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Peng Qiu, PhD

Present Title & Affiliation

Primary Appointment

Assistant Professor, Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX

Education & Training

Degree-Granting Education

2007 University of Maryland, College Park, MD, PHD, Electrical and Computer Engineering
2003 University of Science and Technology of China, Hefei, Anhui, China, BS, Electrical and Computer Engineering

Postgraduate Training

8/2007-3/2010 Postdoctoral Fellow, Integrative Cancer Biology, Stanford University, Stanford, CA, Sylvia K. Plevritis
6/2006-8/2006 Visiting Scholar, University of British Columbia, Vancouver, Canada, Z. Jane Wang
8/2003-8/2007 Graduate Research Assistant, Bioinformatics, University of Maryland, College Park, MD, K.J. Ray Liu

Honors and Awards

2012 Best Paper Award, IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)
2011 Best Performer in DREAM6 Classification of AML Challenge, Dialogue for Reverse Engineering Assessments and Methods
2006-2007 Distinguished Disseration Fellowship in Electrical and Computer Engineering, University of Maryland
2003-2005 Graduate School Super Fellowship, University of Maryland
2002 Microsoft Dean Scholarship, University of Science and Technology of China
1999-2002 Outstanding Undergraduate Student Scholarship First Prize, University of Science and Technology of China

Selected Publications

Peer-Reviewed Original Research Articles
1. Aghaeepour N, Finak G, The FlowCAP Consortium, The DREAM Consortium, Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH. Critical assessment of automated flow cytometry data analysis techniques. Nature Methods 10(3):228-238, 3/2013. PMID: 23396282.
2. Qiu P, Plevritis SK. TreeVis: A MATLAB-based tool for tree visualization. Computer Methods and Programs in Biomedicine 109(1):74-76, 1/2013. PMCID: PMC3508366.
3. Linderman MD, Bjornson Z, Simonds EF, Qiu P, Bruggner RV, Sheode K, Meng TH, Plevritis SK, Nolan GP. CytoSPADE: High-Performance Analysis and Visualization of High-Dimensional Cytometry Data. Bioinformatics 28(18):2400-1, 9/2012. PMCID: PMC3436846.
4. Zheng Y, Yang J, Qian J, Qiu P, Hanabuchi S, Lu Y, Wang Z, Liu Z, Li H, He J, Lin P, Weber D, Davis RE, Kwak L, Cai Z, Yi Q. PSGL-1/Selectin and ICAM-1/CD18 interactions are involved in macrophage-induced drug resistance in myeloma. Leukemia. e-Pub 9/2012. PMID: 22996336.
5. Transtrum MK, Qiu P. Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models. BMC Bioinformatics 13(1). e-Pub 7/2012. PMCID: PMC3536579.
6. Qiu P. Inferring phenotypic properties from single-cell characteristics. PLoS One 7(5):e37038, 5/2012. PMCID: PMC3360688.
7. Qiu P, Zhang L. Identification of markers associated with global changes in DNA methylation regulation in cancers. BMC Bioinformatics 13(Suppl 13):S7, 2012. e-Pub 8/2012. PMCID: PMC3426805.
8. Qiu P, Plevritis SK. Reconstructing Directed Signed Gene Regulatory Network from Microarray Data. IEEE Trans Biomed Eng 58(12):3518 - 3521, 12/2011. PMID: 21803675.
9. Qiu P, Simonds EF, Bendall SC, Gibbs KD, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE. Nat Biotechnol 29(10):886-891, 10/2011. PMCID: PMC3196363.
10. Bendall SC, Simonds EF, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Single Cell Mass Cytometry of Differential Immune and Drug Responses Across the Human Hematopoietic Continuum. Science 332(6030):687-696, 5/2011. PMCID: PMC3273988.
11. Qiu P, Gentles AJ, Plevritis SK. Discovering Biological Progression underlying Microarray Samples. PLoS Comput Biol 7(4):e1001123, 4/2011. PMCID: PMC3077357.
12. Qiu P, Gentles AJ, Plevritis SK. Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks. J Comput Biol 17(2):169-76, 2/2010. PMCID: PMC3148830.
13. Qiu P, Plevritis SK. Simultaneous class discovery and classification of microarray data using spectral analysis. J Comput Biol 16(7):935-44, 7/2009. PMCID: PMC3148134.
14. Qiu P, Gentles AJ, Plevritis SK. Fast calculation of pairwise mutual information for gene regulatory network reconstruction. Comput Methods Programs Biomed 94(2):177-80, 5/2009. e-Pub 1/2009. PMID: 19167129.
15. Qiu P, Wang ZJ, Liu KJ, Szabo Z. An Activity-Subspace Approach for Input Function and Distribution Volume Estimation in PET Parametric Imaging. IEEE Trans Inf Technol Biomed 13(1):25-36, 1/2009. PMID: 19129021.
16. Qiu P, D'Souza WD, McAvoy TJ, Ray Liu KJ. Inferential modeling and predictive feedback control in real-time motion compensation using the treatment couch during radiotherapy. Phys Med Biol 52(19):5831-54, 10/2007. e-Pub 9/2007. PMID: 17881803.
17. Qiu P, Wang ZJ, Liu KJ, Hu ZZ, Wu CH. Dependence network modeling for biomarker identification. Bioinformatics 23(2):198-206, 1/2007. e-Pub 10/2006. PMID: 17077095.
18. Qiu P, Wang Zj, Liu KJR. Genomic Processing for Cancer Classification and Prediction. IEEE signal processing magazine 24(1):100-10, 2007.
19. Qiu P, Wang ZJ, Liu KJ. Polynomial model approach for resynchronization analysis of cell-cycle gene expression data. Bioinformatics 22(8):959-66, 4/2006. e-Pub 1/2006. PMID: 16434439.
20. Qiu P, Wang ZJ, Liu KJ. Ensemble dependence model for classification and prediction of cancer and normal gene expression data. Bioinformatics 21(14):3114-21, 7/2005. e-Pub 5/2005. PMID: 15879455.

Grant & Contract Support

Title: Therapy of AML (Core B1) - "Fluorescence-Activated Cell Sorting (FACS/Molecular Cytogenetics (FISH)/Confocal Microscopy"
Funding Source: NIH/NCI
Role: Co-Investigator
Principal Investigator: Michael Andreeff
Duration: 9/19/2011 - 8/31/2012
 
Title: SPD analysis of s3-D multi-parameter images of brain tissue
Funding Source: NIH (Subcontract from University of Houston)
Role: Co-Investigator
Principal Investigator: Badrinath Roysam
Duration: 3/1/2011 - 3/15/2014
 
Title: ARRA: Integrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC) Admin Supplement
Funding Source: NIH/NCI
Role: Co-Investigator
Principal Investigator: John N Weinstein
Duration: 9/1/2010 - 4/30/2012

Last updated: 3/6/2013