Publications

* corresponding author; + students supervised

2024

Wang, Z., Fang, Y., Liu, Z., Hao N., Zhang H.H., Sun X., Que J., and Ding H. (2024) Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection. Nature Communications 15, 7148 (2024). https://doi.org/10.1038/s41467-024-51639-5
Tang, Y., Zhang, Y., Wang, Y., Zhang, J., and Sun, X. (2024). Zero-inflated Smoothing Spline (ZISS) Models for Individual-level Single-cell Temporal Data. arXiv preprint arXiv:2401.15309.

2023

Zhang M+, Liu Y, Parker J+, An L, and Sun X* (2023) Flexible Analysis of Spatial Transcriptomics Data (FAST): A Deconvolution Approach.
Liu S+, Roemer FW., Ge Y, Bedrick, EJ, Li ZM, Guermazi A, Sharma L, Eaton C, Hochberg MC, Hunter DJ, Nevitt MC, Wirth W, Kwoh CK, and Sun X* (2023) Comparison of evaluation metrics of deep learning for imbalanced imaging data in osteoarthritis studies. Osteoarthritis and Cartilage. Accepted.
Leeper BA, Kern KB, Liu S+, and Sun X, 2023. Electrocardiographic characteristics fail to predict acute coronary occlusions in out-of-hospital cardiac-arrest patients without ST-segment elevation. Resuscitation. Accepted.
Lopez-Pentecost M, Garcia DO, Sun X, Thomson CA, Chow HS, and Martinez JA, 2023. Differences in metabolomic profiles by birthplace in Mexican-origin Hispanic men who participated in a weight loss lifestyle intervention. American Journal of Men's Health.
Jin H, Sun X*, and Du P, 2023. Optimal function-on-function regression with interaction between functional predictors. Statistica Sinica. 33, 1-22.

2022

Steiner H., Carrion K.C., Giles J., Lima A.R., Yee K., Sun X., Cavallari L., Perera M., Duconge J., and Karnes J. (2022) Local ancestry-informed candidate pathway analysis of warfarin stable dose in Latino populations. Clinical Pharmacology & Therapeutics.
Godfrey, T.M., Villavicencio, E.A., Barra, K., Sanderson, P.R., Shea, K., Sun, X., and Garcia, D.O. (2022) Advancing liver cancer prevention for American Indian populations in Arizona: An integrative review. Int. J. Environ. Res. Public Health. 19, 3268.
Liu, Y., Sun, X., Zhong, W., and Li, B. (2022) B-scaling: a novel nonparametric data fusion method. The Annals of Applied Statistics. 16(3), 1292-1312.

2021

Zhong, W., Liu, Y. and Zeng, P., 2021. A model-free variable screening method based on leverage score. Journal of the American Statistical Association, pp.1-12.
Zhang, M., Liu, Y., Zhou, H., Watkins, J. and Zhou, J., 2021. A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data. BMC bioinformatics, 22(1), pp.1-13.
Sun, X., Zhong, W., and Ma, P. (2021) An asympirical smoothing parameters selection approach for smoothing spline ANOVA models in large samples. Biometrika. 108 (1), 149-166.
Ellingson KD, Gerald JK, Sun X, et al. (2021) Incidence of SARS-CoV-2 Infection Among Health Care Personnel, First Responders, and Other Essential Workers During a Prevaccination COVID-19 Surge in Arizona. JAMA Health Forum. 2(10):e213318.
Steiner HE, Giles JB, Patterson HK, Feng J, Rouby NE, Claudio K, Marcatto LR, Tavares LC, Galvez JM, Calderon-Ospina CA, Sun X, Hutz MH, Scott S, Cavallari LH, Fonseca DJ, Duconge J, Botton MR, Santos PCJL, Karnes JH. (2021) Machine Learning for Prediction of Stable Warfarin Dose in US Latinos and Latin Americans. Frontiers in Pharmacology. 12:2735.
Thompson MG, Burgess JL, Naleway AL, Tyner HL, Yoon SK, Meece J, Olsho LEW, Caban-Martinez AJ, Fowlkes A, Lutrick K, Kuntz JL, Dunnigan K, Odean MJ, Hegmann KT, Stefanski ES, Edwards LJ, Schaefer-Solle N, Grant L, Ellingson KD, Groom HC, Zunie T, These MS, Ivacic L, Wesley MG, Mayo Lamberte J, Sun X, Smith ME, Phillips AL, Groover KD, Yoo YM, Gerald J, Brown RT, Herring MK, Joseph G, Beitel S, Morrill TC, Mak J, Rivers P, Harris K, Hunt DR, Arvay ML, Kutty P, Fry AM, Gaglani M. (2021) Prevention and Attenuation of Covid-19 with the BNT162b2 and mRNA-1273 Vaccines. New England Journal of Medicine. 385:320-329.
Thompson MG, Burgess JL, Naleway AL, Tyner HL, Yoon SK, Meece J, Olsho LEW, Caban-Martinez AJ, Fowlkes A, Lutrick K, Kuntz JL, Dunnigan K, Odean MJ, Hegmann KT, Stefanski ES, Edwards LJ, Schaefer-Solle N, Grant L, Ellingson KD, Groom HC, Zunie T, These MS, Ivacic L, Wesley MG, Mayo Lamberte J, Sun X, Smith ME, Phillips AL, Groover KD, Yoo YM, Gerald J, Brown RT, Herring MK, Joseph G, Beitel S, Morrill TC, Mak J, Rivers P, Harris K, Hunt DR, Arvay ML, Kutty P, Fry AM, Gaglani M. (2021) Interim Estimates of Vaccine Effectiveness of BNT 162b2 and mRNA-1273 COVID-19 Vaccines in Preventing SARS-CoV-2 Infection Among Health Care Personnel, First Responders, and Other Essential and Frontline Workers – Eight U.S. Locations, December 2020—March 2021. MMWR. Vol. 70. PMID: 33793460
Lutrick K, Ellingson KD, Baccam Z, Rivers P, Beigel S, Parker J, Sun X, Gerald J, Komatsu K, Kim E, LaFleur B, Grant L, Yoo YM, Kumar A, Mayo Lamberte J, Cowling B, Cobey S, Thornburg NJ, Meece J, Kutty PK, Nikolich J, Thompson MG, Burgess JL. (2021) Protocol for the Arizona Healthcare, Emergency Response, and Other Essential Workers Study (AZ HEROES). JMIR Research Protocols. 10(6):e28925.

2020

Sun, X., Liu, Y., and An, L. (2020) Ensemble dimensionality reduction and feature gene extraction for single-cell RNA-seq data. Nature Communications. 11, 5853. GitHub.
Jin, H., Sun, X.*, and Xu, L. (2020) Decentralized expectation maximization algorithm. 20th International Conference on Algorithms and Architectures for Parallel Processing.

BEFORE 2020

Sun, X., Du, P., Wang, X., and Ma, P. (2018) Optimal penalized function-on-function regression under a reproducing kernel Hilbert space framework. Journal of the American Statistical Association. 113(524),1601-1611.
Liu, Y., Ma, P., Cassidy, P.A., Carmer, R., Zhang, G., Venkatraman, P., Brown, S.A., Pang, C.P., Zhong, W., Zhang, M. and Leung, Y.F., 2017. Statistical Analysis of Zebrafish Locomotor Behaviour by Generalized Linear Mixed Models. Scientific Reports, 7.
Sun, X., Dalpiaz, D., Wu, D., Liu, J. S., Zhong, W., and Ma, P. (2016) Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model. BMC Bioinformatics.17,324.
Zhang, L., Xiang, L., Liu, Y., Venkatraman, P., Chong, L., Cho, J., Bonilla, S., Jin, Z.B., Pang, C.P., Ko, K.M. and Ma, P., 2016. A Naturally-Derived Compound Schisandrin B Enhanced Light Sensation in the pde6c Zebrafish Model of Retinal Degeneration. PLOS ONE, 11(3), p.e0149663.
Liu, Y., Carmer, R., Zhang, G., Venkatraman, P., Brown, S.A., Pang, C.P., Zhang, M., Ma, P. and Leung, Y.F., 2015. Statistical Analysis of Zebrafish Locomotor Response. PLOS ONE, 10(10), p.e0139521.
Ma, P., and Sun, X. (2015) Leveraging for big data regression. Wiley Interdisciplinary Reviews: Computational Statistics. 7(1),70–76.
Kim, D.-H., Xiao, Z., Kwon, S., Sun, X., Ryerson, D., Tkac, D., Ma, P., Wu, S.-Y., Chiang, C.-M., Zhou, E., et al. (2015) A dysregulated acetyl/SUMO switch of FXR promotes hepatic inflammation in obesity. The EMBO Journal, 34(2). 184–199.
Ji, L., Sasaki, T., Sun, X., Ma, P., Lewis, Z. A., and Schmitz, R. J. (2014) Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics. 5(341).
Seok, S., Fu, T., Choi, S.-E., Li, Y., Zhu, R., Kumar, S., Sun, X., Yoon, G., Kang, Y., Zhong, W., et al. (2014) Transcriptional regulation of autophagy by an FXR-CREB axis. Nature. 516(7529),108–111.

Book Chapters

Parker, J.+, Zhang, Y.+, LaFleur, B., and Sun, X.* (2022) Computationally efficient Kalman filter approaches for fitting smoothing splines. InTechOpen
Liu, Y., Xing, X. and Zhong, W., 2018. Sufficient Dimension Reduction for Tensor Data, in Handbook of Big Data Analytics. Springer.
Zhang, J., Jin, H., Wang, Y., Sun, X., Ma, P., and Zhong, W. (2018) Smoothing spline ANOVA models and their applications in complex and massive datasets. InTechOpen.

Abstracts

Liu, S.+, Sun, X.*, Roemer, F., Guermazi, A., Kwoh C K. (2022) Comparison of various metrics for evaluating the performance of deep learning binary classification, particularly when underlying imaging data are imbalanced. International Workshop on Osteoarthritis Imaging.
Liu, S.+, Sun, X.*, Roemer, F., Ashbeck, L E., Bedrick, J E., Li, ZM., Guermazi, A., Kwoh C K. (2021) Automatic Detection of Bone Marrow Lesions from Knee MRI Data from the OAI Study. International Workshop on Osteoarthritis Imaging.
Liu, S.+, Sun, X.*, Roemer, F., Ashbeck, L E., Bedrick, J E., Li, ZM., Guermazi, A., Kwoh C K. (2021) Automatic Detection of Bone Marrow Lesions from Knee MRI Data from the OAI Study. American College of Rheumatology (ACR) Convergence.
Kwoh, C K., Ashbeck, L E., Bedrick, J E., Sun, X., Duryea, J. (2021) Variance of Joint Space Width Across the Joint on Knee Radiographs: A Novel Measure of Structural Progression. American College of Rheumatology (ACR) Convergence.

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