Publications
Published
Lu, J., Satten, G.A., Meyer, K.A., Launer, L.J., Ling, W., Zhao, N. (2026). Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT). Microbiome.
Pareek, E., Pershad, Y., Zhao, K., Uddin, M.M., Xue, L., Vlasschaert, C., Mack, T.M., Haessler, J., Collins, J.M., Glick, E., Glaser, V., Heise, R., Ling, W., Haring, B., Shadyab, A., Beydoun, H., Wallace, R., Jaiswal, S., Manson, J.E., Natarajan, P., Honigberg, M.C., Kooperberg, C., Whitsel, E.A., Kitzman, J.O., Bick, A.G., Reiner, A.R., Desai, P. (2026). Metformin does not significantly alter longitudinal dynamics of clonal hematopoiesis. Clinical Cancer Research.
Samorodnitsky, S., Campbell, K.M., Little, A., Ling, W., Zhao, N., Chen, Y.C., Wu, M.C. (2026). Detecting clinically relevant topological structures in multiplexed spatial proteomics imaging using TopKAT. Patterns, 7(1).
Little, A., Ling, W., Plantinga, A.M., Samorodnitsky, S., Wu, M.C., Zhao, N. (2026). Statistical analysis of -omics data. In: Crowley, J., Hoering, A., Othus, M. (eds): Handbook of Statistics in Clinical Oncology, 4th Ed., 443-470. Chapman & Hall/CRC Press, Boca Raton, FL.
Liu, C., Han, H., Qi, Y., Ling, W. (2025). A knowledge-guided large language model framework for microbiome-based disease diagnosis. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
Desai, P., Li, Z., Li, Y., Mencia-Trinchant, N., Gorski, K., Ling, W., Ritchie, E., Samuel, M., Canaani, J., Bar-Natan, M., Elemento, O. (2025). Characterization of antecedent clonal hematopoiesis (CH) mutations in lymphoid and plasma cell neoplasms. Blood, 146, 1399.
Selbach, F., Li, C., Dong, H., Ling, W., Dadhania, D. M., Lee, J. R. (2025). Negative impact of antibiotics on fecal short chain fatty acid levels: implications for gut health in kidney transplant recipients. American Journal of Transplantation, 25(8), S913-S914.
Wang, Z., Ling, W., Wang, T. (2025). A semiparametric quantile regression rank score test for zero-inflated data. Biometrics, 81(2), ujaf050.
Han, H., Li, Y., Qi, Y., Mangiola, S., Ling, W. (2025). Deciphering gut microbiome in colorectal cancer via robust learning methods. Genes, 16(4), 452.
* Guo, B., * Ling, W., Kwon, S.H., Panwar, P., # Ghazanfar, S., # Martinowich, K., # Hicks, S.C. (2025). Integrating spatially-resolved transcriptomics data across tissues and individuals: challenges and opportunities. Small Methods, 2401194. [ * Joint First Author; # Joint Senior/Corresponding Author ]
Little, A., Zhao, N., Mikhaylova, A., Zhang, A., Ling, W., Curran, J., Blangero, J., O’Connell, J.R., Xu, H., Thornton, T., Wu, M.C. (2025). General kernel machine methods for multi-omics integration and genome-wide association testing with related individuals. Genetic Epidemiology, 49(1), e22610.
Li, S., Li, R., Lee, J.R., # Zhao, N., # Ling, W. (2025). ZINQ-L: a zero-inflated quantile approach for differential abundance analysis of longitudinal microbiome data. Frontiers in Genetics, 15, 1494401. [ # Joint Senior/Corresponding Author ]
Little, A., Deek, R.A., Zhang, A., Zhao, N., Ling, W., Wu, M.C. (2024). Enhanced visualization of microbiome data in repeated measures designs. Frontiers in Genetics, 15, 1480972.
Li, Y., Lee, T., Marin, K., Hua, X., Srinivasan, S., Fredricks, D.N., Lee, J.R., Ling, W. (2024). SurvBal: compositional microbiome balances for survival outcomes. Bioinformatics, 40(10), btae612.
* Dong, H., * Li, R., Zhao, N., Dadhania, D.M., Suthanthiran, M., # Lee, J.R., # Ling, W. (2024). Antibiotic subclasses differentially perturb the gut microbiota in kidney transplant recipients. Frontiers in Transplantation, 3, 1400067. [ * Joint First Author; # Joint Senior/Corresponding Author ]
* Zhang, Y., * Luth, E.A., Phongtankuel, V., Ling, W., Zhang, M., Shao, H. (2023). Factors associated with preventable hospitalizations after hospice live discharge among medicare patients with ADRD. Journal of the American Geriatrics Society (JAGS), 71(11), 3631-3635. [ * Joint First Author ]
Liu, H., Ling, W., Hua, X., Moon JY, Williams-Nguyen, J.S., Zhan, X., Plantinga, A.M., Zhao, N., Zhang, A., Knight, R., Qi, Q., Burk, R.D., Kaplan, R.C., Wu, M.C. (2023). Kernel-based genetic association analysis for microbiome phenotype identifies host genetic drivers of beta-diversity. Microbiome, 11(1), 1-19.
Song, H., Ling, W., Zhao, N., Plantinga, A.M., Broedlow, C.A., Klatt, N.R., Hensley-McBain, T., Wu, M.C. (2023). Accommodating multiple potential normalizations in microbiome associations studies. BMC Bioinformatics, 24, 22.
Ling, W., Lu, J., Zhao, N., Plantinga, A.M., Lulla, A., Fu, W., Zhang, A., Liu, H., Song, H., Li, Z., Chen, J., Randolph, T., Koay, WL.A., White, J.R., Launer, L.J., Fodor, A.A., Meyer, K.A., Wu, M.C. (2022). Batch effects removal for microbiome data via conditional quantile regression. Nature Communications, 13, 5418.
Ling, W., Cheng, B., Wei, Y., Willey, J.Z., Cheung, YK. (2022). Statistical inference in quantile regression for zero-inflated outcomes. Statistica Sinica, 32, 1411-1433.
Wang, T., Ling, W., Wu, M.C., Plantinga, A.M., Zhan, X. (2022). Testing microbiome association using integrated quantile regression models. Bioinformatics, 38(2), 419-425.
Ling, W., Zhang, W., Cheng, B., Wei, Y. (2021). Zero-inflated quantile rank-score based test (ZIQRank) with application to scRNA-seq differential gene expression analysis. Annals of Applied Statistics, 15(4), 1673-1696.
Ling, W., Qi, Y., Hua, X., Wu, M.C. (2021). Deep ensemble learning over the microbial phylogenetic tree (DeepEn-Phy). 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 470-477.
Hudson, P.L., Ling, W., Wu, M.C., Hayward, M.R., Mitchell, A.J., Larson, J., Guthrie, K.A., Reed, S.D., Kwon, D.S., Mitchell, C.M. (2021). Comparison of the vaginal microbiota in postmenopausal Black and White women. The Journal of Infectious Diseases, 224(11), 1945-1949.
Ling, W., Zhao, N., Plantinga, A.M., Launer, L.J., Fodor, A.A., Meyer, K.A., Wu, M.C. (2021). Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ). Microbiome, 9(1), 1-19.
Cheung, K., Ling, W., Karr, C.J., Weingardt, K., Schueller, S.M., Mohr, D.C. (2018). Evaluation of a recommender app for apps for the treatment of depression and anxiety: an analysis of longitudinal user engagement. Journal of the American Medical Informatics Association (JAMIA), 25(8), 955-962.
Lee, C.C., Ling, W., Wu, N., Xu, M. (2012). A note to Zhi-Wei Sun's supercongruences on binomial coefficients. Journal of Combinatorics and Number Theory, 4(3), 137.
Under review and in revision
Fu, C., Lu, J., Zhao, N., Ling, W. (2026+). MOSAIC: a pipeline for microbiome studies analytical integration and correction. Genome Biology, Under review.
Zhang, A., Ling, W., Little, A., Williams-Nguyen, J.S., Moon, J.Y., Burk, R.D., Knight, R., Wang, D.D., Qi, Q., Kaplan, R., Zhao, N., Wu, M.C. (2026+). Weighted variance component test for the integrative multi-omics analysis of microbiome data. mSystems, In revision
Patents
Tang, Q., Ling, W., Qi, Y. (2023). Methods to estimate effectiveness of a medical treatment. US Patent, US 11694773.