Publications
* as corresponding author
High dimensional data integration
Zhou, Y.H.*, Gallins, P., Etheridge, A., Jima, D., Scholl, E., Wright, F.A., Innocenti, F. (2022) "A resource for integrated genomic analysis of the human liver." Scientific Reports, accepted
Wang, W., Zhou, Y.H.* (2021) "Eigenvector-based sparse canonical correlation analysis: Fast computation for estimation of multiple canonical vectors." Journal of Multivariate Analysis, 104781.
Gallins, P., Saghapour, E., Zhou, Y.H.* (2020) "Exploring the limits of combined image/`omics analysis for non-cancer histological phenotypes." Frontiers in Genetics doi.org/10.3389/fgene.2020.555886
GTEx Consortium (2018) “Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics”, Nature communications, 9 (1): 1825.
GTEx Consortium, (2017) “Landscape of X chromosome inactivation across human tissues”, Nature, 550(7675): 244.
GTEx Consortium, (2017) “Genetic effects on gene expression across human tissues”, Nature, 550(7675): 204.
GTEx Consortium (2017) “Dynamic landscape and regulation of RNA editing in mammals.” Nature, 550(7675): 249.
GTEx Consortium (2017) “Co-expression networks reveal the tissue-specific regulation of transcription and splicing.” Genome Research, 27(11): 1843-1858.
GTEx Consortium (2017) “Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.” Genome research, 27(11): 1859-1871.
Machine Learning and Statistical methods in biomedical data analysis
Ting, B., Wright, F., and Zhou, Y.H.* (2023) "Simultaneous Modeling of Multivariate Heterogeneous Responses & Heteroskedasticity via a Two-Stage Composite Likelihood." Biometrical Journal, accepted.
Sun, Y., Zhou, Y.H.* (2022) "A machine learning pipeline for mortality prediction in the ICU." International Journal of Digital Health, 2(1): 3 doi.org/10.29337/ijdh.44
Ting, B., Wright, F.A., Zhou, Y.H.* (2022) "Fast Multivariate Probit Estimation via a Two-Stage Composite Likelihood." Statistics in Biosciences, doi.org/10.1007/s12561-022-09338-6
Zhou, Y.H.*, Saghapour, E. (2021) "ImputEHR: A visualization tool for imputation and prediction of biomedical data." Frontiers in Genetics, doi.org/10.3389/fgene.2021.691274.
Zhou, Y.H.* (2019) "Set-based differential covariance testing for genomics." Stat DOI:10.1002/sta4.235.
Zhou, Y.H.* (2019) "A note on cyclic shift permutation testing for large eigenvalues ." Stat DOI: 10.1002/sta4.257.
Zhou, Y.H.*, Marron, J.S., Wright, F.A. (2018) “Eigenvalue significance testing for genetic association.” Biometrics, 74 (2):439-337.
Aoshima, M., Shen, D., Shen, H., Yata, K., Zhou, Y.H., Marron, J.S. (2018) “A survey of high dimension low sample size asymptotics”, Australian & New Zealand Journal of Statistics, 60 (1): 4-19.
Zhou, Y.H.*, Marron, J.S., Wright, F.A. (2017) “Computation of ancestry scores with mixed families and unrelated individuals.” Biometrics, 74 (1): 155-164.
Zhou, Y.H.*, Marron, J.S. (2016) “Visualization of robust L1PCA.” Stat, 5 (1), 173-184.
Zhou, Y.H.* (2016) “Pathway analysis for RNA-Seq data using a score-based approach.” Biometrics, 72 (1): 165-74.
Microbiome data analysis
Song, K., and Zhou, Y.H.* (2023) "Leveraging scheme for cross-study microbiome machine learning prediction and feature evaluations." Bioengineering, 10 (2), 231.
Song, K., and Zhou, Y.H.* (2022) "C3NA – correlation and consensus-based cross-taxonomy network analysis for compositional microbial data." BMC Bioinformatics, 23:468.
Song, K., Wright, F.A., Zhou, Y.H.* (2020) "Systematic comparisons for composition profiles, taxonomic levels, and machine learning methods for microbiome-based disease prediction." Frontiers in Molecular Biosciences, doi.org/10.3389/fmob.2020.610845.
Zhou, Y.H.*, and Gallins, P. (2019) "A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction." Frontiers in Genetics 10 : 579.
Hu, T., Zhou, Y.H.* (2018) “A zero-inflated beta-binomial model for microbiome data analysis”, Stat, 10.1002.sta4.185
Zhou, Y.H.*, Brooks, P., and Wang, X. (2017) “A two-stage hidden Markov model design for biomarker detection, with application to microbiome research.” Statistics in Biosciences, 10 (1): 41-58.
Brooks. J.P., Buck, G.A., Chen, G., Edwards, D.J., Fettweis, J.M., Rakitin, A., Satten, G.A., Waks, Z., Wright, M.L., Yanover, C., and Zhou, Y.H. (2017) “Changes in vaginal community state types reflect major shifts in the microbiome.” Microbial Ecology in Health and Disease, 28 (1), 1303265.
Computational Toxicology
Cordova, A., Klaren, W.D., Ford, L.C., Grimm, F.A., Baker, E.S., Zhou, Y.H., Wright, F.A., Rusyn, I. (2023) "Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams." Toxics, 10.3390/toxics11070586
Chen, Z., Jang, S., Kaihatu, J., Zhou, Y.H., Wright, F.A.., Chiu, W., Rusyn, I. (2021) " Potential human health hazard of post-hurricane Harvey sediments in Galveston Bay and Houston Ship Channel: A case study of using in vitro bioactivity data to inform risk management decisions." International Journal of Environmental Research and Publich Health
Luo, Y., Chen, Z., Blanchette, A., Zhou, Y.H., Wright, F.A., Baker, E., Chiu, W., Ruysn, I. (2021) "Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC) - Derived cardiomyocytes." Food and Chemical Toxicology, 149, 111979.
Marvel, S.W., House, J.S., Wheeler, M., Song, K., Zhou, Y.H., Wright, F.A., Chiu, W.A., Rusyn, I., Motsinger-Reif, A., Reif, D.M. (2021) "The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning." Environmental Health Perspectives, 129 (1), 017701.
Chen, Z., Lloyd, D., Zhou, Y.H., Chiu, W., Wright, F.A., Rusyn, I. (2020) "Risk characterization of environmental samples using in vitro bioactivity and polycyclic aromatic hydrocarbon (PAH) concentrations data." Toxicological Sciences, doi.org/10.1093/toxsci/kffa166
Zhou, Y.H., Cichocki, J., Soldatow, V., Scholl, E., Gallins, P., Jima, D., Yoo, H.S., Chiu, W., Wright, F.A., Rusyn, I. (2017) “Comparative dose-response analysis of liver and kidney transcriptomic effects of trichloroethylene and tetrachloroethylene in B6C3F1 mouse.” Toxicological Sciences, 160(1),95-110
Cystic Fibrosis-related collaboration
Zhou, Y.H.*, Gallins, P.J., Pace, R.G., Dang, H., Aksit, M., Blue, E.E., Buckingham, K.J., Collaco, J.M., Faino, A., Gordon, W.W., Hetrick, K.N., Ling, H., Liu, W., Onchiri, F., Pagel, K., Pugh, E.W., Raraigh, K. S., Rosenfeld, M., Sun, Q., Wen, J., Li, Y., Corvol, H., Strug, L., Bamshad, M.J., Blackman, S., Cutting, G.R., Gibson, R.L., O’Neal, W.K., Wright, F.A., Knowles, M.R. (2023) "Genetic modifiers of cystic fibrosis lung disease severity: whole genome analysis of 7,840 patients. " American Journal of Respiratory and Critical Care Medicine (impact factor 30+) doi: 10.1164/rccm.202209-1653OC.
Zhou, Y.H.*, Gallins, P., Pace, R., Dang, H., O’Neal, W., Li, Y., Ling, H., Corvol, H., Strug, L., Bamshad, M. and Gibson, R., (2021). "644: Genetic variants that modify severity of CF lung disease: Update from the CF genome project. " Journal of Cystic Fibrosis, 20, p.S306.
Aksit, M., Ling, H., Pace, R., Raraigh, K., Onchiri, F., Pagel, K., Pugh, E., Faino, A., Stilp, A., Blue, E., Wright, F., Bamshad, M.J., Zhou, Y.H., Gibson, R.L., Knowles, M.R., Cutting, G.R., Blackman, S.M. (2021). "654: Missense variant within SLC26A9 increases risk of meconium ileus but not age at onset of cystic fibrosis–related diabetes." Journal of Cystic Fibrosis, 20, p.S310.
Raraigh, K.S., Aksit, M.A., Hetrick, K., Pace, R.G., Ling, H., O'Neal, W., Blue, E., Zhou, Y.H., Bamshad, M., Blackman, S.M., Gibson, R.L., Knowles, M.R., Cutting, G.R. (2021) "Complete CFTR gene sequencing in 5,058 individuals with Cystic Fibrosis informs variant-specific treatment." Journal of Cystic Fibrosis, S1569-1993 (21) 02113-5.
Rosenfeld, M., Faino, A., Onchiri, F., Aksit, M., Blackman, S., Blue, E., Collaco, J., Gordon, W., Pace, R., Raraigh, K.S., Zhou, Y.H., Cutting, G.R., Knowles, M.R., Bamshad, M.J., Gibson, R.L. (2021) "Comparing encounter-based and annualized chronic pseudomonas infection definitions in cystic fibrosis." Journal of Cystic Fibrosis, doi.org/10.1016/j.jcf.2021.07.020.
Aksit, M.A., Ling, H., Pace, R.G., Mikeasky, R., Raraigh, K.S., Bamshad, M., Gibson, R., Zhou, Y.H., Knowles, M., Cutting, G.R., Blackman, S.M. (2020) “Genome-wide association detects new genetic modifiers of meconium ileus and suggests a pleiotropic modifier of meconium ileus, CF-related diabetes, and type 2 diabetes.” In Pediatric Pulmonology Vol. 55, pp. S114-S114.
Aksit, M.A., Hetrick, K., Ling, H., Raraigh, K.S., Pace, R.G., Buckingham, K., Zhou, Y.H., Blue, E., Bamshad, M., Knowles, M., Blackman, S.M. (2020) “Whole genome sequencing of individuals with cystic fibrosis reveals unexpected levels of homozygosity encompassing the entire CFTR gene.” In Pediatric Pulmonology Vol. 55, pp. S59-S60.
Raraigh, K.S., Aksit, M.A., Hetrick, K., Pace, R.G., Bamshad, M., Zhou, Y.H., Blackman, S.M., Gibson, R., Knowles, M., Cutting, G.R. (2020) “The complexity of CFTR: Findings from whole genome sequencing in 5,058 individuals with CF.” In Pediatric Pulmonology Vol. 55, pp. S118-S118.
Ling, H., Sun, Q., Gordon, W.W., Aksit, M.A., Buckingham, K., Pace, R.G., Raraigh, K.S., Zhang, P., Hetrick, K., Faino, A., Onchiri, F.M., Gallins, P, Liu, W., Xie, M., Li, Y., Blue, E., Zhou, Y.H., Pugh, E, Wright, F.A., Gibson, R, Blackman, S.M., Bamshad, M., Knowles, M, Cutting, G.R.(2020) “The cystic fibrosis genome project: A multi-phenotype whole genome sequencing resource.” In Pediatric Pulmonology Vol. 55, pp. S114-S114.
Zhou, Y.H.*, Gallins, P., Pace, R.G., Dang, H., O'Neal, W., Li, Y., Ling, H., Bamshad, M., Gibson, R., Cutting, G.R., Blackman, S.M. (2020) “Genetic modifiers of cystic fibrosis lung disease: initial results from the cystic fibrosis genome project.” In Pediatric Pulmonology Vol. 55, pp. S117-S117.
Sun, Q., Liu, W., Pace, R.G., Dang, H., Gallins, P., Blue, E., Ling, H., Bamshad, M., Gibson, R., Pugh, E., Blackman, S.M., Cutting, G.R., Zhou, Y.H., Wright, F.A., Knowles, M., Li, Y. (2020) “Leveraging similar to 200,000 haplotypes to perform genotype imputation for the Cystic Fibrosis Genome Project.” In Pediatric Pulmonology Vol. 55, pp. S116-S117.
Polineni, D., Dang, H., Gallins, P., Jones, L., Pace, R.G., Stonebraker, J.R., Corvol, H., Cutting, G.R., Drumm, M.L., Strug, L.J., Boyle, M.P., Durie, P.R., Chmiel, J.F., Zhou, Y.H., Zou, F., Wright, F.A., O’Neal, W., Knowles, M. (2017) "A31 Mechanisms in Cystic Fibrosis and other bronchiectatic diseases: Integrative Transcriptomic And Genomic Analysis Reveals Gene Networks Associated With Cystic Fibrosis Lung Disease Severity." American Journal of Respiratory and Critical Care Medicine 195.