Amanda Yi-Hui Zhou

Computational Framework for Therapeutic Target Discovery via Perturbation Simulation: Application to Cystic Fibrosis Airway Disease

Sun, G., & Zhou, Y.-H. (2026, March 3).

Hierarchical Multi-Omics Trajectory Prediction for Fecal Microbiota Transplantation: A Novel Machine Learning Framework for Small-Sample Longitudinal Multi-Omics Integration

Zhou, Y.-H., & Sun, G. (2026, February 23).

Computation of Ancestry Scores with Mixed Families and Unrelated Individuals

Marron, J. S., & Wright, F. A. (2025, October 25). UNC Libraries.

Detecting Algorithmic Bias in ICU Clinical Decision: A Doubly-Robust Framework for Auditing Treatment Recommendation Disparities

Zhou, Y.-H., & Sun, G. (2025, November 17). BioRxiv (Cold Spring Harbor Laboratory).

Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients.

Zhou, Y.-H., Gallins, P. J., Pace, R. G., Dang, H., Aksit, M. A., Blue, E. E., … Knowles, M. R. (2025, October 22). UNC Libraries.

HAP-SAMPLE2: data-based resampling for association studies with admixture

Sun, G., Ting, B. W., Wright, F. A., & Zhou, Y.-H. (2025, June 1). (J. Kelso, Ed.). Bioinformatics.

Identifying novel therapeutic targets in cystic fibrosis through advanced single-cell transcriptomics analysis

Sun, G., & Zhou, Y.-H. (2025, February 8). Computers in Biology and Medicine.

MagicalRsq: Machine-learning-based genotype imputation quality calibration

Yang, Y., Jiang, M.-Z., Chen, J., Liu, W., Wen, J., Raffield, L. M., … Li, Y. (2025, May 1). UNC Libraries.

Organophosphate Flame Retardants Disrupt Autism-Relevant Gene Networks Across Development: A Cross-Species Multi-Omics Study

Zhou, Y.-H., & Sun, G. (2025, September 3). Environmental Research.

Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy

Ford, L. C., Lin, H.-C., Zhou, Y.-H., Wright, F. A., Gombar, V. K., Sedykh, A., … Rusyn, I. (2024, September 2). Human Genomics, Vol. 18.

Control of false discoveries in grouped hypothesis testing for eQTL data

Rudra, P., Zhou, Y.-H., Nobel, A., & Wright, F. A. (2024, April 11). BMC Bioinformatics, Vol. 25.

Control of false discoveries in grouped hypothesis testing for eQTL data

Rudra, P., Zhou, Y.-H., Nobel, A., & Wright, F. A. (2024, April 11). Springer Nature.

Genetic variation in severe cystic fibrosis liver disease is associated with novel mechanisms for disease pathogenesis

Stonebraker, J. R., Pace, R. G., Gallins, P. J., Dang, H., Aksit, M. A., Faino, A. V., … Knowles, M. R. (2024, March 27). Hepatology, Vol. 3.

Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types

Ford, L. C., Lin, H.-C., Tsai, H.-H. D., Zhou, Y.-H., Wright, F. A., Sedykh, A., … Rusyn, I. (2024, February 27). Toxicology, Vol. 503.

Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits

Broadaway, K. A., Brotman, S. M., Rosen, J. D., Currin, K. W., Alkhawaja, A. A., Etheridge, A. S., … Mohlke, K. L. (2024, August 22). The American Journal of Human Genetics, Vol. 111.

Predicting Microbiome Growth Dynamics under Environmental Perturbations

Sun, G., & Zhou, Y.-H. (2024, June 10). Applied Microbiology.

AI in healthcare: navigating opportunities and challenges in digital communication

Sun, G., & Zhou, Y.-H. (2023, December 19). Frontiers in Digital Health, Vol. 5.

Association of Pseudomonas aeruginosa infection stage with lung function trajectory in children with cystic fibrosis

Rosenfeld, M., Faino, A. V., Qu, P., Onchiri, F. M., Blue, E. E., Collaco, J. M., … Gibson, R. L. (2023, May 20). Journal of Cystic Fibrosis, Vol. 22, pp. 857–863.

Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients

Zhou, Y.-H., Gallins, P. J., Pace, R. G., Dang, H., Aksit, M. A., Blue, E. E., … Knowles, M. R. (2023, March 15). American Journal of Respiratory and Critical Care Medicine, Vol. 207, pp. 1324–1333.

Integrative Chemical–Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams

Cordova, A. C., Klaren, W. D., Ford, L. C., Grimm, F. A., Baker, E. S., Zhou, Y.-H., … Rusyn, I. (2023, July 5). Toxics, Vol. 11.

Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations

Song, K., & Zhou, Y.-H. (2023, February 8). Bioengineering, Vol. 10.

Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two‐stage composite likelihood

Ting, B. W., Wright, F. A., & Zhou, Y. H. (2023, May 22). Biometrical Journal.

A Double Penalty Model for Ensemble Learning

Wang, W., & Zhou, Y.-H. (2022, November 30). Mathematics, Vol. 10.

A Machine Learning Pipeline for Mortality Prediction in the ICU

Sun, Y., & Zhou, Y.-H. (2022, January 1). International Journal of Digital Health, Vol. 2.

A Population-Based Human In Vitro Approach to Quantify Inter-Individual Variability in Responses to Chemical Mixtures

Ford, L. C., Jang, S., Chen, Z., Zhou, Y.-H., Gallins, P. J., Wright, F. A., … Rusyn, I. (2022, August 1). Toxics, Vol. 8.

A resource for integrated genomic analysis of the human liver

Zhou, Y.-H., Gallins, P. J., Etheridge, A. S., Jima, D., Scholl, E., Wright, F. A., & Innocenti, F. (2022, September 7). Scientific Reports, Vol. 9.

Accounting for population structure in genetic studies of cystic fibrosis

Kingston, H., Stilp, A. M., Gordon, W., Broome, J., Gogarten, S. M., Ling, H., … Blue, E. E. (2022, May 12). Human Genetics and Genomics Advances, Vol. 7.

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data

Song, K., & Zhou, Y.-H. (2022, November 8). BMC Bioinformatics, Vol. 11.

Fast Multivariate Probit Estimation via a Two-Stage Composite Likelihood

Ting, B., Wright, F., & Zhou, Y.-H. (2022, February 15). Statistics in Biosciences, Vol. 2.

Improve the Colorectal Cancer Diagnosis Using Gut Microbiome Data

Zhou, Y.-H., & Sun, G. (2022, August 12). Frontiers in Molecular Biosciences, Vol. 8.

Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients

Sun, Q., Liu, W., Rosen, J. D., Huang, L., Pace, R. G., Dang, H., … Li, Y. (2022, January 11). Human Genetics and Genomics Advances, Vol. 4.

Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients

Sun, Q., Liu, W., Rosen, J. D., Huang, L., Pace, R. G., Dang, H., … Project, C. F. G. (2022, January 11). Elsevier.

MagicalRsq: Machine-learning-based genotype imputation quality calibration

Sun, Q., Yang, Y., Rosen, J. D., Jiang, M.-Z., Chen, J., Liu, W., … Li, Y. (2022, October 4). The American Journal of Human Genetics, Vol. 109, pp. 1986–1997.

Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis

Aksit, M. A., Ling, H., Pace, R. G., Raraigh, K. S., Onchiri, F., Faino, A. V., … Zhou, Y.-H. (2022, October 1). The American Journal of Human Genetics, Vol. 10.

Comparing encounter-based and annualized chronic pseudomonas infection definitions in cystic fibrosis

Rosenfeld, M., Faino, A. V., Onchiri, F., Aksit, M. A., Blackman, S. M., Blue, E. E., … Gibson, R. L. (2021, August 12). Journal of Cystic Fibrosis, Vol. 1.

Complete CFTR gene sequencing in 5,058 individuals with cystic fibrosis informs variant-specific treatment

Raraigh, K. S., Aksit, M. A., Hetrick, K., Pace, R. G., Ling, H., O'Neal, W., … Cutting, G. R. (2021, November 12). Journal of Cystic Fibrosis, Vol. 1.

Eigenvector-based sparse canonical correlation analysis: Fast computation for estimation of multiple canonical vectors

Wang, W., & Zhou, Y.-H. (2021, June 18). Journal of Multivariate Analysis, Vol. 185, p. 104781.

ImputEHR: A Visualization Tool of Imputation for the Prediction of Biomedical Data

Zhou, Y.-H., & Saghapour, E. (2021, July 2). Frontiers in Genetics, Vol. 7.

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

Chen, Z., Jang, S., Kaihatu, J. M., Zhou, Y.-H., Wright, F. A., Chiu, W. A., & Rusyn, I. (2021, December 19). International Journal of Environmental Research and Public Health, Vol. 12.

Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes

Luo, Y.-S., Chen, Z., Blanchette, A. D., Zhou, Y.-H., Wright, F. A., Baker, E. S., … Rusyn, I. (2021, January 13). Food and Chemical Toxicology, Vol. 149.

The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning

Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y.-H., Wright, F. A., … Reif, D. M. (2021, January 1). Environmental Health Perspectives, Vol. 129, pp. 017701–017701-017701–017703.

Exploring the Limits of Combined Image/'omics Analysis for Non-cancer Histological Phenotypes

Gallins, P., Saghapour, E., & Zhou, Y.-H. (2020, October 23). Frontiers in Genetics, Vol. 11.

Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction

Song, K., Wright, F. A., & Zhou, Y.-H. (2020, December 16). Frontiers in Molecular Biosciences, Vol. 7.

A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex‐Biased Phenotypes

Etheridge, A. S., Gallins, P. J., Jima, D., Broadaway, K. A., Ratain, M. J., Schuetz, E., … Innocenti, F. (2019, December 23). Clinical Pharmacology & Therapeutics.

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

Zhou, Y.-H., & Gallins, P. (2019, June 25). Frontiers in Genetics, Vol. 10.

A note on cyclic shift permutation testing for large eigenvalues

Zhou, Y. H. (2019, January 1). Stat, Vol. 8.

Marker-Trait Complete Analysis

Zhou, Y.-H., Gallins, P., & Wright, F. (2019, November 9). (Vol. 11). Vol. 11.

Set‐based differential covariance testing for genomics

Zhou, Y. H. (2019, January 1). Stat, Vol. 8.

A common allele in FGF21 associated with sugar intake is associated with body shape, lower total body-fat percentage, and higher blood pressure

Cell Reports, 23(2), 327–336.

A common allele in FGF21 associated with sugar intake is associated with body shape, lower total body-fat percentage, and higher blood pressure

Cell Reports, 23(2), 327–336.

A survey of high dimension low sample size asymptotics

Aoshima, M., Shen, D., Shen, H., Yata, K., Zhou, Y. H., & Marron, J. S. (2018, March 1). Australian & New Zealand Journal of Statistics, Vol. 60, pp. 4–19.

A zero-inflated beta-binomial model for microbiome data analysis

Stat, 7(1).

A zero‐inflated beta‐binomial model for microbiome data analysis

Hu, T., Gallins, P., & Zhou, Y. H. (2018, January 1). Stat, Vol. 7, p. e185.

Airway mucosal host defense is key to genomic regulation of cystic fibrosis lung disease severity

American Journal of Respiratory and Critical Care Medicine, 197(1), 79–93.

Airway mucosal host defense is key to genomic regulation of cystic fibrosis lung disease severity

American Journal of Respiratory and Critical Care Medicine, 197(1), 79–93.

Computation of ancestry scores with mixed families and unrelated individuals

Biometrics, 74(1), 155–164.

A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics

Frontiers in Genetics, 8, 168.

A Two-Stage Hidden Markov Model Design for Biomarker Detection, with Application to Microbiome Research

Statistics in Biosciences, 10(1), 41–58.

A procedure to detect general association based on concentration of ranks

Stat, 6(1), 88–101.

Changes in vaginal community state types reflect major shifts in the microbiome

Microbial Ecology in Health and Disease, 28(1), 1303265.

Changes in vaginal community state types reflect major shifts in the microbiome

Microbial Ecology in Health and Disease, 28(1), 1303265.

Computation of Ancestry Scores with Mixed Families and Unrelated Individuals

Zhou, Y.-H., Marron, J. S., & Wright, F. A. (2017, April 27). Biometrics, Vol. 74, pp. 155–164.

Dynamic landscape and regulation of RNA editing in mammals

Nature, 550(7675), 249–254.

Editor’s Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse

Zhou, Y.-H., Cichocki, J. A., Soldatow, V. Y., Scholl, E. H., Gallins, P. J., Jima, D., … Rusyn, I. (2017, August 11). Toxicological Sciences.

Editor’s Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse

Toxicological Sciences, 160(1), 95–110.

Eigenvalue Significance Testing for Genetic Association

Zhou, Y.-H., Marron, J. S., & Wright, F. A. (2017, August 29). Biometrics.

Estimation of cis-eQTL Effect Sizes Using a Log of Linear Model

Palowitch, J., Shabalin, A., Zhou, Y.-H., Nobel, A. B., & Wright, F. A. (2017, October 26). Biometrics, Vol. 74, pp. 616–625.

Genetic effects on gene expression across human tissues

Nature, 550(7675), 204–213.

The impact of rare variation on gene expression across tissues

Nature, 550(7675), 239–243.

Estimation of interpretable eQTL effect sizes using a log of linear model

ArXiv Preprint ArXiv:1605.08799.

Genomic characterization of metformin hepatic response

PLoS Genetics, 12(11), e1006449.

Homologous recombination and translesion DNA synthesis play critical roles on tolerating DNA damage caused by trace levels of hexavalent chromium

PLoS One, 11(12).

Homologous recombination and translesion DNA synthesis play critical roles on tolerating DNA damage caused by trace levels of hexavalent chromium

PloS One, 11(12), e0167503.

Pathway analysis for RNA-Seq data using a score-based approach

Biometrics, 72(1), 165–174.

Poster: risk-based attack surface approximation

Symposium and Bootcamp on the Science of Security, 121–123.

The projack: a resampling approach to correct for ranking bias in high-throughput studies

Biostatistics (Oxford, England), 17(1), 54–64.

Visualization of robust L1PCA

Stat, 5(1), 173–184.

Effect of predicted protein-truncating genetic variants on the human transcriptome

Science, 348(6235), 666–669.

Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci

Human Molecular Genetics, 24(15), 4464–4479.

Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci

Human Molecular Genetics, 24(15), 4464–4479.

Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes

The American Journal of Human Genetics, 96(2), 318–328.

Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes

The American Journal of Human Genetics, 96(2), 318–328.

Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis

Nature Communications, 6(1).

Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis

Nature Communications, 6.

Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis

Nature Communications, 6, 8382.

High dimension low sample size asymptotics of robust PCA

Zhou, Y.-H., & Marron, J. S. (2015, January 1). Electronic Journal of Statistics, Vol. 9, pp. 204–218.

High dimension low sample size asymptotics of robust PCA

Electronic Journal of Statistics, 9(1), 204–218.

Hypothesis testing at the extremes: fast and robust association for high-throughput data

Zhou, Y.-H., & Wright, F. A. (2015, March 18). Biostatistics.

Hypothesis testing at the extremes: fast and robust association for high-throughput data

Biostatistics, 16(3), 611–625.

Identification of Novel Gene Targets and Putative Regulators of Arsenic-Associated DNA Methylation in Human Urothelial Cells and Bladder Cancer

Chemical Research in Toxicology, 28(6), 1144–1155.