Peng Qiu

Summary

Affiliation: The University of Texas
Country: USA

Publications

  1. pmc Identification of thresholds for dichotomizing DNA methylation data
    Yihua Liu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    EURASIP J Bioinform Syst Biol 2013:8. 2013
  2. pmc Inferring phenotypic properties from single-cell characteristics
    Peng Qiu
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
    PLoS ONE 7:e37038. 2012
  3. pmc Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, CA, USA
    Nat Biotechnol 29:886-91. 2011
  4. doi request reprint Reconstructing directed signed gene regulatory network from microarray data
    Peng Qiu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    IEEE Trans Biomed Eng 58:3518-21. 2011
  5. pmc Discovering biological progression underlying microarray samples
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, California, USA
    PLoS Comput Biol 7:e1001123. 2011
  6. pmc CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data
    Michael D Linderman
    Department of Electrical Engineering, Stanford University, Stanford, CA, USA
    Bioinformatics 28:2400-1. 2012
  7. pmc Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    Sean C Bendall
    Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
    Science 332:687-96. 2011
  8. pmc Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, California 94305, USA
    J Comput Biol 17:169-76. 2010
  9. doi request reprint Fast calculation of pairwise mutual information for gene regulatory network reconstruction
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, CA, United States
    Comput Methods Programs Biomed 94:177-80. 2009
  10. pmc TreeVis: a MATLAB-based tool for tree visualization
    Peng Qiu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, USA
    Comput Methods Programs Biomed 109:74-6. 2013

Collaborators

Detail Information

Publications14

  1. pmc Identification of thresholds for dichotomizing DNA methylation data
    Yihua Liu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    EURASIP J Bioinform Syst Biol 2013:8. 2013
    ..We notice that the appropriate thresholds vary across different CpG sites. In addition, the negative association between methylation and expression is highly tissue specific...
  2. pmc Inferring phenotypic properties from single-cell characteristics
    Peng Qiu
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, Houston, Texas, United States of America
    PLoS ONE 7:e37038. 2012
    ..This solution was among the top-performing methods that achieved 100% prediction accuracy...
  3. pmc Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, CA, USA
    Nat Biotechnol 29:886-91. 2011
    ..SPADE facilitates the analysis of cellular heterogeneity, the identification of cell types and comparison of functional markers in response to perturbations...
  4. doi request reprint Reconstructing directed signed gene regulatory network from microarray data
    Peng Qiu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    IEEE Trans Biomed Eng 58:3518-21. 2011
    ..Simulation results suggested a novel biological hypothesis that in gene knockout experiments, repressing protein synthesis to a certain extent may lead to better expression data and higher network reconstruction accuracy...
  5. pmc Discovering biological progression underlying microarray samples
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, California, USA
    PLoS Comput Biol 7:e1001123. 2011
    ....
  6. pmc CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data
    Michael D Linderman
    Department of Electrical Engineering, Stanford University, Stanford, CA, USA
    Bioinformatics 28:2400-1. 2012
    ..10 onwards for Linux, OSX and Windows. CytoSPADE is implemented in R, C++ and Java. CONTACT: michael.linderman@mssm.edu SUPPLEMENTARY INFORMATION: Additional documentation available at http://cytospade.org...
  7. pmc Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum
    Sean C Bendall
    Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
    Science 332:687-96. 2011
    ..Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention...
  8. pmc Reducing the computational complexity of information theoretic approaches for reconstructing gene regulatory networks
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, California 94305, USA
    J Comput Biol 17:169-76. 2010
    ..The proposed method can be used with any method that relies on the mutual information to reconstruct networks...
  9. doi request reprint Fast calculation of pairwise mutual information for gene regulatory network reconstruction
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, CA, United States
    Comput Methods Programs Biomed 94:177-80. 2009
    ..6 hours. The increased efficiency of our algorithm improves the feasibility of applying mutual information based approaches for reconstructing large regulatory networks...
  10. pmc TreeVis: a MATLAB-based tool for tree visualization
    Peng Qiu
    Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, USA
    Comput Methods Programs Biomed 109:74-6. 2013
    ..We present a new visualization algorithm to generate two-dimensional layouts for complex tree structures. Implementations in both MATLAB and R are provided...
  11. pmc Simultaneous class discovery and classification of microarray data using spectral analysis
    Peng Qiu
    Department of Radiology, Stanford University, Stanford, California 94305, USA
    J Comput Biol 16:935-44. 2009
    ..We demonstrate the effectiveness of SPACC for class discovery and classification on microarray data of lymphomas and leukemias. SPACC software is available at http://icbp.stanford.edu/software/SPACC/...
  12. doi request reprint An activity-subspace approach for estimating the integrated input function and relative distribution volume in PET parametric imaging
    Peng Qiu
    Department of Radiology, Stanford University, CA 94305, USA
    IEEE Trans Inf Technol Biomed 13:25-36. 2009
    ..The proposed method is compared with a blind estimation method, iterative quadratic maximum-likelihood (IQML) via simulation, and the proposed method outperforms IQML. The proposed method is also evaluated in a brain PET dataset...
  13. pmc Identification of markers associated with global changes in DNA methylation regulation in cancers
    Peng Qiu
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
    BMC Bioinformatics 13:S7. 2012
    ..We also generated a library of the significant CCRs that may be of interest to future studies of the regulation network of DNA methylation in cancer...
  14. pmc Optimal experiment selection for parameter estimation in biological differential equation models
    Mark K Transtrum
    Department of Bioinformatics and Computational Biology, University of Texas M, d, Anderson Cancer Cneter, Houston, Texas, USA
    BMC Bioinformatics 13:181. 2012
    ..We explore the question to what extent parameters can be efficiently estimated by appropriate experimental selection...