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Xing Qiu, Ph.D.

Xing Qiu, Ph.D.

Contact

Office (585) 275-0666

About Me

Professional Background

2018-present University of Rochester, Rochester, New York, Professor, Biostatistics and Computational Biology
2013-2018 University of Rochester, Rochester, New York, Associate Professor, Biostatistics and Computational Biology
2007-2013 University of Rochester, Rochester, New York, Assistant P...
2018-present University of Rochester, Rochester, New York, Professor, Biostatistics and Computational Biology
2013-2018 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

Faculty Appointments

Professor - Department of Biostatistics and Computational Biology (SMD)

Credentials

Post-doctoral Training & Residency

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

Education

PhD | University of Rochester. Mathematics. 2004

MA | University of Rochester. Mathematics. 2000

ME | South China University of Technology. Civil Engineering. 1996

Awards

University Research Award. 2022 - 2023

Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award. 2018

Graphics Processing Unit Grant. 2018

Best Mentor Award. 2017

Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award. 2016

Behrooz A. Akbarnia, MD Award for the Best Paper. 2015

The best Basic Science E-Poster. 2014

Novel Biostatistical and Epidemiologic Methods (NBEM) Pilot Award. 2013

Provost's Multidisciplinary Award. 2011

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...
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 (2023), I have published more than 100 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.

Publications

Journal Articles

Adverse Childhood Experiences Predict Diurnal Cortisol Throughout Gestation.

Panisch LS, Murphy HR, Wu Q, Brunner JL, Duberstein ZT, Arnold MS, Best M, Barrett ES, Miller RK, Qiu X, O'Connor TG

Psychosomatic medicine.. 2023 May 18 Epub 05/18/2023.

Consagra, W.; Venkataraman, A.; Qiu, X.

Efficient Multidimensional Functional Data Analysis

Initiation of combined antiretroviral therapy confers suboptimal beneficial effects on neurovascular function in people with HIV.

Singh MV, Uddin MN, Singh VB, Peterson AN, Murray KD, Zhuang Y, Tyrell A, Wang L, Tivarus ME, Zhong J, Qiu X, Schifitto G

Frontiers in neurology. 2023 14 :1240300. Epub 08/31/2023.

Longitudinal Effects of Combination Antiretroviral Therapy on Cognition and Neuroimaging Biomarkers in Treatment-Naive People With HIV.

Weber MT, Finkelstein A, Uddin MN, Reddy EA, Arduino RC, Wang L, Tivarus ME, Zhong J, Qiu X, Schifitto G

Neurology.. 2022 September 699 (10):e1045-e1055. Epub 06/22/2022.

FastMix: A Versatile Data Integration Pipeline for Cell Type-Specific Biomarker Inference.

Zhang Y, Sun H, Mandava A, Aevermann BD, Kollmann TR, Scheuermann RH, Qiu X, Qian Y

Bioinformatics.. 2022 August 26 Epub 08/26/2022.

Prenatal diurnal cortisol: Normative patterns and associations with affective symptoms and stress.

Murphy HR, Gu Y, Wu Q, Brunner J, Panisch LS, Best M, Arnold MS, Duberstein ZT, Putzig J, Carnahan J, Groth SW, Barrett ES, Qiu X, O'Connor TG

Psychoneuroendocrinology.. 2022 June 30143 :105856. Epub 06/30/2022.

Qiu, X.; Xu, T.; Soltanalizadeh, B.; Wu, H.

Identifiability Analysis of Linear Ordinary Differential

A systems genomics approach uncovers molecular associates of RSV severity.

McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qiu X, Mariani TJ

PLoS computational biology.. 2021 December 2817 (12):e1009617. Epub 12/28/2021.

Increased risk for cerebral small vessel disease is associated with quantitative susceptibility mapping in HIV infected and uninfected individuals.

Murray KD, Uddin MN, Tivarus ME, Sahin B, Wang HZ, Singh MV, Qiu X, Wang L, Spincemaille P, Wang Y, Maggirwar SB, Zhong J, Schifitto G

NeuroImage. Clinical.. 2021 August 2832 :102786. Epub 08/28/2021.

Genomic analysis of Clostridioides difficile in two regions of the United States reveals a diversity of strains and limited transmission.

Pecora N, Holzbauer S, Wang X, Gu Y, Taffner S, Hatwar T, Hardy D, Dziejman M, D'Heilly P, Pung K, Guh A, Qiu X, Gill S, Dumyati G

The Journal of infectious diseases.. 2021 June 9 Epub 06/09/2021.

Mitochondrial toxicity before and after combination antiretroviral therapy, a Magnetic Resonance Spectroscopy study.

Tivarus ME, Zhuang Y, Wang L, Murray KD, Venkataraman A, Weber MT, Zhong J, Qiu X, Schifitto G

NeuroImage. Clinical.. 2021 May 731 :102693. Epub 05/07/2021.

A longitudinal analysis of brain extracellular free water in HIV infected individuals.

Uddin MN, Faiyaz A, Wang L, Zhuang Y, Murray KD, Descoteaux M, Tivarus ME, Weber MT, Zhong J, Qiu X, Schifitto G

Scientific reports.. 2021 April 1511 (1):8273. Epub 04/15/2021.

Cohort profile: Understanding Pregnancy Signals and Infant Development (UPSIDE): a pregnancy cohort study on prenatal exposure mechanisms for child health.

O'Connor T, Best M, Brunner J, Ciesla AA, Cunning A, Kapula N, Kautz A, Khoury L, Macomber A, Meng Y, Miller RK, Murphy H, Salafia CM, Vallejo Sefair A, Serrano J, Barrett E,

BMJ open.. 2021 April 111 (4):e044798. Epub 04/01/2021.

CX3CR1 Engagement by Respiratory Syncytial Virus Leads to Induction of Nucleolin and Dysregulation of Cilia-related Genes.

Anderson CS, Chirkova T, Slaunwhite CG, Qiu X, Walsh EE, Anderson LJ, Mariani TJ

Journal of virology.. 2021 March 17 Epub 03/17/2021.

Super-delta2: An Enhanced Differential Expression Analysis Procedure for Multi-Group Comparisons of RNA-seq Data.

Cui Z, Liu Y, Zhang J, Qiu X

Bioinformatics.. 2021 March 8 Epub 03/08/2021.

Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants.

Wang L, Chu CY, McCall MN, Slaunwhite C, Holden-Wiltse J, Corbett A, Falsey AR, Topham DJ, Caserta MT, Mariani TJ, Walsh EE, Qiu X

BMC medical genomics.. 2021 February 2514 (1):57. Epub 02/25/2021.

Functional MRI Correlates of Sleep Quality in HIV.

Venkataraman A, Zhuang Y, Marsella J, Tivarus ME, Qiu X, Wang L, Zhong J, Schifitto G

Nature and science of sleep.. 2021 13 :291-301. Epub 03/02/2021.

Fixel-Based Analysis and Free Water Corrected DTI Evaluation of HIV-Associated Neurocognitive Disorders.

Finkelstein A, Faiyaz A, Weber MT, Qiu X, Uddin MN, Zhong J, Schifitto G

Frontiers in neurology. 2021 12 :725059. Epub 11/04/2021.

Biological Network Inference With GRASP: A Bayesian Network Structure Learning Method Using Adaptive Sequential Monte Carlo.

Yu K, Cui Z, Sui X, Qiu X, Zhang J

Frontiers in genetics.. 2021 12 :764020. Epub 11/29/2021.

Whole-brain computational modeling reveals disruption of microscale brain dynamics in HIV infected individuals.

Zhuang Y, Zhang Z, Tivarus M, Qiu X, Zhong J, Schifitto G

Human brain mapping.. 2020 September 17 Epub 09/17/2020.

Airway gene expression correlates of RSV disease severity and microbiome composition in infants.

Chu CY, Qiu X, McCall MN, Wang L, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Pryhuber GS, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Mariani TJ

The Journal of infectious diseases.. 2020 September 14 Epub 09/14/2020.

Spatial regression analysis of MR diffusion reveals subject-specific white matter changes associated with repetitive head impacts in contact sports.

Asselin PD, Gu Y, Merchant-Borna K, Abar B, Wright DW, Qiu X, Bazarian JJ

Scientific reports.. 2020 August 1210 (1):13606. Epub 08/12/2020.

Unbiased analysis of peripheral blood mononuclear cells reveals CD4 T cell response to RSV matrix protein.

Thakar J, Qian Y, Benoodt L, Roumanes D, Qiu X, Laniewski N, Chu C, Slaunwhite C, Wang L, Mandava A, Chang I, Falsey AR, Caserta MT, Mariani TJ, Scheuermann RH, Walsh EE, Topham DJ

Vaccine: X.. 2020 August 75 :100065. Epub 04/21/2020.

MatchMixeR: A Cross-platform Normalization Method for Gene Expression Data Integration.

Zhang S, Shao J, Yu D, Qiu X, Zhang J

Bioinformatics.. 2020 January 6 Epub 01/06/2020.

Pathomechanisms of HIV-Associated Cerebral Small Vessel Disease: A Comprehensive Clinical and Neuroimaging Protocol and Analysis Pipeline.

Murray KD, Singh MV, Zhuang Y, Uddin MN, Qiu X, Weber MT, Tivarus ME, Wang HZ, Sahin B, Zhong J, Maggirwar SB, Schifitto G

Frontiers in neurology. 2020 11 :595463. Epub 12/15/2020.

Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection.

Sonawane AR, Tian L, Chu CY, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill SR, Caserta MT, Falsey AR, Topham DJ, Walsh EE, Mariani TJ, Weiss ST, Silverman EK, Glass K, Liu YY

Scientific reports.. 2019 September 259 (1):13824. Epub 09/25/2019.

Measuring the Severity of Respiratory Illness in the First 2 Years of Life in Preterm and Term Infants.

Caserta MT, Yang H, Bandyopadhyay S, Qiu X, Gill SR, Java J, McDavid A, Falsey AR, Topham DJ, Holden-Wiltse J, Scheible K, Pryhuber G

The Journal of pediatrics.. 2019 July 31 Epub 07/31/2019.

Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.

Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT

JMIR research protocols.. 2019 June 68 (6):e12907. Epub 06/06/2019.

Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure.

Zhang Y, Bandyopadhyay G, Topham DJ, Falsey AR, Qiu X

BMC bioinformatics.. 2019 April 1520 (1):185. Epub 04/15/2019.

Skeletal muscle mitoflashes, pH, and the role of uncoupling protein-3.

McBride S, Wei-LaPierre L, McMurray F, MacFarlane M, Qiu X, Patten DA, Dirksen RT, Harper ME

Archives of biochemistry and biophysics.. 2019 March 15663 :239-248. Epub 01/16/2019.

Differences in the influenza-specific CD4 T cell immunodominance hierarchy and functional potential between children and young adults.

Shannon I, White CL, Murphy A, Qiu X, Treanor JJ, Nayak JL

Scientific reports.. 2019 January 289 (1):791. Epub 01/28/2019.

Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis.

Chen G, Ramírez JC, Deng N, Qiu X, Wu C, Zheng WJ, Wu H

Database : the journal of biological databases and curation.. 2019 January 12019 Epub 01/01/2019.

Parameter Estimation and Variable Selection for Big systems of High-Dimensional Linear ordinary Differential Equations: A Matrix-Based Approach

Wu, L., Qiu, X., Yuan, Y.X., and Wu, H.

Journal of American Statistical Association. 2019; 114(526): 657-667.

Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach.

Wu L, Qiu X, Yuan YX, Wu H

Journal of the American Statistical Association.. 2019 114 (526):657-667. Epub 07/11/2018.

Comparison of the Michigan Hand Outcomes Questionnaire, Boston Carpal Tunnel Questionnaire, and PROMIS Instruments in Carpal Tunnel Syndrome.

Mahmood B, Chongshu C, Qiu X, Messing S, Hammert WC

The Journal of hand surgery.. 2018 December 20 Epub 12/20/2018.

Neonatal gut and respiratory microbiota: coordinated development through time and space.

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

Microbiome.. 2018 October 266 (1):193. Epub 10/26/2018.

Senescent Phenotype Induced by p90RSK-NRF2 Signaling Sensitizes Monocytes and Macrophages to Oxidative Stress in HIV Individuals: Implications for Atherogenesis.

Singh MV, Kotla S, Le NT, Ko KA, Heo KS, Wang Y, Fujii Y, Vu HT, McBeath E, Thomas TN, Gi YJ, Tao Y, Medina JL, Taunton J, Carson N, Dogra V, Doyley MM, Tyrell A, Lu W, Qiu X, Stirpe NE, Gates K, Hurley C, Fujiwara K, Maggirwar S, Schifitto G, Abe JI

Circulation.. 2018 October 26 Epub 10/26/2018.

Virus-Specific Antibody, Viral Load, and Disease Severity in Respiratory Syncytial Virus Infection.

Walsh EE, Wang L, Falsey AR, Qiu X, Corbett A, Holden-Wiltse J, Mariani TJ, Topham DJ, Caserta MT

The Journal of infectious diseases.. 2018 June 20218 (2):208-217. Epub 1900 01 01.

Publication Rate of Podium Presentations From the North American Spine Society Annual Meetings.

Raudenbush B, Frost C, Okafor R, Chen C, Qui X, Mesfin A

Global spine journal.. 2018 May 8 (3):273-278. Epub 06/23/2017.

Some equivalence relationships of regularized regressions

Zhang, Y.; Thakar, J.; Topham, D.J.; Falsey, A.R.; Zeng, D.; Qiu, X.

Mathematics for Applications. 2018; 7: 3-10.

Alteration of brain network topology in HIV-associated neurocognitive disorder: A novel functional connectivity perspective.

Abidin AZ, DSouza AM, Nagarajan MB, Wang L, Qiu X, Schifitto G, Wismüller A

NeuroImage. Clinical.. 2018 17 :768-777. Epub 12/07/2017.

Super-delta: a new differential gene expression analysis procedure with robust data normalization.

Liu Y, Zhang J, Qiu X

BMC bioinformatics.. 2017 December 2118 (1):582. Epub 12/21/2017.

Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth.

Grier A, Qiu X, Bandyopadhyay S, Holden-Wiltse J, Kessler HA, Gill AL, Hamilton B, Huyck H, Misra S, Mariani TJ, Ryan RM, Scholer L, Scheible KM, Lee YH, Caserta MT, Pryhuber GS, Gill SR

Microbiome.. 2017 December 115 (1):158. Epub 12/11/2017.

The Uniform Pattern of Growth and Skeletal Maturation during the Human Adolescent Growth Spurt.

Sanders JO, Qiu X, Lu X, Duren DL, Liu RW, Dang D, Menendez ME, Hans SD, Weber DR, Cooperman DR

Scientific reports.. 2017 December 17 (1):16705. Epub 12/01/2017.

The preliminary radiogenomics association between MR perfusion imaging parameters and genomic biomarkers, and their predictive performance of overall survival in patients with glioblastoma.

Liu X, Mangla R, Tian W, Qiu X, Li D, Walter KA, Ekholm S, Johnson MD

Journal of neuro-oncology.. 2017 December 135 (3):553-560. Epub 09/09/2017.

Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants.

Mariani TJ, Qiu X, Chu CY, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE

The Journal of infectious diseases.. 2017 November 15216 (8):1027-1037. Epub 1900 01 01.

Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection.

Connor R, Jones LD, Qiu X, Thakar J, Maggirwar SB

Journal of leukocyte biology.. 2017 October 102 (4):953-964. Epub 06/29/2017.

Combination antiretroviral therapy improves cognitive performance and functional connectivity in treatment-naïve HIV-infected individuals.

Zhuang Y, Qiu X, Wang L, Ma Q, Mapstone M, Luque A, Weber M, Tivarus M, Miller E, Arduino RC, Zhong J, Schifitto G

Journal of neurovirology.. 2017 October 23 (5):704-712. Epub 08/08/2017.

FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.

Zhang Y, Topham DJ, Thakar J, Qiu X

Bioinformatics.. 2017 July 133 (13):1944-1952. Epub 1900 01 01.

Development of a Global Respiratory Severity Score for Respiratory Syncytial Virus Infection in Infants.

Caserta MT, Qiu X, Tesini B, Wang L, Murphy A, Corbett A, Falsey AR, Holden-Wiltse J, Walsh EE

The Journal of infectious diseases.. 2017 March 1215 (5):750-756. Epub 1900 01 01.

Selective pre-priming of HA-specific CD4 T cells restores immunological reactivity to HA on heterosubtypic influenza infection.

Alam S, Chan C, Qiu X, Shannon I, White CL, Sant AJ, Nayak JL

PloS one.. 2017 12 (5):e0176407. Epub 05/11/2017.

High-dimensional linear state space models for dynamic microbial interaction networks.

Chen I, Kelkar YD, Gu Y, Zhou J, Qiu X, Wu H

PloS one.. 2017 12 (11):e0187822. Epub 11/15/2017.

Total Hip Arthroplasty for Femoral Neck Fractures: Improved Outcomes With Higher Hospital Volumes.

Maceroli M, Nikkel LE, Mahmood B, Ketz JP, Qiu X, Ciminelli J, Messing S, Elfar JC

Journal of orthopaedic trauma.. 2016 November 30 (11):597-604. Epub 1900 01 01.

Controllability and stability analysis of large transcriptomic dynamic systems for host response to influenza infection in human.

Sun X, Hu F, Wu S, Qiu X, Linel P, Wu H

Infectious Disease Modelling.. 2016 October 1 (1):52-70. Epub 09/13/2016.

The Healthy Infant Nasal Transcriptome: A Benchmark Study.

Chu CY, Qiu X, Wang L, Bhattacharya S, Lofthus G, Corbett A, Holden-Wiltse J, Grier A, Tesini B, Gill SR, Falsey AR, Caserta MT, Walsh EE, Mariani TJ

Scientific reports.. 2016 September 236 :33994. Epub 09/23/2016.

Improved spatial regression analysis of diffusion tensor imaging for lesion detection during longitudinal progression of multiple sclerosis in individual subjects.

Liu B, Qiu X, Zhu T, Tian W, Hu R, Ekholm S, Schifitto G, Zhong J

Physics in medicine and biology.. 2016 March 2161 (6):2497-513. Epub 03/07/2016.

Ion-Current-Based Temporal Proteomic Profiling of Influenza-A-Virus-Infected Mouse Lungs Revealed Underlying Mechanisms of Altered Integrity of the Lung Microvascular Barrier.

Shen S, Li J, Hilchey S, Shen X, Tu C, Qiu X, Ng A, Ghaemmaghami S, Wu H, ZAnd M, Qu J

Journal of proteome research.. 2016 February 515 (2):540-53. Epub 01/08/2016.

Moments of Distance from a Vertex to a Random Point within Arbitrary Triangles

Li, H.; Qiu, X.

Mathematical Problems in Engineering. 2016; : 8371750.

Spatial regression analysis of serial DTI for subject-specific longitudinal changes of neurodegenerative disease.

Liu B, Qiu X, Zhu T, Tian W, Hu R, Ekholm S, Schifitto G, Zhong J

NeuroImage. Clinical.. 2016 11 :291-301. Epub 02/21/2016.

Reducing Prenatal Phthalate Exposure Through Maternal Dietary Changes: Results from a Pilot Study.

Barrett ES, Velez M, Qiu X, Chen SR

Maternal and child health journal.. 2015 September 19 (9):1936-42. Epub 1900 01 01.

A new information criterion based on Langevin mixture distribution for clustering circular data with application to time course genomic data

Qiu, X.; Wu, S.; Wu, H.

Statistica Sinica. 2015; 25: 1459-1476.

Platelet Activation in Human Immunodeficiency Virus Type-1 Patients Is Not Altered with Cocaine Abuse.

Kiebala M, Singh MV, Piepenbrink MS, Qiu X, Kobie JJ, Maggirwar SB

PloS one.. 2015 10 (6):e0130061. Epub 06/15/2015.

Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice.

Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS

PloS one.. 2015 10 (9):e0138110. Epub 09/28/2015.

Intima modifier locus 2 controls endothelial cell activation and vascular permeability.

Smolock EM, Burke RM, Wang C, Thomas T, Batchu SN, Qiu X, Zettel M, Fujiwara K, Berk BC, Korshunov VA

Physiological genomics.. 2014 September 146 (17):624-33. Epub 07/01/2014.

ERK5 activation in macrophages promotes efferocytosis and inhibits atherosclerosis.

Heo KS, Cushman HJ, Akaike M, Woo CH, Wang X, Qiu X, Fujiwara K, Abe J

Circulation.. 2014 July 8130 (2):180-91. Epub 04/28/2014.

Using the health belief model to illustrate factors that influence risk assessment during pregnancy and implications for prenatal education about endocrine disruptors

Chen, S.R.; Barrett, E.; Velez, M.; Conn, K.; Heinert, S.; Qiu, X.

Policy, Futures, and Education. 2014; 12(7): 961-974.

Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations.

Wu S, Liu ZP, Qiu X, Wu H

PloS one.. 2014 9 (5):e95276. Epub 05/06/2014.

Evaluation of bias-variance trade-off for commonly used post-summarizing normalization procedures in large-scale gene expression studies.

Qiu X, Hu R, Wu Z

PloS one.. 2014 9 (6):e99380. Epub 06/18/2014.

SPatial REgression Analysis of Diffusion tensor imaging (SPREAD) for longitudinal progression of neurodegenerative disease in individual subjects.

Zhu T, Hu R, Tian W, Ekholm S, Schifitto G, Qiu X, Zhong J

Magnetic resonance imaging.. 2013 December 31 (10):1657-67. Epub 10/05/2013.

The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis.

Qiu X, Wu H, Hu R

BMC bioinformatics.. 2013 April 1114 :124. Epub 04/11/2013.

A Geometric Illustration of Differential Gene Association Analysis for Microarray Data

Hu, R.; Qiu, X.

Journal of Unified Statistical Techniques. 2013; 1(1).

High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.

Henn AD, Wu S, Qiu X, Ruda M, Stover M, Yang H, Liu Z, Welle SL, Holden-Wiltse J, Wu H, Zand MS

Scientific reports.. 2013 3 :2327. Epub 1900 01 01.

Ribosomal protein L17, RpL17, is an inhibitor of vascular smooth muscle growth and carotid intima formation.

Smolock EM, Korshunov VA, Glazko G, Qiu X, Gerloff J, Berk B

Circulation.. 2012 November 13126 (20):2418-27. Epub 10/12/2012.

Correlation analysis of quantitative diffusion parameters in ipsilateral cerebral peduncle during Wallerian degeneration with motor function outcome after cerebral ischemic stroke.

Liu X, Tian W, Qiu X, Li J, Thomson S, Li L, Wang HZ

Journal of neuroimaging : official journal of the American Society of Neuroimaging.. 2012 July 22 (3):255-60. Epub 06/23/2011.

Hyperintensity on diffusion weighted image along ipsilateral cortical spinal tract after cerebral ischemic stroke: a diffusion tensor analysis.

Liu X, Tian W, Li L, Kolar B, Qiu X, Chen F, Dogra VS

European journal of radiology.. 2012 February 81 (2):292-7. Epub 01/17/2011.

Functionally Distinct Subpopulations of CpG-Activated Memory B Cells.

Henn AD, Laski M, Yang H, Welle S, Qiu X, Miao H, Barry CT, Wu H, Zand MS

Scientific reports.. 2012 2 :345. Epub 03/30/2012.

Identical de novo mutation in the type 1 ryanodine receptor gene associated with fatal, stress-induced malignant hyperthermia in two unrelated families.

Groom L, Muldoon SM, Tang ZZ, Brandom BW, Bayarsaikhan M, Bina S, Lee HS, Qiu X, Sambuughin N, Dirksen RT

Anesthesiology.. 2011 November 115 (5):938-45. Epub 1900 01 01.

Hierarchical parallelization of gene differential association analysis.

Needham M, Hu R, Dwarkadas S, Qiu X

BMC bioinformatics.. 2011 September 2112 :374. Epub 09/21/2011.

HER2 amplification, overexpression and score criteria in esophageal adenocarcinoma.

Hu Y, Bandla S, Godfrey TE, Tan D, Luketich JD, Pennathur A, Qiu X, Hicks DG, Peters JH, Zhou Z

Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc.. 2011 July 24 (7):899-907. Epub 04/01/2011.

Quantification of accuracy and precision of multi-center DTI measurements: a diffusion phantom and human brain study.

Zhu T, Hu R, Qiu X, Taylor M, Tso Y, Yiannoutsos C, Navia B, Mori S, Ekholm S, Schifitto G, Zhong J

NeuroImage.. 2011 June 156 (3):1398-411. Epub 02/18/2011.

Comparison of the Paley method using chronological age with use of skeletal maturity for predicting mature limb length in children.

Sanders JO, Howell J, Qiu X

The Journal of bone and joint surgery. American volume.. 2011 June 193 (11):1051-6. Epub 1900 01 01.

MR diffusion tensor and perfusion-weighted imaging in preoperative grading of supratentorial nonenhancing gliomas.

Liu X, Tian W, Kolar B, Yeaney GA, Qiu X, Johnson MD, Ekholm S

Neuro-oncology.. 2011 April 13 (4):447-55. Epub 02/04/2011.

A population-based analysis of emergent vs. elective hospital admissions for an intrathoracic stomach.

Polomsky M, Hu R, Sepesi B, O'Connor M, Qui X, Raymond DP, Litle VR, Jones CE, Watson TJ, Peters JH

Surgical endoscopy.. 2010 June 24 (6):1250-5. Epub 12/24/2009.

Are endoscopic therapies appropriate for superficial submucosal esophageal adenocarcinoma? An analysis of esophagectomy specimens.

Sepesi B, Watson TJ, Zhou D, Polomsky M, Litle VR, Jones CE, Raymond DP, Hu R, Qiu X, Peters JH

Journal of the American College of Surgeons.. 2010 April 210 (4):418-27. Epub 1900 01 01.

A new gene selection procedure based on the covariance distance.

Hu R, Qiu X, Glazko G

Bioinformatics.. 2010 February 126 (3):348-54. Epub 12/08/2009.

Cobb angle progression in adolescent scoliosis begins at the intervertebral disc.

Will RE, Stokes IA, Qiu X, Walker MR, Sanders JO

Spine.. 2009 December 134 (25):2782-6. Epub 1900 01 01.

Does the value of PET-CT extend beyond pretreatment staging? An analysis of survival in surgical patients with esophageal cancer.

Sepesi B, Raymond DP, Polomsky M, Watson TJ, Litle VR, Jones CE, Hu R, Qiu X, Peters JH

Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract.. 2009 December 13 (12):2121-7. Epub 10/01/2009.

Genomic responses from the estrogen-responsive element-dependent signaling pathway mediated by estrogen receptor alpha are required to elicit cellular alterations.

Nott SL, Huang Y, Li X, Fluharty BR, Qiu X, Welshons WV, Yeh S, Muyan M

The Journal of biological chemistry.. 2009 May 29284 (22):15277-88. Epub 03/24/2009.

Detecting intergene correlation changes in microarray analysis: a new approach to gene selection.

Hu R, Qiu X, Glazko G, Klebanov L, Yakovlev A

BMC bioinformatics.. 2009 January 1510 :20. Epub 01/15/2009.

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.

Li X, Nott SL, Huang Y, Hilf R, Bambara RA, Qiu X, Yakovlev A, Welle S, Muyan M

Journal of molecular endocrinology.. 2008 May 40 (5):211-29. Epub 1900 01 01.

Testing differential expression in nonoverlapping gene pairs: a new perspective for the empirical Bayes method.

Klebanov L, Qiu X, Yakovlev A

Journal of bioinformatics and computational biology.. 2008 April 6 (2):301-16. Epub 1900 01 01.

CNS delivery of vectored prion-specific single-chain antibodies delays disease onset.

Wuertzer CA, Sullivan MA, Qiu X, Federoff HJ

Molecular therapy : the journal of the American Society of Gene Therapy.. 2008 March 16 (3):481-6. Epub 01/08/2008.

Discussion of: Treelets - An adaptive multi-scale basis for sparse unordered data

Qiu, X.

Annals of Applied Statistics. 2008; 2(2): 484-488.

Comments on probabilistic models behind the concept of false discovery rate.

Qiu X, Yakovlev A

Journal of bioinformatics and computational biology.. 2007 August 5 (4):963-75. Epub 1900 01 01.

Statistical methods and microarray data.

Klebanov L, Qiu X, Welle S, Yakovlev A

Nature biotechnology.. 2007 January 25 (1):25-6; author reply 26-7. Epub 1900 01 01.

Control of the mean number of false discoveries, Bonferroni and stability of multiple testing

Gordon, A.; Glazko, G.; Qiu, X.; Yakovlev, A.

The Annals of Applied Statistics. 2007; 1(1): 179-190.

Some comments on instability of false discovery rate estimation.

Qiu X, Yakovlev A

Journal of bioinformatics and computational biology.. 2006 October 4 (5):1057-68. Epub 1900 01 01.

Utility of correlation measures in analysis of gene expression.

Almudevar A, Klebanov LB, Qiu X, Salzman P, Yakovlev AY

NeuroRx : the journal of the American Society for Experimental NeuroTherapeutics.. 2006 July 3 (3):384-95. Epub 1900 01 01.

Assessing stability of gene selection in microarray data analysis.

Qiu X, Xiao Y, Gordon A, Yakovlev A

BMC bioinformatics.. 2006 February 17 :50. Epub 02/01/2006.

The effects of normalization on the correlation structure of microarray data.

Qiu X, Brooks AI, Klebanov L, Yakovlev N

BMC bioinformatics.. 2005 May 166 :120. Epub 05/16/2005.

Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes.

Qiu X, Klebanov L, Yakovlev A

Statistical applications in genetics and molecular biology. 2005 4 :Article34. Epub 11/22/2005.

An Improvement on the concentration-compactness principle

Qiu, X.; Hong, Y.; Shen, Y.

Mathematicae Applicatae Sinica. 2001; 17: 60-67.

Books

Statistical Modeling for Biological Systems: In Memory of Andrei Yakovlev (2020)

Chapter: Correlation between the true and false discoveries in a positively dependent multiple comparison problem

Authors: Qiu, X. and Hu, Rui

Publisher: Springer Nature, Cham, Switzerland 2020

Topics in Applied Statistics (2013)

Chapter: High-Dimensional Ordinary Differential Equation Models for Reconstructing Genome-Wide Dynamic Regulatory Networks

Authors: Wu, S.; Liu, Z. P.; Qiu, X.; Wu, H.

Publisher: Springer, New York 2013

Statistical Methods for Microarray Data Analysis (2012)

Chapter: Gene selection with the delta-sequence method

Authors: Xing Qiu and Lev Klebanov

Publisher: Humana Press 2012