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Xing Qiu, Ph.D.

Contact Information

Phone Numbers

Office: (585) 275-0666

Faculty Appointments

Biography

Professional Background

2013-present University of Rochester, Rochester, New York, Associate Professor, Biostatistics and Computational Biology
2007-2013 University of Rochester, Rochester, New York, Assistant Professor, Biostatistics and Computational Biology
2004-2007 University of Rochester, Rochester, New York, PostDoc, Biostatistics and Computational Biology
1998-2004 University of Rochester, Rochester, New York, PhD, Mathematics
1996-1998 South China University of Technology, China, Applied Mathematics
1992-1996 South China University of Technology, China, BE, Civil Engineering

Research

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). By now (2018), 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. Below please find some examples of my ongoing research projects:
• A Multi-step Integrative Analysis Pipeline for Multi-Omics Data
o Multi-site data integration based on novel batch effect removal method and cross-platform normalization method;
o A robust normalization and differential expression analysis pipeline (the super-delta method)
o A penalized multi-set CCA method for dimension reduction
o 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
o A robust meta-analysis framework to combine results from multiple studies
o 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

I am also 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); the Bioinformatics and Computational Biology Unit Leader of Center for AIDS Research (CFAR) at the University of Rochester.

Credentials

Education

1996
ME | South China University of Technology
Civil Engineering

2000
MA | University of Rochester
Mathematics

2004
PhD | University of Rochester
Mathematics

Post-doctoral Training & Residency

2004 - 2007
Postdoctoral Research Trainee, Department of Biostatistics and Computational Biology, the University of Rochester

Awards

2018
Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award
Sponsor: The University of Rochester
Location: Rochester, New York

2018
Graphics Processing Unit Grant
Sponsor: NVIDIA's Academic Programs
Location: Santa Clara, CA

2017
Best Mentor Award
Sponsor: Upstate Chapters of the American Statistical Association
Location: Buffalo, NY

2016
Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award
Sponsor: The University of Rochester
Location: Rochester, New York

2015
Behrooz A. Akbarnia, MD Award for the Best Paper
Sponsor: International Congress on Early Onset Scoliosis

2014
The best Basic Science E-Poster
Sponsor: Scoliosis Research Society

2013
Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award
Sponsor: The University of Rochester
Location: Rochester, New York

2011
Provost's Multidisciplinary Award
Sponsor: The University of Rochester
Location: Rochester, New York

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Publications

Journal Articles

2019
Wu, L., Qiu, X., Yuan, Y.X., and Wu, H. "Parameter Estimation and Variable Selection for Big systems of High-Dimensional Linear ordinary Differential Equations: A Matrix-Based Approach". Journal of American Statistical Association. 2019; : in press.

2019
Singh, M.; Kotla, S.; Le, N.T.; Ko, K.; Heo, K.S.; Wang, Y.; Fujii, Y.; Vu, H.; McBeath, E.; Thomas, T.; Gi, Y.J.; Tao, Y.; Medina, J.; Taunton, J.; Carson, N.; Dogra, V.; Doyley, M.; Tyrell, A.; Lu, W.; Qiu, X.; Stirpe, N.; Gates, K.; Hurley, C.; Fujiwara, K.; Maggirwar, S.; Schifitto, G.; Abe, J. "Senescent phenotype induced by p90RSK-NRF2 signaling sensitizes monocytes and macrophages to oxidative stress in HIV+ individuals: implications for atherogenesis". Circulation. 2019; : in press.

10/26/2018
Grier A, McDavid A, Wang B, Qiu X, Java J, Bandyopadhyay S, Yang H, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR. "Neonatal gut and respiratory microbiota: coordinated development through time and space." Microbiome.. 2018 Oct 26; 6(1):193. Epub 2018 Oct 26.

Books & Chapters

2013
Chapter Title: High-Dimensional Ordinary Differential Equation Models for Reconstructing Genome-Wide Dynamic Regulatory Networks
Book Title: Topics in Applied Statistics
Author List: Wu, S.; Liu, Z. P.; Qiu, X.; Wu, H.
Published By: Springer 2013 in New York

2012
Chapter Title: Gene selection with the delta-sequence method
Book Title: Statistical Methods for Microarray Data Analysis
Author List: Xing Qiu and Lev Klebanov
Published By: Humana Press 2012

VIEW ALL PUBLICATIONS