Past Faculty - Xiangqin Cui, Ph.D.

Xiangqin Cui, Ph.D. Department of Biostatistics
Ryals Public Health Bldg, 317
University of Alabama at Birmingham
Birmingham, AL 35294
Phone: (205) 996-4154
Fax: (205) 975-2540
Full CV

Dr. Cui received her Ph.D in Genetics at Iowa State University in 2001. She was then trained in in statistical genetics as a postdoc at the Jackson Laboratory. Dr. Cui joined SSG in Aug 2004 as an Assistant Professor with a joint appointment in the Biostatistics Department and the Department of Medicine (Division of Genetic and Translational Medicine). Her research interest includes statistical genomics, epigenomics, proteinomics, metabolomics, microbiomic, immune-Repertoire, and other high throughput study design and data analyses.

  • Research
  • Teaching
  • Mentoring

Methodology Research

  1. Equivalence testing of high dimensional data:

    The conventional supervised analysis of high dimensional expression data (microarras, proteomics, RNA-seq etc) often identifies differentially expressed genes by rejecting the null hypothesis of equality at each gene. The genes that are not significantly different are often discarded as uninteresting. However, when the goal of the experiment is to discover genes, pathways, or networks that are consistent (not changing), such as evaluating model systems and seeking common mechanisms between related diseases, the conventional "testing for difference" framework does not provide a valid test directly answering these questions. Many people have the misconception that genes failing to be categorized as differentially expressed according to the statistical tests for differential expression must be equivalently expressed. This misconception fails to recognize that the reason that a gene is not categorized as a differentially expressed gene is most likely due to the lack of power caused by high noise level or lack of replication in the experimental design, or both. The lack of statistical evidence of differential expression does not provide evidence of equivalence in gene expression. In this project, we are trying to develop, evaluate, and apply sound equivalence testing methods for identifying equivalently expressed and equivalently changed genes, pathways, and networks. Our current application of this method is in evaluating the consistency of gene expression change between primary human brain tumor (GBM) and their xenografts in mice, which is critical for the successful transfer of drugs tested on xenografts to human patients.

    Related publications:

    • Cui, X., J. Qiu, J. Zhou, and M. Mrug (2009). Validation of Endogenous Internal Real-Time PCR Controls in Renal Tissues. The American Journal of Nephrology. Am J Nephrol 30:413–417. [DOI: 10.1159/000235993] [PMID: 19729889] [PMCID: PMC2818397]
    • Qiu, J. and X Cui (2010). Evaluation of a Statistical Equivalence Test Applied to Microarray Data. Journal of Biopharmaceutical Statistics. Journal of Biopharmaceutical Statistics, 20(2):240-66. [DOI: 10.1080/10543400903572738] [PMID: 20309757]
    • Qiu, Jing; Qi, Yue; Cui, Xiangqin (2014) “Applying shrinkage variance estimators to the TOST test in high dimensional settings” Statistics in Genetics and Molecular Biology, 13(3):323-41. [doi: 10.1515/sagmb-2013-0045]
    • Yang C, Bartolucci AA, Cui X (2015) Multigroup Equivalence Analysis for High-Dimensional Expression Data. Cancer Inform. 2015 Nov 23;14 (Suppl 2):253-263. [PMCID: PMC4659441]
  2. Next Generation Sequencing Design and Data Analysis:

    Next Generation Sequencing is a booming technology that has many applications in Biological Sciences, such as RNA-seq for quantifying transcript expression, ChIP-seq for interrogating protein binding sites in the genome, exome-seq for sequencing all the exons in the genome, as well as whole genome sequencing and whole genome DNA-methylation sequencing etc. For this technology, we are mainly working on the experimental design and data analysis of RNA-seq data and ChIP-seq data.

    We were funded for the organization of a conference focusing on the Statistical Analysis of NGS data.

    Statistical Analyses for Next Generation Sequencing
    Sept 26-27, 2011
  3. Epigenomics:

    Modifications to DNA or chromatin that affects the gene expression but without altering the DNA sequence are often referred to epigenetics. The whole collection of this type of modifications is referred as epigenomics. Since epigenetic modification can be results of environment factors, it is often considered to be the bridge between genetics and environment in human disease. We are interested in the data analysis of epigenomics data as well as study the role of epigenetic alterations in human cardiovascular and neural disease. The technologies we work with are mostly DNA methylation microarrays.

Major Collaborators

  • Zhide Fang, PhD, Professor and Director, LSUHSC School of Public Health
  • Jing Qiu, PhD, Assistant Professor, Applied Economics and Statistics, University of Delaware
  • Michal Mrug, MD, Associate Professor, Division of Nephrology, UAB
  • Glen C Ulett, PhD, Associate Professor, School of Medical Sciences, Centre for Medicine and Oral Health, Griffith University, Australia
  • Marcas Bamman, PhD, Professor, Departments of Physiology & Biophysics, Medicine and Nutrition Sciences, UAB
  • S. Louis Bridges, MD, PhD, Professor of Medicine, Director, Division of Clinical Immunology and Rheumatology, UAB
  • Louis Dell'Italia, PhD, Professor of Medicine, Director of the Center for Heart Failure Research, UAB
  • G. Yancey Gillespie, PhD, Professor of Surgery with secondary appointments in the Departments of Microbiology and Cell Biology, UAB
  • Anupam Agarwal, MD, Professor and Director, Department of Medicine, Division of Nephrology, UAB.
  • Trygve O. Tollefsbol, PhD, Professor, Dept. of Biology, UAB.
  • Lisa Guay-Woodford, MD, Children's National Medical Center, Washington DC.
  • Wendy Demark-Wahnefried, PhD, RD, Professor and Webb Endowed Chair of Nutrition Sciences, Associate Director, UAB Comprehensive Cancer Center, UAB
  • Peter King, MD, Professor and Vice Chair, Department of Neurology, UAB
  • Peter J. Mannon, MD, MPH, Professor of Medicine, Division of Gastroenterology & Hepatology, UAB
  • Roslyn B. Mannon, MD, Professor of Medicine and Surgery, Director of Research, Alabama Transplant Center.
  • Stephen Barnes, PhD. Professor of Pharmacology & Toxicology, UAB
  • Elizabeth E. Brown, Ph.D, Professor. Department of Pathology, UAB.


  • Classes:

    BST 675 - Introduction to Statistical Genetics (offered in the spring of odd years)

    This is an elective course in the Biostatistics Department. It is to introduce students to basic concepts in population genetics, genetic epidemiology analysis, Mendelian laws of inheritance, heritability, test cross, linkage analysis, QTL analysis, human linkage and human association methods for discrete and quantitative traits. Students are expected to critically read and present current statistical research papers and to write a mini-review summarizing an area of statistical genetics research that is of interest to the student.

    BST 676 – Genomics Data Analysis (offered in the spring of even years)

    This is an elective course in the Biostatistics Department. The purpose of this course is to teach graduate students statistical methods that underlie the analysis of data generated by high throughput genomic technologies, as well as issues in the experimental design and implementation of these technologies. High throughput technologies that are covered include: microarrays, proteomics, and second generation sequencing. Many of real data analysis projects will be provided as the class projects. After the students go through each step of the analysis and finish the project, they are expected to take on new but similar data analysis projects.

    BST 611 – Intermediate Statistical Analysis I (Spring 2015-online, Fall 2015-inclass)

    This is a service course for non-biostatistics student from School of Public Health and other schools at UAB. It is the first of the three course sequence. Students will gain a thorough understanding of basic analysis methods, elementary concepts, statistical models and applications of probability, commonly used sampling distributions, parametric and non-parametric one and two sample tests, confidence intervals, applications of analysis of two-way contingency table data, simple linear regression, and simple analysis of variance.

  • Guest Lectures:
    • "Introduction to Microarray Technology (Biology and Experimental Design)", CS640 (course title: Bioinformatics; primary instructor: Chengcui Zhang). Fall 2004
    • "Image processing,analysis,QC and normalization -Two color" in NSF Plant Microarray Short Course, June 14, 2005, Madison, WI. 6/13/06
    • "Inferential Statistical Procedures - Linear Models" in NSF Plant Microarray Short Course, June 14, 2005, Madison, WI NIDDK short course at UAB: Demonstration and Supervised Practice (Microarray). May 4th, 2005. Birmingham, AL.
    • "Genomics, Bioinformatics, and Medicine" in UAB K30 genetics lectures (organizer: Bruce Korf), Spring 05, 06,07, 08
    • "Inferencial Statistical Procedures--Linear Models" in the 2nd NSF Plant Microarray Short Course, August 2, 2006. Boston, MA.
    • "Statistical Analysis of Microarray Data: Design, Normalization, and Statistical Inference" in Genet702 (course title: Animal Model Systems for Genetic and Genomic Analyses). Spring 05, 07
    • "Design of microarray experiments" in International Microarray Workshop, January 11, 2007. January 10th 2008, Tucson, AZ.
    • "Statistical Aspects for the polycystic kidney study" in HMG703 (Title: Hughes Med-Grad "Quantitative Methods"). March 28, 2007, April 1st 2009
    • "Basic Statistics" in Genetics Core Lecture Series (organizer: Scott Austin). August 17, 2007. Fall 2008.
    • "Introduction to QTL mapping" in NSF Statistical Genetics Short Course, July 12th 2008, Birmingham, AL
    • "Software Demonstration of MAANOVA package" in the NSF Statistical Genetics Short Course, July 12th 2008, Birmingham, AL
    • "Permutation Methods" in BST 765 (course name: Advanced Computational Methods; primary instructor: Rui Feng). Oct 1st 2008
    • "Arrays and Bioinformatics" in Combined Fellow's Physiology Conference (organizer: James Hagood), February 19th, 2009
    • "Microarray Analysis and Related Topics" in EPI 788 (course name: Molecular Epidemiology; primary instructor: Elizabeth Brown). Summer 2009, Summer 2011.
    • "Introduction to Epigenetics/Epigenomics" in Introduction to Statistical Genetics Workshop. New Orleans, LA. Feb 12th 2009 Lecture is at
    • "Bioinformatics, Genomics, and Medicine" in Vocabulary of Clinical & Translational Science (organizer: Jacqueline Ann Moss). Sep 18th, 2009
    • "Analysis Issues of Microarray and Next-Generation Sequencing Data" in the Genomics Block of GBS 722 (course name: GGS Bioinformatics: course master: Michael Crowley). Jan 26th, 2011.
    • "Microarray Data Analysis Software – R Based" in the Bioinformatics Block of GBS 722 (course name: GGS Bioinformatics: course master: Chiquito Crasto). Feb 28th, 2011
    • "Statistical Analyses of RNA-seq Data" in BST 695 (course name: Special Topics; primary instructor: Degui Zhi). April 6th, 2011.
    • "Software packages Affy, maanova, and PowerAtlas" in the NIGMS short course , Birmingham, AL, July 20th, 2011.
    • "Analysis of Whole Genome Transcriptome Sequencing Data" in the NHGRI short course on Next Generation Sequencing, Birmingham, AL. December 19th, 2011. (
    • “Introduction to R & Bio-conductor”. For NIGMS short course at UAB 7/9/2012 “Affy, RMANOVA package demo”. For NIGMS short course at UAB 7/11/2012
    • “Analysis of Whole Genome Transcriptome Sequencing Data,” in the NHGRI short course on Next Generation Sequencing, Birmingham, AL. December 12, 2012.
    • “Introduction to R and Bioconductor”, in the NIGMS short course on Statistical Genetics and Genomics, Birmingham, AL, 7/8/2013
    • “RNAseq: Experimental Design and Data Analysis”, in the NIGMS short course on Statistical Genetics and Genomics, Birmingham, AL, 7/11/2013
    • “Bowtie/TopHat, SAMTools, IGV, R packages for RNA-seq and ChIP-seq”, together with Hao Wu in the NIGMS short course on Statistical Genetics and Genomics, Birmingham, AL, 7/11/2013
    • “Transcriptome Analysis” in 3rd Short Course on Next-Generation Sequencing: Technology and Statistical Methods, Birmingham, Al, 12/18/2013
    • “Software Demonstration (RNA-Seq & Galaxy)” in 3rd Short Course on Next-Generation Sequencing: Technology and Statistical Methods, Birmingham, Al, 12/18/2013
    • “About RNA-seq” in WINGS Workshop in Next Generation Science,  UNC Charlotte, May 13-14, 2014
    • “Introduction to R & Bio-conductor” in Short Course on Statistical Genetics and Genomics. Birmingham, AL, 4th 7/7/2014, 5th 7/27/2015
    • “Transcriptome Analyses: Microarray and RNAseq” in Short Course on Statistical Genetics and Genomics. Birmingham, AL, 4th 7/10/2014, 5th 7/29/2015
    • “Introduction to R & Bio-conductor” in Short Course on Next-Generation Sequencing: Technology and Statistical Methods. Birmingham, AL, 4th 12/15/2014, 5th 12/14/2015
    • “Transcriptome Analysis Using NGS” in Short Course on Next-Generation Sequencing: Technology and Statistical Methods. Birmingham, AL, 4th  12/17/2014, 5th 12/19/2015
    • “Experimental Design of Omics Experiments” in GBS 748: Advanced Graduate Course in Metabolomics, January 17th 2015; January 6th, 2016
    • “Interpretation of Metabolomics Analysis Results” in GBS 748: Advanced Graduate Course in Metabolomics, Feb. 9th 2015;
    • “Introduction to R and Bioconductor” in GBS 722: Bioinformatics, Feb. 11th-12th 2015; March 8-9, 2-016.
    • “Training in Experimental Design” 6/15/2015 in 3rd Annual Workshop on Metabolomics.
    • “Designing a Metabolomics Experiment” 12/2/2015 in One-Day Metabolomics Workshop
    • “Experimental Design & Statistics” 9/11/2015 in MIC 741:Topics in Professional Development

Student/Post-docs advised

  • Master students
    • Kathakali Ghosh (2005–2006) M.S. student research project advisor
    • Liyan Gao (2009–2010 ) M.S. student academic and research advisor
    • Luqin Deng (2009–2012) M.S. student academic and research advisor
    • Ligong Chen (2010–2012) M.S. student research advisor
    • Xuelin Li (2013) M.S. student research advisor
    • Shaohua Yu (2013-present) M.S. student academic and research advisor
    • Amanda Hall (2014- present) M.S. academic and research advisor
    • Justin Leach (2014-present) M.S. academic advisor
    • Holly Hartman (2015) M.S. research project advisor
    • Lauren Wood (2015-) M.S. academic advisor
  • Ph.D students:
    • Henry Roberson (2005–2008) academic advisor
    • Lang Chen (2006-2008) dissertation Co-chair
    • Jun Li (2005–2011) academic advisor
    • Guoqiao Wang (2010–2013) academic advisor
    • Celeste Yang (2010-2013) dissertation Chair
  • Postdocs
    • Richard Kennedy (2008–2011) Co-mentor
    • Armrit Karki (2012-2012) mentor
    • Jason Guichard (2012-present) Co-mentor
  • Graduate disertation committees:
    • Hong Gao (Ph.D.) Department of Vision Science (2007-2009)
    • Jacquelyn Zimmerman (Ph.D.) Department of Medicine, Division of Hematology & Oncology (2009–2012)
    • Elizabeth Perkins (Ph.D.) Clinical Immunology and Rheumatology (2011–2012)
    • Kathryn Royse (Ph.D.) Department of Epidemiology (2011–present)
    • Lindsey Jones (Ph.D) Biostatistics (2013-present)
    • Michael Behring (Ph.D) Biostatistics (2015- present)
    • Stephen Gragg (MD/Ph.D) NIH Medical Scientist Training (2016-present)
  • Summer interns
    • Tarik Trend, Emery University, (2007) Intern advisor



  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • pre 2006
  1. Wang Y, Kapoor P, Parks R, Silva-Sanchez A, Alam SM, Verkoczy L, Liao HX, Zhuang Y, Burrows P, Levinson M, Elgavish A, Cui X, Haynes BF, Schroeder H Jr. (2016) HIV-1 gp140 epitope recognition is influenced by immunoglobulin DH gene segment sequence. Immunogenetics. ;68(2):145-55. [doi: 10.1007/s00251-015-0890-x] [PMCID: PMC4729650]
  1. Rojnueangnit K, Mikhail FM, Cui X, Yu S, Robin NH. (2015) Predictor(s) of Abnormal Array Comparative Genomic Hybridization Results in Patients with Cleft Palate Craniofac J. 2015 Nov;52(6):724-31. [doi: 10.1597/14-088] Epub 2014 Dec 9.
  2. Cui X**, Yu S, Tamhane A, Causey ZL, Steg A, Danila MI, Reynolds RJ, Wang J, Wanzeck KC, Tang Q, Ledbetter SS, Redden DT, Johnson MR, Bridges SL Jr. (2015) “Simple Regression for Correcting ΔCt Bias in RT-qPCR Low-Density Array Data Normalization”. BMC-Genomics. BMC Genomics. 2015 Feb 14;16:82. [doi: 10.1186/s12864-015-1274-1]
  3. Tang Q, Danila MI, Cui X, Parks L, Baker BJ, Reynolds RJ, Raman C, Wanseck KC, Redden DT, Johnson MR; CLEAR Investigators, Bridges SL Jr. (2015) “Expression of Interferon-gamma Receptor Genes in PBMCs is Associated with Rheumatoid Arthritis and Its Radiographic Severity in African Americans” Arthritis Rheumatol. 2015 May;67(5):1165-70. [doi:10.1002/art.39056].
  4. Yan Q, Tiwari HK, Yi N, Gao G, Zhang K, Lin WY, Lou XY, Cui X, Liu N. (2015) A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model. Hum Hered. 2015;79(2):60-8. [doi:10.1159/000375409] Epub 2015 Mar 10.
  5. Si Y, Kim S, Cui X, Zheng L, Oh SJ, Anderson T, AlSharabati M, Kazamel M,Volpicelli-Daley L, Bamman MM, Yu S, King PH. (2015) Transforming Growth Factor Beta(TGF-β) Is a Muscle Biomarker of Disease Progression in ALS and Correlates with Smad Expression. PLoS One. 10(9):e0138425. [doi:10.1371/journal.pone.0138425] [PMCID: PMC4574401]
  6. Mrug M, Zhou J, Yang C, Aronow BJ, Cui X, Schoeb TR, Siegal GP, Yoder BK,Guay-Woodford LM. (2015) Genetic and Informatic Analyses Implicate Kif12 as a Candidate Gene within the Mpkd2 Locus That Modulates Renal Cystic Disease Severity in the Cys1cpk Mouse. PLoS One. 10(8):e0135678. [doi:10.1371/journal.pone.0135678] Central [PMCID: PMC4546649]
  7. Plyler ZE, Hill AE, McAtee CW, Cui X, Moseley LA, Sorscher EJ. (2015) SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution. Genome Biol Evol. 2015 Aug 6;7(9):2506-19. [doi:10.1093/gbe/evv150] [PMCID: PMC4607513]
  8. Yang C, Bartolucci AA, Cui X**. (2015) Multigroup Equivalence Analysis for High-Dimensional Expression Data. Cancer Inform. 2015 Nov 23;14(Suppl 2):253-263. [PMCID: PMC4659441]
  1. Johnson SL, SO. Hughes, X Cui, X Li, DB Allison, Y Liu, S Goodell, T Nicklas, T Power, KL Vollrath (2014) Portion sizes for children are associated with parental characteristics and the amounts parents serve themselves. The American Journal of Clinical Nutrition. 99(4):763-70. [doi: 10.3945/ajcn.113.078311] [PMCID: PMC3953879]
  2. Yang S, Cui X, Fang Z. (2014) “BCRgt: a Bayesian cluster regression-based genotyping algorithm for the samples with copy number alterations.” BMC Bioinformatics 15: 74.[ doi:10.1186/1471-2105-15-74] [PMCID: PMC4003822]
  3. Yan Q, Tiwari HK, Yi N, Lin WY, Gao G, Lou XY, Cui X, Liu N. (2014) Kernel-machine testing coupled with a rank-truncation method for genetic pathway analysis. Genetic Epidemiology, 38(5):447-56. [doi: 10.1002/gepi.21813] [PMCID: PMC4073214]
  4. Justin Barnes, Betty Pat, Yaun-wen Chen, Pamela C Powell, Wayne E Bradley, Junying Zheng, Amrit Karki, Xiangqin Cui, James Collawn, Chih-Cheng Wei, Jason Guichard, Louis J Dell’Italia (2014) “Whole-Genome Profiling Highlights the Complexity Underlying Eccentric Cardiac Hypertrophy” Ther Adv Cardiovasc Dis. 2014 Mar 31. [Epub ahead of print]
  5. Qiu, Jing; Qi, Yue; Cui, Xiangqin (2014) “Applying shrinkage variance estimators to the TOST test in high dimensional settings” Statistics in Genetics and Molecular Biology, 13(3):323-41. [doi: 10.1515/sagmb-2013-0045]
  6. Peng Y, Song L, Zhao M, Harmelink C, Debenedittis P, Cui X, Wang Q, Jiao K. (2014) “Critical roles of miRNA-mediated regulation of TGFβ signalling during mouse cardiogenesis.” Cardiovasc Res. 103(2):258-67. [doi: 10.1093/cvr/cvu126] [PMCID: PMC4110444]
  7. Boddu R, Yang C, O'Connor AK, Hendrickson RC, Boone B, Cui X, Garcia-Gonzalez M, Igarashi P, Onuchic LF, Germino GG, Guay-Woodford LM (2014) “Intragenic motifs regulate the transcriptional complexity of Pkhd1/PKHD1.” J Mol Med (Berl) 92(10):1045-56. [doi: 10.1007/s00109-014-1185-7] [PMCID: PMC4197071]
  8. Barnes J, Pat B, Chen YW, Powell PC, Bradley WE, Zheng J, Karki A, Cui X, Guichard J, Wei CC, Collawn J, Dell'Italia LJ. (2014) “Whole-genome profiling highlights the molecular complexity underlying eccentric cardiac hypertrophy.” Ther Adv Cardiovasc Dis. 8(3):97-118
  9. Kitiwan Rojnueangnit, Fady M. Mikhail, Xiangqin Cui, Shaohua Yu, Nathaniel H. Robin. (2014) Predictor(s) of Abnormal Array Comparative Genomic Hybridization Results in Patients with Cleft Lip and/or Palate. The Cleft Palate-Craniofacial Journal 2014 Dec 9. [Epub ahead of print]
  10. Cuna A, B Halloran, O Faye-Petersen, D Kelly, D Crossman, X Cui, K Pandit, N Kaminski, S Bhattacharya, A Ahmad, T J. Mariani and N Ambalavanan (2014). Alterations in Gene Expression and DNA Methylation During Murine and Human Lung Alveolar Septation. Am J Respir Cell Mol Biol 2014 Nov 11. [Epub ahead of print] PMCID-in process
  11. Matthew L Stoll, Ranjit Kumar, Casey D Morrow, Elliot J Lefkowitz, Xiangqin Cui, Anna Genin, Randy Q Cron, Charles O Elson. Dysbiosis triggering abnormal humoral immune responses to commensal organisms in juvenile spondyloarthritis. (Arthritis Research & Therapy) 2014 Nov 30;16(6):486 [PMCID: PMC4272554]
  12. Ying Si, Xianqin Cui, Soojin Kim, Robert Wians, Robert Sorge, Shin J. Oh, Mohammad Al-Sharabati, Liang Lu, Gwen Claussen, Tina Anderson, Shaohua Yu, Dylan Morgan, Mohamed Kazamel, Peter H. King (2014) “Smads as Muscle Biomarkers in Amyotrophic Lateral Sclerosis” Annals of Clinical and Translational Neurology. 1:778-787
  1. Fox ER, Musani SK, Barbalic M, Lin H, Yu B, Ogunyankin KO, Smith NL, Kutlar A, Glazer NL, Post WS, Paltoo DN, Dries DL, Farlow DN, Duarte CW, Kardia SL, Meyers KJ, Sun YV, Arnett DK, Patki AA, Sha J, Cui X, Samdarshi TE, Penman AD, Bibbins-Domingo K, Bůžková P, Benjamin EJ, Bluemke DA, Morrison AC, Heiss G, Carr JJ, Tracy RP, Mosley TH, Taylor HA, Psaty BM, Heckbert SR, Cappola TP, Vasan RS (2013) Genome-wide association study of cardiac structure and systolic function in African Americans: The Candidate Gene Association Resource (CARe) Study. Circ Cardiovasc Genet. 2013 Feb;6(1):37-46. [doi: 10.1161/CIRCGENETICS.111.962365] [PMID: 23275298]
  2. Thalacker-Mercer A, Stec M, Cui X, Cross J, Windham S, Bamman M. (2013) Cluster analysis reveals differential transcript profiles associated with resistance training-induced human skeletal muscle hypertrophy. Physiological Genomics 17;45(12):499-507. [doi: 10.1152/physiolgenomics.00167.2012] [PMID: 23632419]
  1. Duell BL, Carey AJ, Tan CK, Cui X, Webb RI, Totsika M, Schembri MA, Derrington P, Irving-Rodgers H, Cripps AW, Crowley M, and Ulett GC. (2012) Innate transcriptional networks activated in bladder in response to uropathogenic Escherichia coli drive diverse biological pathways and rapid synthesis of IL-10 for defense against bacterial urinary tract infection. Journal of Immunology Jan 15;188(2):781-92. Epub 2011 Dec 19. [PMID: 22184725]
  2. Duarte CW, CD Willey, D Zhi D, X Cui, JJ Harris, LK Vaughan, T Mehta, RO McCubrey, NN Khodarev, RR Weichselbaum, and GY Gillespie. (2012). Expression signature of ifn/stat1 signaling genes predicts poor survival outcome in Glioblastoma Multiforme in a subtype-specific manner. PLoS One 2012; 7(1):e29653. Epub 2012 Jan 5. [PMCID: PMC3252343]
  3. Reynolds RJ, X Cui, LK Vaughan, DT Redden, Z Causey, E Perkins, T Shah, LB Hughes; CLEAR Investigators, A Damle, M Kern, PK Gregersen, MR Johnson, and SL Bridges Jr. (2012). Gene expression patterns in peripheral blood cells associated with radiographic severity in African Americans with early rheumatoid arthritis. Rheumatology International. Jan. 12. [Epub ahead of print]
  4. Moskowitz-Kassai E, L Mackelaite, J Chen, K Patel, DM Dadhania, SS Gross, P Chander, V Delaney, L Deng, L Chen, X Cui, M Suthanthiran, and MS Goligorsky MS. (2012) Excretion of anti-angiogenic proteins in patients with chronic allograft dysfunction. Nephrology Dialysis Transplantation. 2012 Feb;27(2):494-7. Epub 2012 Jan 17. [PMCID: PMC3275786] [doi: 10.1093/ndt/gfr638]
  5. Fang Z., R Du, and X Cui.** (2012) Uniform approximation is more appropriate for Wilcoxon Rank-Sum Test in Gene Set Analysis. PLoS One. 7(2):e31505 Epub 2012 Feb 7. [PMCID: PMC3274536]
  6. Zhou J, Ouyang X, Schoeb TR, Bolisetty S, Cui X, Mrug S, Yoder BK, Johnson MR, Szalai AJ, Mrug M. (2012) Kidney Injury Accelerates Cystogenesis via Pathways Modulated by Heme Oxygenase and Complement. J Am Soc Nephrol. Jul;23(7):1161-71
  7. Tan CK, AJ Carey, X Cui, RI Webb, WH Benjamin Jr., AW Cripps, M Crowley, KB Ulett, and GC Ulett. (2012) Genome-wide mapping of cystitis due to Streptococcus agalactiae and Escherichia coli in mice identifies a unique bladder transcriptome signifying pathogenspecific antimicrobial defense against urinary tract infection. Infection and Immunity. 80(9):3145-60. [PMCID: PMC3418756] [doi: 10.1128/IAI.00023-12]
  8. Wu H, M. Wu, D Zhi, S A Santorico, X Cui**, (2012) Statistics for Next Generation Sequencing---- Meeting Report. Frontiers in Statistical Genetics and Methodology [doi:10.3389/fgene.2012.00128]
  9. Krejčí E, Pesevski Z, Dealmeida AC, Mrug M, Fresco VM, Argraves WS, Barth JL, Cui X, Sedmera D. (2012) Microarray analysis of normal and abnormal chick ventricular myocardial development. Physiol Res. 2012 Jul 24;61 Suppl 1:S137-44.
  1. Wu X, Patki A, Lara-Castro C, Cui X, Zhang K, Walton RG, Osier MV, Gadbury GL, Allison DB, Martin M, Garvey WT. (2011) Genes and Biochemical Pathways in Human Skeletal Muscle Affecting Resting Energy Expenditure and Fuel Partitioning. J Appl Physiol. Mar;110(3):746-55. [PMID: 21109598] [doi:10.1152/japplphysiol.00293.2010]
  2. Gao L, Fang Z, Zhang K, Zhi D, Cui X. (2011) Length Bias Correction for RNA-seq Data in Gene Set Analyses. Bioinformatics. 7 (5): 662-669. [doi: 10.1093/bioinformatics/btr005] [PMID: 21252076] [PMCID: PMC3042188] [R-Codes]
  3. Fang Z. and X Cui**. (2011) Design and Validation Issues in Next Generation Sequencing Experiments. Briefings in Bioinformatics 12(3) 280-287 [PMID: 21498551]
  4. Chen Y, Pat B, Gladden JD, Zheng J, Powell P, Wei C-C, Cui X, Husain A, LJ Dell'Italia. (2011) Dynamic Molecular and Histopathological Changes in Extracellular Matrix and Inflammation in the Transition to Heart Failure in Isolated Volume Overload. Circulation. AJP-Heart and Circulatory Physiology 300(6):H2251-60. [PMID: 21421827] [PMCID: PMC3119090]
  1. Ulett GC, Webb RI, Ulett KB, Cui X, Benjamin WH, Crowley M, Schembri MA (2010). Group B Streptococcus (GBS) Urinary Tract Infection Involves Binding of GBS to Bladder Uroepithelium and Potent but GBS-Specific Induction of Interleukin 1alpha. J Infect Dis. 201(6):866-70.[PMID: 20132033] [DOI: 10.1086/650696]
  2. Anna Thalacker_Mercer, Louis J Dell’Italia, Xiangqin Cui, James M. Cross, and Marcas M. Bamman (2010) Differential Genomic Responses in Old vs. Young Humans Despite Similar Levels of Modest Muscle Damage After Resistance Loading. Physiological Genomics. 40(3):141-9. Epub 2009 Nov 10. [PMID: 19903761]
  3. Jing Qiu and Xiangqin Cui. (2010) Evaluation of a Statistical Equivalence Test Applied to Microarray Data. Journal of Biopharmaceutical Statistics. 20(2):240-66. [PMID: 20309757] [DOI: 10.1080/10543400903572738]
  4. Juling Zhou, Xiaosen Ouyang, Xiangqin Cui, Trenton R. Schoeb, Lesley E. Smythies, Martin R. Johnson, Lisa M. Guay-Woodford, Arlene B. Chapman and Michal Mrug. (2010) Renal CD14 expression correlates with rates of cystic kidney disease progression. Kidney International 78(6):550-60. [PMID: 20555320]
  1. Xiangqin Cui, Jing Qiu, and Juling Zhou, and Michal Mrug (2009). Validation of Endogenous Internal Real-Time PCR Controls in Renal Tissues. The American Journal of Nephrology. Am J Nephrol 2009;30:413–417. [DOI: 10.1159/000235993] [PMID: 19729889] [PMCID: PMC2818397]
  2. Xiangqin Cui, Ann, E. Loraine (2009) Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing. PLoS ONE 4(1): e4229. [PMID: 19165320]
  3. P.A. Ioannidis, David B. Allison, Catherine Ball, Cesare Furlanello, Jon Mangion, Grier P. Page, Vera van Noort, Issa Coulibaly, Xiangqin Cui, Aedin Culhane, Mario Falci, Laurence Game, Giuseppe Jurman, Tapan Mehta, Enrico Petretto, Jelai Wang, Myles Axton (2009) Repeatability of published microarray gene expression analyses. Nature Genetics 41, 149 – 155. [PMID: 19174838] [DOI:10.1038/ng.295]
  4. Huifen Zhu, Guo-Jing Li1, Lei Ding, Xiangqin Cui, Howard Berg, Sarah M. Assmann, Yiji Xia (2009) Arabidopsis Extra Large G Protein 2 (XLG2) interacts with the Gβ subunit of heterotrimeric G protein and functions in disease resistance. Molecular Plant 2(3):513-525 [DOI:10.1093/mp/ssp001]
  5. Lang Chen, Grier P. Page, Tapan Mehta, Rui Feng, Xiangqin Cui (2009). Single Nucleotide Polymorphisms Affect both cis- and trans-eQTLs. Genomics 93(6):501-8 [PMID: 19248827]
  1. Michal Mrug, Juling Zhou, Yong Woo, Xiangqin Cui, Alexander J. Szalai1, Jan Novak, Gary A. Churchill, and Lisa M. Guay-Woodford "Overexpression of innate immune response genes in a model of recessive polycystic kidney disease" Kidney International (2008) 73, 63–76; [PMID: 17960140]
  1. Brand J.P.L., Chen L, Cui, XQ., Bartolucci, A.A, Page, G.P., Kim, K., Barnes, S., Srinivasasainagendra, V., Beasley, T.M., Allison, D.B. (2007) "An Adaptive Alpha-spending Algorithm Improves the Power of Statistical Inference in Microarray Data Analysis" Bioinformation, 1(10) 384-389 [PMID: 17597927]
  2. Ruden, D. M., XQ Cui, A. Loraine, A., Ye, J., Bynum, K., Kim, N. C., De Luca, M., Garfinkel, M. D., Lu, X. (2007). Methods for nutrigenomics and longevity studies in Drosophila: effects of diets high in sucrose, palmitic acid, soy, or beef. Methods Mol Biol. 2007;371:111-41 [PMID: 17634578]
  3. Wu, X., Wang, J., Cui, XQ., Maianu, L., Rhees, B., Rosinski, J., So, W.V., Willi, S.M., Osier M.V., Hill, H.S., Page, G.P., Allison, D.B., Martin, M., and Timothy Garvey, WT. (2007) The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle: Endocrine; Volume 31, No. 1, pp. 5 – 17. [PMID: 17709892]
  4. Gao YZ, Guo SY, Yin QZ, Cui XQ, Hisamitsu T, Jiang XH (2007) Possible involvement of integrin signaling pathway in the process of recovery from restraint stress in rats. Neurosci Bull. 2007 Jul;23 (4):229-35. [PMID: 17687398]
  1. Allison DB, Cui XQ, Page GP, Sabripour M (2006). Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. Jan. 7:55-65. [PMID: 16369572]
  2. Cui, XQ. and A. E. Loraine (2006) Global Correlation Analysis Between Redundant Probe Sets Using A Large Collection Of Arabidopsis Ath1 Expression Profiling Data. CSB2006 Proceedings of the LSS Computational Systems Bioinformatics Conference. Stanford, CA, August, p 223-226. [PMID: 17369640]
  3. Cui, XQ, Jason Affourtit, Keith R. Shockley, Yong Woo, and Gary A. Churchill(2006) Inheritance Patterns of Transcript Levels in F1 Hybrid Mice, Genetics 174:627-637. [PMID: 16888332]
  4. Laudencia-Chingcuanco, Debbie L., Stamova B.S., Laxo G.R., Cui XQ, and Anderson OD (2006) Analysis of the wheat endosperm transcriptome, J. Appl. Genet 47:287-302. [PMID: 17132893]
  1. Song WQ, XQ Cui, WS Xu, XL Li, YK Peng and RY Chen (1996) Micro-dissection and amplification of the terminal region from the long arm of the big M chromosome in Vica faba. Chinese Science Bulletin 41: 361-364
  2. Cui XQ, RP Wise and PS Schnable (1996) The rf2 nuclear restorer gene of male sterile T-cytoplasm maize. Science 272:1334-1336. [PMID: 8650543]
  3. Liu F *, XQ Cui *, HT Horner, H Weiner and PS Schnable (2001) Mitochondrial aldehyde dehydrogenase activity is required for male fertility in maize. Plant Cell 13: 1063-1078 * These authors contributed equally to this work. [PMID: 11340182]
  4. Skibbe DS, Liu F, Wen TJ, Yandeau MD, Cui XQ, Jun Cao J, Simmons CR, and PS Schnable (2002) Characterization of the Aldehyde Dehydrogenase Gene Families of Zea mays and Arabidopsis. Plant Molecular Biology 48: 751-764. [PMID: 11999848]
  5. Cui XQ, AP Hsia, DA Ashlock, RP Wise and PS Schnable. (2003) Alternative transcription initiation sites and polyadenylation sites are recruited during Mu suppression at the rf2a locus of maize. Genetics, 163: 685-698. [PMID: 12618406]
  6. Cui XQ, BE Scheffler, C Simmons, RB Meeley, and PS Schnable. Mutations in the maize pdc3 gene reduce tolerance to anaerobic stress (in preparation).
  7. Cui XQ, MK Kerr and GA Churchill. Transformations for cDNA microarray data.(2003) Statistical Applications in Genetics and Molecular Biology. vol 2, issue 1 article 4. [PMID: 16646782]
  8. Wu H, MK Kerr, XQ Cui, and GA Churchill. (2003) MAANOVA: A Software Package for the Analysis of Spotted cDNA Microarray Experiments. Chapter 14 in The analysis of gene expression data. Edited by Parmigiani G. et al. Springer, New York. [DOI: 10.1007/0-387-21679-0_14]
  9. Cui XQ and GA Churchill. (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biology, 4:210. [PMID: 12702200]
  10. Cui XQ and GA Churchill. (2003) How many mice and how many arrays? replication in mouse cDNA microarray experiments. in “Methods of Microarray Data Analysis III”, Edited by Kimberly F. Johnson and Simon M. Lin. Kluwer Academic Publishers, Norwell, MA. pp 139-154.
  11. Lobenhofer E.K., XQ Cui, L. Bennett, P.L. Cable, G.A. Churchill and C.A. Afshari (2004) Exploration of Low Dose Estrogen Effects: Identification of No Observed Transcriptional Effect Level (NOTEL). Toxicol Pathol. Jul-Aug; 32(4):482-92. [PMID: 15223774]
  12. Cui XQ, J. T.G. Hwang, J. Qiu, N.J. Blades and G. Churchill (2005) Improved statistical tests for differential gene expression by shrinking variance component estimates. Biostatistics Jan. 6(1):59-75. [PMID: 15618528]
  13. Yao H, Guo L, Fu Y, Borsuk LA, Wen TJ, Skibbe DS, Cui XQ, Scheffler BE, Cao J, Emrich SJ, Ashlock DA, Schnable PS. (2005) Evaluation of five ab initio gene prediction programs for the discovery of maize genes. Plant Mol Biol. Feb 57(3):445-60. [PMID: 15830133]
  14. Mrug M., R. Li, XQ Cui, T. R. Schoeb, G. A. Churchill, and L. M.Guay-Woodford (2005) Kinesin-Related Protein 12 is a Candidate Polycystic Kidney Disease Modifier in the cpk Mouse. J Am Soc Nephrol. 16(4):905-16. [PMID: 15728779]
  15. Mrug M , Schoeb TR, Li R, Cui X, Churchill GA , Guay-Woodford LM (2005) Kinesin 12 is predicted to modulate multiple phenotypes in the cpk mouse model of ARPKD. J Am Soc Nephrol 15:216A. [PMID: 15728779]