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Xing Qiu, PhD

Xing QiuAssociate Professor of Biostatistics and Computational Biology
Ph.D. (2004) University of Rochester


Contact Information

University of Rochester
Dept of Biostatistics and Computational Biology
265 Crittenden Boulevard, CU 420630 
Rochester, New York 14642-0630
 
Office: Saunders Research Building 4220
Phone: (585) 275-0666
Fax: (585) 273-1031
E-mail: xing_qiu@urmc.rochester.edu

Research Interests

I am a statistician and computational biologist working in the field of BigData analytics (high-throughput data analysis). I received my PhD in Mathematics (area: stochastic differential equations) from the University of Rochester in 2004. I joined the faculty of the Department of Biostatistics and Computational Biology at the University of Rochester in 2007.

I have developed many statistical and computational methods for analyzing and integrating large-scale data with complex correlation structures such as various Omics data (gene expression, protein expression, microbiota abundance and diversity, etc) and medical image data (primarily structural MRI data).

I have published 70 journal articles and book chapters, covering research topics such as Omics data pre-processing, hypothesis testing, multiple testing adjustment, functional data analysis, cluster analysis, network analysis, gene set enrichment analyses, and spatial statistical analysis for Diffusion Tensor Imaging data.

Examples of my ongoing research projects:

  • A Multi-step Integrative Analysis Pipeline for Multi-Omics Data
    • Multi-site data integration based on novel batch effect removal method and cross-platform normalization method
    • A robust normalization and differential expression analysis pipeline (the super-delta method)
    • A penalized multi-set CCA method for dimension reduction
    • A computationally efficient linear mixed effects regression framework based on moment method, which can be used to estimate parameters and make correct inferences for correlated data with heterogeneous variance-covariance structure

    • A robust meta-analysis framework to combine results from multiple studies

    • Machine learning techniques for building predictive models based on features exacted from various datasets.

  • Gene Set Enrichment Analysis with Capability of Defining Condition-specific Gene Sets
  • Network Analysis Based on High-dimensional Ordinary Differential Equations and State Space Modeling
  • Personalized Analyses for Longitudinal Imaging Data Based on Partial Differential Equations
  • Multiple Testing Procedure for Data with Rank-deficient Correlation Structure
  • Using Lie Groups and Haar Measure in High-dimensional and Functional Data Analysis

Collaborative research:

I am an active participant in collaborative research. Over the years, I have been involved in 20+ collaborative research projects; most of them are related to infectious diseases such as influenza, respiratory syncytial virus, and HIV. Currently, I am the Data Management, Informatics and Computational Biology Core Leader of the University of Rochester Respiratory Pathogens Research Center (RPRC) and the Bioinformatics and Computational Biology Unit Leader of Center for AIDS Research (CFAR) at the University of Rochester.

Full List of Publications

Please visit my URMC Profile or download my CV for a full list of my publications.


Selected Publications

Novel Methodologies for Omics Data Analysis

  • Qiu, X., Brooks, A. I., Klebanov, L. and Yakovlev, A. (2005). The effects of normalization on the correlation structure of microarray data, BMC Bioinformatics 6:120. PMID: 15904488, PMCID: PMC 1156869.
  • Gordon, A., Glazko, G., Qiu, X. and Yakovlev, A. (2007).  Control of the Mean Number of False Discoveries, Bonferroni, and Stability of Multiple Testing, Annals of Applied Statistics, 1(1):179-190.
  • Klebanov, L., Qiu, X., Welle, S., and Yakovlev, A. (2007).  Statistical methods and microarray data, Nature Biotechnology, 25(1):25-26. PMID: 17211383
  • Hu, R., Qiu, X., and Glazko, G. (2010). A new gene selection procedure based on the covariance distance. Bioinformatics, 26(3):348-354. PMCID:  PMC2815661
  • Needham, M., Hu, R., Dwarkadas, S., and Qiu, X. (2011) Hierarchical parallelization of gene differential association analysis. BMC Bioinformatics, 12(1):374. PMID: 21936916, PMCID: PMC3248234
  • Qiu, X., Hu, R., and Wu, H. (2013) The Impact of Quantile and Rank Normalization on the Testing Power of Gene Differential Expression Analysis, BMC Bioinformatics, 14(1):124. PMID: 23578321
  • Qiu, X., Wu, S., and Wu, H. (2015). A new information criterion based on Langevin mixture distribution for clustering circular data with application to time course genomic data. Statistica Sinica, 25:1459-1476.
  • Zhang, Y., Topham, J.D., Thakar*, J., and Qiu*, X. (2017) FUNNEL-GSEA: FUNctioNal ELastic-net Regression in time-course Gene Set Enrichment Analysis. Bioinformatics, 33(13): 1944-1952. [*Senior authorship shared] PMID: 28334094.
  • Liu, Y., Zhang*, J., and Qiu*, X. (2017) Super-delta: A new approach that combines gene expression data normalization and differential expression test. BMC Bioinformatics, in press. [*Senior authorship shared]
  • Chen, I., Kelkar, Y.D., Gu, Y, Zhou, J., Qiu*, X., and Wu, H*. (2017) High-Dimensional Linear State Space Models for Dynamic Microbial Interaction Networks. PloS One, in press. [*Senior authorship shared]
  • Wu*, L., Qiu*, X., Yuan, Y.X., and Wu, H. (2017) Parameter Estimation and Variable Selection for Big systems of High-Dimensional Linear ordinary Differential Equations: A Matrix-Based Approach. Journal of American Statistical Association, in press. [*First authorship shared]

Novel Methodologies for Diffusion Tensor Imaging Analysis

  • Zhu, T., Hu, R., Qiu, X., Taylor, M., Tso, Y., Yiannoutsos, C., Navia, B., Mori, S., Ekholm, S., Schifitto, G., and Zhong, J. (2011) Quantification of accuracy and precision of multi-center DTI measurements: A diffusion phantom and human brain study. Neuroimage, 56(3):1398–1411. PMID:21316471; PMCID: PMC3085553
  • Zhu, T., Hu, R., Tian, W., Ekholm, S., Schifitto, G., Qiu*, X., and Zhong*, J. (2013) Spatial regression analysis of diffusion tensor imaging (spread) for longitudinal progression of neurodegenerative disease in individual subjects. Magnetic Resonance Imaging, 31(10), 1657-1667. [*Senior authorship shared] PMID: 24099667
  • Liu*, B., Qiu*, X., Zhu, T., Tian, W., Hu, R., Ekholm, S., Schifitto, G., Zhong, J. (2016) Spatial regression analysis of serial DTI for subject-specific longitudinal changes of neurodegenerative disease, NeuroImage: Clinical 11: 291-301. [*First authorship shared] PMID: 26977399, PMCID: PMC4782002.
  • Liu*, B., Qiu*, X., Zhu, T., Tian, W., Hu, R., Ekholm, S., Schifitto, G., Zhong, J. (2016) Improved spatial regression analysis of diffusion tensor imaging for lesion detection during longitudinal progression of multiple sclerosis in individual subjects, Physics in Medicine and Biology, 61(6): 2497. [*First authorship shared] PMID: 26948513.

Collaborative Research Related to Infectious Diseases

  • Qiu*, X., Wu*, S., Hilchey, S. P., Thakar, J., Liu, Z. P., Welle, S. L., Henn, A.D., Wu, H., and Zand, M. S. (2015). Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PloS one, 10(9), e0138110. [*First authorship shared] PMID: 26413862; PMCID: PMC4586376
  • Chu*, C., Qiu*, X., Wang, L., Bhattacharya, S., Lofthus, G., Corbett, A., Holden-Wiltse, J., Grier, A., Tesini, B., Gill, S.R., Falsey, A.R., Caserta, M.T., Walsh, E.E., and Mariani, T.J. (2016) The Healthy Infant Nasal Transcriptome: A Benchmark Study. Scientific Reports 6. [*First authorship shared]  PMCID: PMC5034274
  • Mariani, T.J., Qiu, X., Chu, C., Wang, L., Thakar, J., Holden-Wiltse, J., Corbett, A., Topham, D.J., Falsey, A.R., Caserta, M.T., Walsh, E.E. (2017) Dynamic changes in the CD4 T cell transcriptome are associated with disease severity during primary RSV infection in young infants. Journal of Infectious Diseases, in press.
  • Grier, A., Qiu, X., Bandyopadhyay, S., Holden-Wiltse, J.,  Kessler, H, Gill, A.L., Hamilton, B., Huyck, H., Misra, S., Mariani, T.J., Ryan, R., Scholar, L., Scheible, K., Lee, Y.H., Caserta, M., Pryhuber, G.S., and Gill, S.R. (2017+) Impact of Prematurity and Nutrition on the Developing Gut Microbiome and Preterm Infant Growth. Microbiome, in press.
  • Abidin, A.Z., Dsouza, A.M., Nagarajan, M.B., Lu, W., Qiu, X., Schifitto, G., Wismüller, A. (2017) Alteration of Brain Network Topology in HIV Associated Neurocognitive Disorder: A Novel Functional Connectivity Perspective. NeuroImage:Clinical, in press.

Last updated: September 18, 2018