Research

Publications

Invited book chapters

  1. Cui, Y.H., G.X. Li, S.Y. Li and R.L. Wu. (2010) Designs for Linkage Analysis and Association Studies of Complex Diseases. In: Statistical Methods in Molecular Biology (Eds.: H. Bang, X.K. Zhou, H.L. Van Epps and M. Mazumdar) Humana Press.

Peer-referred journal articles (*: corresponding author)

  1. Xue Wang, Vivekananda Sarangi, Daniel P. Wickland, Shaoyu Li, Duan Chen, E. Aubrey Thompson, Garrett Jenkinson, Yan W. Asmann, Identification of gene regulatory networks associated with breast cancer patient survival using an interpretable deep neural network model, Expert Systems with Applications, Volume 262, 2025, 125632, ISSN 0957-4174, https://doi.org/10.1016/j.eswa.2024.125632.
  2. Park A, Sayed F, Robinson P, Elopre L, Ge Y, Li S, Grov C, Sullivan PS. Health Information on Pre-Exposure Prophylaxis From Search Engines and Twitter: Readability Analysis. JMIR Public Health Surveill. 2023 Sep 4;9:e48630. doi: 10.2196/48630. PMID: 37665621; PMCID: PMC10507523.
  3. Kepple D, Ford CT, Williams J, Abagero B, Li S, Popovici J, Yewhalaw D, Lo E. Comparative transcriptomics reveal differential gene expression in Plasmodium vivax geographical isolates and implications on erythrocyte invasion mechanisms. bioRxiv [Preprint]. 2023 Feb 16:2023.02.16.528793. doi: 10.1101/2023.02.16.528793. Update in: PLoS Negl Trop Dis. 2024 Jan 29;18(1):e0011926. PMID: 36824754; PMCID: PMC9949051.
  4. Duan Chen, Shaoyu Li, Xue Wang. Geometric structure guided model and algorithms for complete deconvolution of gene expression data. Foundations of Data Science, 2022, 4(3): 441-466. doi: 10.3934/fods.2022013 .
  5. Li, S*., Sun, Y., Diao, L. and X., Wang, Distance-Based Analysis with Quantile Regression Models. Stat Biosci 13, 291–312 (2021). https://doi.org/10.1007/s12561-021-09306-6.
  6. Kazemi DM, Li S, Levine MJ, Auten B, Granson M. Systematic Review of Smartphone Apps as a mHealth Intervention to Address Substance Abuse in Adolescents and Adults. J Addict Nurs. (2021) Jul-Sep 01;32(3):180-187. doi: 10.1097/JAN.0000000000000416. PMID: 34473447.
  7. Chen D., Li S., Wang W., and Xia Kelin, Fast random algorithms for manifold based optimization in reconstructing 3D chromosomal structures, Communications in Information and Systems, Vol. 21, No. 1 (2021), pp. 1-29.
  8. Wang, X., Allen, M., Li, S. et al. Deciphering cellular transcriptional alterations in Alzheimer’s disease brains. Mol Neurodegeneration 15, 38 (2020). https://doi.org/10.1186/s13024-020-00392-
  9. Deng, Y., He, T., Fang, R., Li, S., Cao, H., and Cui, Y. (2020) Genome-Wide Gene-Based Multi-Trait Analysis, Frontiers in Genetics. https://doi.org/10.3389/fgene.2020.00437.
  10. Kazemi, D. M., Borsari, B., Levine, M., Li, S., Shehab, M., Fang, F., and Norona, J.C. (2020) Effectiveness of a Theory-Based mHealth Intervention for High-Risk Drinking in College Students, Substance Use and Misuse.  https://doi.org/10.1080/10826084.2020.1756851
  11. Ren, J., Du, Y., Li, S., Ma, S., Jiang,Y., and Wu, C. (2019)  Robust network-based regularization and variable selection for high dimensional genomics data in cancer prognosis, Genetic Epidemiology, 43(3):276-291, doi:10.1002/gepi.22194.
  12. Tao He, Shaoyu Li, Ping-Shou Zhong, and Yuehua Cui. (2019) An optimal kernel-based U-statistic method for gene set association analysis, Genetic Epidemiology, 43(2):137-149.
  13. Kazemi, D.M., Borsari, B., Levine M.J., Shehab, M., Nelson, M.,  Dooley, B., Stinson, B., Fang, F., Li, S. (2019) Real-Time Demonstration of a mHealth app Designed to Reduce College Students Hazardous Drinking, Psychological Services, 16(2):255-259.
  14. Kazemi DM, Borsari B, Levine MJ, Li S, Lamberson KA, Matta LA, A Systematic Review of the mHealth Interventions to Prevent Alcohol and Substance Abuse, J Health Commun. (2017), 22(5): 413-432
  15. Shaoyu Li *, Tao He, Iwona Pawlikowska, and Tong Lin, Correcting length-bias in gene set enrichment analysis for DNA methylation data, Statistics and Its Interface (2017), Vol. 10, No. 2, pp. 279-289.
  16. Haitao Yang, Shaoyu Li, Hongyan Cao, Chichen Zhang, and Yuehua Cui (2017) Predicting disease trait with genomic data: a composite kernel approach. Briefings in Bioinformatics, 18(4):591-601.
  17. Salloum R, Hummel TR, Kumar SS, Dorris K, Li S, Lin T, Daryani VM, Stewart CF, Miles L, Poussaint TY, Stevenson C, Goldman S, Dhall G,Packer R, Fisher P, Pollack IF, Fouladi M, Boyett J, Drissi R, A molecular biology and phase II study of imetelstat (GRN163L) in children with recurrent or refractory central nervous system malignancies: a pediatric brain tumor consortium study, J Neurooncol (2016) doi:10.1007/s11060-016-2189-7.
  18. Wetmore C, Boyett J, Li S, Lin T, Bendel A, Gajjar A, Orr BA., Alisertib is active as single agent in recurrent atypical teratoid rhabdoid tumors in children. Neuro Oncol (2015), 17(6):882-8.
  19. Li S*, Cui Y and Romero R., Entropy-based selection for maternal-fetal genotype incompatibility with application to preterm prelabor rupture of membranes. BMC Genetics (2014), 15:66.
  20. Pounds S, Cheng C, Li S, Liu Z, Zhang J and Mullighan C., A Genomic Random Interval Models for Statistical Analysis of Genomic Lesion Data. Bioinformatics (2013), 29(17): 2088-95.
  21. Wu C, Li S and Cui Y., Genetic association studies: an information content perspective. Current Genomics (2012), 13(7): 566-573.
  22. Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ., Novel mutations target distinct subgroups of medulloblastoma. Nature (2012), 488(7409):43-8.
  23. Li S and Cui Y., Gene-centric gene-gene interaction: a model-based kernel machine method.  Annals of Applied Statistics (2012), 6(3): 1134-1161.
  24. Qaddoumi I, Sane M, Li S, Kocak M, Pai-Panandiker A, Harreld J, Klimo P, Wright K, Broniscer A, Gajjar A. Diagnostic utility and correlation of tumor markers in the serum and cerebrospinal fluid of children with intracranial germ cell tumors. Childs Nery Syst. (2012), 28(7): 1017-24.
  25. Li S, Williams B and Cui Y., A combined p-value approach to infer pathway regulations in eQTL mapping. Statistics and Its Interface (2011), 4(3): 389-402.
  26. Li S, Lu Q and Cui Y., A systems biology approach for identifying novel pathway regulators in an eQTL mapping study. Journal of Biopharmaceutical Statistics (2010), 20(2): 373–400.
  27. Li S, Lu Q, Fu W, Romero R and Cui Y.,  A regularized regression approach for dissecting genetic conflicts that increase disease risk in pregnancy. Statistical Applications in Genetics and Molecular Biology. (2009), Vol. 8: Iss. 1, Article 45.
  28. Cui Y, Li S, and Li G., Functional mapping imprinted quantitative trait loci underlying developmental characteristics. Theoretical Biology and Medical Modeling (2008), 5:6.
  29. Li S and Liu C.,  Empirical Bayesian estimator for the parameter of the linear exponential model. Journal of Huazhong University of Science and Technology (2006) 34: 3 (English Abstract).

Abstracts

1. Amar J. Gajjar, Sridharan Gururangan, Ibrahim A Qaddoumi, Roger Packer, Stewart Goldman, Michael Prados, Annick Desjardins, Maryam Fouladi, Naoko Takebe, Shaoyu Li, David W. Ellison, Tom Curran, Richard J. Gilbertson, James M. Boyett. A prospective phase II study to determine the efficacy of GDC0449 (vismodegib) in adults with recurrent medulloblastoma (MB): A pediatric Brain Tumor Consortium study (PBTC-025B), ASC

2. Donna M. Kazemi, Maureen Levine, Shaoyu Li, Brian Borsari, and Beau Dooley, Mobile mHealth Interventions for Alcohol and Substance Uses: A Systematic Review, American Public Health Association (APHA) 2016 Annual Meeting & Expo

3. Donna, M. Kazemi, Maureen Levine, Brian Borsari, Beau Dooley, Shaoyu Li, and Mohanmed Shehab, MHealth Intervention delivered in Real Time to Reduce Alcohol Use among College Students: A Mixed Methods Study, Public Health Nursing program of the APHA’s 2018 Annual Meeting & Expo (Nov. 10 – Nov. 14), San Diego, CA.

4. Xue Wang, Mariet Allen, Jeremy Burgess, Minerva Carrasquillo, Nilüfer Ertekin-Taner, Shaoyu Li, and Yan Asmann, Application of refined brain cell type marker gene analysis identifies differentially expressed genes in Alzheimer’s disease. International Society for Computational Biology (ISCB) 2017, July 21-July 25, Prague, Czech Republic.

5. Xue Wang, Mariet Allen, Minerva M. Carrasquillo, Jeremy D. Burgess, Shaoyu Li, Yan W. Asmann, and Nilüfer Ertekin-Taner, Identification of cell-type specific differentially expressed genes in Alzheimer’s disease. Alzhemer’s Association International Conference, 2018, Chicago.