*Denotes I am corresponding author

@Denotes publication with my graduate student as first author


A.    Statistical Theory and Methods

*Cui X, Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, Close TJ 2005. Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit, Bioinformatics, 21(20), 3852-3858

*Xu J, Cui X 2008. Robustified MANOVA in detecting differentially expressed genes from oligonucleotide arrays. Bioinformatics, 24(8), 1056-1062

*Cui X, Wilson J 2008. On the probability of correct selection for large k populations with application to Microarray data, Biometrical Journal, 50(5), 870-883

*Xu J, Cui X, Gupta AK 2009. Improved statistics for contrasting means of two samples under non-normality. British Journal of Mathematical and Statistical Psychology, 62 (1), 21-40

*Cui X  and Wilson J 2009. A simulation study on the probability of correct selection for large k populations. Communications in Statistics - Simulation and Computation, 38(6), 1244-1255

*Cui X, Zhao H, Wilson J 2010. Optimized ranking and selection methods for feature selection with application in microarray experiments. Journal of Biopharmaceutical statistics, 20(2), 223-239

*Cui X, You N, Girke T, Michelmore R, Van Deynze A 2010. Single feature polymorphism detection using recombinant inbred line microarray expression data. Bioinformatics, 26(16), 1983-1989

*Zhao H, Wang B, Cui X 2010. General solutions to consistency problems in multiple hypothesis testing. Biometrical Journal, 52(6), 735-746

*@Wang B and Cui X  2010. Consonant closed likelihood ratio test procedures with application to dose-response study. Statistics in Medicine, 29(25), 2617-2630

*@Wang B and Cui X 2012. A New Partition Testing Strategy for Multiple Endpoints.  Statistics in Medicine. 31(20), 2151-2168

*You N, Murillo G, Su X, Zeng X, Xu J, Ning K, Zhang S, Zhu JK, Cui X 2012. SNP calling using genotype model selection on high-throughput sequencing data. Bioinformatics, 28(5), 643-650

@Zhang Z, Jeske DR, Cui X, Hoddle MS 2012.  Co-clustering spatial data using a generalized linear mixed model with application to the integrated pest management. Journal of Agricultural, Biological, and Environmental Statistics, 17(2), 265-282

*@Zhang Z, Cui X, Jeske DR, Li X, Braun J, Borneman J  2013. Clustering scatter plots using data depth measures. Journal of Biometrics and Biostatistics, S5-001. doi: 10.4172/2155-6180.S5-001

*@Zhang Z, Cui X, Jeske DR, Borneman J 2013.  Biclustering scatter plots using data depth measures. Statistical Analysis and Data Mining, 6(2) 102-115

*Zhao, H., Peddada, S., Cui, X. 2015. Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p-values.Biometrical Journal.57(1) 144-158.             

*Wang, X., Su, X.,Cui, X., Kang, N. 2015 MetaBoot: A machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data. PeerJ. Doi:10.7717/peerj.993

*@Cacho A, Smirnova E., Huzurbazar,Cui X 2015. A Comparison of Base-calling Algorithms for Illumina Sequencing Technology.Briefings in Bioinformatics, doi: 10.1093/bib/bbv088             

*@Xiao, Z., Brunel, N., Yang, Z.,Cui, X. 2015. A Constrained Mixed Effects Model Based on Semilinear Differential Equation for Cell Polarity Signaling in Tip Growth of Pollen TubesUnder Revision.

*@Murillo G., You, N., Su, X., Cui, W., Ning, K., Reilly, M.P., Li, M., Cui X 2015. MultiGeMS: Detection of SNVs from Multiple Samples Using Model Selection on High-Throughput Sequencing Datadoi:10.1093/bioinformatics/btv753 


B.    Domain Expertise Related Collaborative Research

Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J,   Xu J, Cui X, Close TJ 2005. Comparative transcriptional profiling of two contrasting rice (Oryza sativa L.) genotypes under salinity stress during vegetative growth stage. Plant Physiology, 139(2), 822-835

Walia H, Wilson C, Condamine P, Ismail AM, Xu J, Cui X, Close TJ 2007. Array-Based genotyping and expression analysis of barley cv. maythorpe and salt-tolerant golden promise. BMC Genomics, 8:87

Das S, Bhat P, Sudhakar C, Ehlers J, Wanamaker S, Roberts P, Cui X, Close TJ 2008. Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L.Walp) using a soybean genome array. BMC Genomics, 9: 107

Kim SH, Bhat PR, Cui X, Walia H, Xu J, Wanamaker S, Ismail AM, Wilson C, Close T 2009. Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. BMC Plant Biology, 9:65  doi:10.1186/1471-2229-9-65

Walia H, Wilson C, Ismail AM, Close T, Cui X 2009. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. BMC Genomics, 10:398 doi:10.1186/1471-2164-10-398

Saxena RK, Cui X, Thakur V, Walter B, Close TJ, Varshney RK 2011. Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea (Cajanus spp.). Funct Integr Genomics, 11(4), 651-657

Presley L, Ye J, Li X, LeBlanc J, Zhang Z, Ruegger PM, Allard J, McGovern D,  Lpolliti A, Roth B, Cui X, Jeske DR, Elashoff D, Goodglick L, Braun J, Borneman J 2011. Host-Microbe Relationships in Inflammatory Bowel Disease Detected by Bacterial and Metaproteomic Analysis of the Mucosal-Luminal Interface. Inflammatory Bowel Diseases, 18(3), 409-417

Stoffel K, van Leeuwen H, Kozik A, Caldwell D, Ashrafi H, Cui X, Tan X, Hill T, Reyes-Chin-Wo S,  Truco MJ, Michelmore RW, Van Deynze A  2012.  Development and application of a 6.5 Million Feature Affymetrix GeneChip(R) for Massively Parallel Discovery of Single Position Polymorphisms in Lettuce (Lactuca spp.). BMC Genomics, 13:185

Placido D, Campbell MT, Jin J, Cui X, Kruger GR, Baenziger PS, Walia H  2013. Introgression of novel traits from a wild wheat relative improves drought adaptation in wheat (Triticum aestivum). Plant Physiology, 161(4), 1806-1819

Yang, F., Ning, K., Chang, X., Yuan, X., Tu, Q., Yuan, T., Deng, Y., Hemme, CL., Nostrand, JV., Cui, X., He, Z., Chen, Z., Guo, D., Yu, J., Zhang, Y., Zhou, J., Xu, J. 2014 Saliva Microbiota Carry Caries-Specific Functional Gene Signatures. PloS one. 9(2), e76458

Ashby, J., Flack, K., Jimenez, L.A., Duan, Y., Khatib, A., Somlo,G., Wang, S.Z., Cui, X., Zhong, W. 2014 Distribution Profiling of Circulating MicroRNAs in Serum. Analytical Chemistry. 86(18), 9343-9349

Wang, X., Zhang, H., Zhou, Q., Su, X., Cui, X., Bu, D., Poetsch, A., and Ning, K. 2015. Bi-clustering interpretation and prediction of correlation from gene expression and protein abundance. Scientific Report. Under revision.


C. Genetics,Genomics Collaborative Research

Tsuchiya T, Dhahbi JM, Cui X, Mote PL, Bartke A, Spindler SR 2004. Additive regulation of hepatic gene expression by dwarfism and caloric restriction. Physiol. Genomics, 17(3), 307-315

Walia H, Wilson C, Condamine P, Wahid A, Cui X, Close TJ 2006. Expression analysis of barley (Hordeum vulgare L.) during salinity stress.  Functional & Integrative Genomics, 6(2), 143-156

Bhat P, Lukaszewski A, Cui X, Xu J, Wanamaker S, Svensson JT, Wanamaker S, Waines G, Close T 2007. Mapping translocation breakpoints using a wheat microarray.  Nucleic Acids Research. 35(9), 2936-2943

Kempema LA, Cui X, Holzer FM, Walling LL 2007. Arabidopsis Transcriptome changes in response to phloem-feeding silverleaf whitefly nymphs: similarities and distinctions in response to aphids. Plant Physiology. 143(2), 849-865

Li WX, Oono Y, Zhu J, He XJ, Wu JM, Iida K, Lu XY, Cui X, Jin H, Zhu JK 2008. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. Plant Cell.  20(8), 2238-2251

He XJ, Hsu YF, Zhu S, Liu HL, Pontes O, Zhu J, Cui X, Wang CS, Zhu JK 2009. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev. 23(23), 2717-2722 doi:10.1101/gad.1851809

Ren Z, Zheng Z, Chinnusamy V, Zhu J, Cui X, Lida K, Zhu JK 2010. RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. Proceedings of the National Academy of Sciences, 107(22), 5669-5674

Zhu J, Lee BH, Dellinger M, Cui X, Zhang C, Wu S, Nothnagel EA, Zhu JK 2010. A cellulose synthase-like protein is required for osmotic stress tolerance in Arabidopsis. The Plant Journal, 63(1), 128-140

Ruegger PM, Bent E, Li W, Jeske DR, Cui X, Braun J, Jiang T, Borneman J 2012. Improving oligonucleotide fingerprinting of rRNA genes by implementation of polony microarray technology. Journal of Microbiological Methods. 90(3) , 235-240.

MacWilliam, D., Arensburger, P., Higa, J.,Cui, X., and Adams, M. E. 2015. Behavioral and Genomic Characterization of Molt-Sleep in the Tobacco Hornworm, Manduca sexta. Insect Biochemistry and Molecular Biology. 62,154-167, doi:10.1016/j.ibmb.2015.01.012


D. Health Service Collaborative Research

Cheng E, Myers L, Wolf S, Shatin D, Cui X, Ellison G, Belin T, Vickrey BG 2001.  Mobility impairments and use of preventive services in women with multiple sclerosis:  observational study.  British Medical Journal 323(7319), 968-969

Gjertson DW, Dabrowska DM, Cui X, Cecka JM  2002.  Four causes of cadaveric kidney transplant failure:  A competing risk analysis.  American Journal of Transplantation 2(1), 84-93

Birbeck GL, Hays RD, Cui X, Vickrey BG 2002.  Seizure reduction and quality of life improvements in people with epilepsy. Epilepsia 43(5), 535-38

Birbeck GL, Cui X, Zingmond DS, Vickrey BG 2004. Intravenous tissue plasminogen activator for acute stroke in California: recipients and resources. Cerebrovasc Dis 17(4), 341-343

Birbeck GL, Zingmond DS, Cui X, Vickrey BG  2006. Multispecialty stroke services in California hospitals are associated with reduced mortality. Neurology. 66(10), 1527-1532

Vickrey BG, Mittman BS, Connor KI, Pearson ML, Della Penna RD, Ganlats TG, DeMonte RW Jr, Chodosh J, Cui X, Vassar S, Duan N, Lee M 2006. The effect of a disease management intervention on quality and outcomes of dementia care - a randomized, controlled trial. Annals of Internal Medicine. 145(10), 713-726