overexpression and score criteria in esophageal adenocarcinoma
    Yingchuan Hu
    Department of Pathology, University of Rochester, Rochester, NY, USA
    Mod Pathol 24:899-907. 2011
    ..A modified two-step model for esophageal adenocarcinoma HER2 testing is recommended for clinical esophageal adenocarcinoma HER2 trial...
  14. pmc Hierarchical parallelization of gene differential association analysis
    Mark Needham
    Department of Computer Science, University of Rochester, New York 14627, USA
    BMC Bioinformatics 12:374. 2011
    ....
  15. pmc The effects of normalization on the correlation structure of microarray data
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, New York 14642, USA
    BMC Bioinformatics 6:120. 2005
    ..A potential impact of between-gene correlations on the performance of such methods has yet to be explored...
  16. pmc High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature
    Alicia D Henn
    Department of Medicine, Division of Nephrology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
    Sci Rep 3:2327. 2013
    ..With robust statistical methods, time-varying response characteristics of individual subjects were effectively captured along with a shared plasma cell gene signature. ..
  17. pmc Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations
    Shuang Wu
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, United States of America
    PLoS ONE 9:e95276. 2014
    ..The application to the influenza infection data elucidates the potentials of our pipeline in providing valuable insights into systematic modeling of complicated biological processes. ..
  18. pmc Gene expression profiling reveals that the regulation of estrogen-responsive element-independent genes by 17 beta-estradiol-estrogen receptor beta is uncoupled from the induction of phenotypic changes in cell models
    Xiaodong Li
    Departments of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
    J Mol Endocrinol 40:211-29. 2008
    ..These findings suggest that the ERE-dependent pathway is a required signaling route for E(2)-ERbeta to induce cellular responses...
  19. pmc Evaluation of bias-variance trade-off for commonly used post-summarizing normalization procedures in large-scale gene expression studies
    Xing Qiu
    Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York, United States of America
    PLoS ONE 9:e99380. 2014
    ..Based on our findings, we provide some practical guidance for selecting a suitable normalization procedure under different scenarios. ..
  20. pmc Quantification of accuracy and precision of multi-center DTI measurements: a diffusion phantom and human brain study
    Tong Zhu
    Department of Imaging Sciences, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642 8648, USA
    Neuroimage 56:1398-411. 2011
    ..This approach will provide a more effective integration of datasets from multi-center DTI studies...
  21. doi request reprint Does the value of PET-CT extend beyond pretreatment staging? An analysis of survival in surgical patients with esophageal cancer
    Boris Sepesi
    Division of Thoracic and Foregut Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
    J Gastrointest Surg 13:2121-7. 2009
    ..The role of PET in predicting survival has received less attention. We sought to assess the relationship of pretreatment maximum standard uptake value (SUV(max)) to survival in surgical patients with esophageal cancer...