Research

RESEARCH INTERESTS

Statistical learning, High-dimensional data analysis, Semiparametric models, Large-scale statistical test, Statistical genomics, Bioinformatics

Ke, C., Shin, S., Lou, Y., & Ahn, M. A Generalized Formulation for Group Selection via ADMM. Journal of Scientific Computing, 100, 15 (2024). https://doi.org/10.1007/s10915-024-02571-9

Yang, J., Jiang, X., Jin, K.W., Shin, S., & Li, Q. Bayesian hidden mark interaction model for detecting spatially variable genes in imaging-based spatially resolved transcriptomics data. Frontiers in Genetics, 15, 1356709 (2024). https://doi.org/10.3389/fgene.2024.1356709

The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology, 25, 53 (2024). https://doi.org/10.1186/s13059-023-03113-6

Ke, C., Ahn, A., Shin, S., & Lou, Y. Iteratively reweighted group lasso based on log-composite regularization. SIAM Journal on Scientific Computing, 43(5), S655-S678 (2021). https://doi.org/10.1137/20M1349072

Simonett, S.P., Shin, S., Bacher, R., Dong, C., Smith, L., Rabaglia, M., Stapleton, D., Schueler, K., Choi, J., Bernstein, M., Perez-Cervantes, C., Herring, J., Spaeth, J., Stein, R., Tessem, J., Kendziorski, C., Keles, S, Moskowitz, I., Attie, A., & Keller, M. Identification of direct transcriptional targets of Nfatc2 that promote β-cell proliferation in human islets. Journal of Clinical Investigation, 131(21):e144833 (2021). https://doi.org/10.1172/JCI144833

Dong, C., Simonett, S.P., Shin, S., Stapleton, D.S., Schueler, K.L., Churchill, G.A., Lu, L., Liu, X., Jin, F., Li, Y. Attie, A.D., Keller, M.P. & Keles, S. INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. Genome Biology, 22, 241 (2021). https://doi.org/10.1186/s13059-021-02450-8

Abascal, F., Acosta, R., Addleman, N.J., et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583, 699-710 (2020). https://doi.org/10.1038/s41586-020-2493-4

Abascal, F., Acosta, R., Addleman, N.J. et al. Perspectives on ENCODE. Nature, 583, 693-698 (2020). https://doi.org/10.1038/s41586-020-2449-8

Shin, S., Liu, Y., Cole, S.R. & Fine, J.P. Ensemble estimation and variable selection with semiparametric regression models. Biometrika, 107(2), 433-448 (2020). https://doi.org/10.1093/biomet/asaa012

Shin, S., Hudson, R., Harrison, C., Craven, M. & Keles, S. atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. Bioinformatics, 35(15), 2657-2659 (2019). https://doi.org/10.1093/bioinformatics/bty1010

Harrison, C., Keles, S., Hudson, R., Shin, S. & Dutra, I. atSNPInfrastructure, a case study for searching billions of records while providing significant cost savings over cloud providers. Proceedings of IEEE International Parallel and Distributed Processing Symposium Workshops, 497-506 (2018). https://doi.org/10.1109/IPDPSW.2018.00086

Shin, S. & Keles, S. Annotation regression for genome-wide association studies with an application to Psychiatric Genomics Consortium data. Statistics in Biosciences, 9(1), 50-72 (2017). https://doi.org/10.1007/s12561-016-9154-z

Guduru, A., Fleischman, D., Shin, S., Zeng, D., Baldwin, J.B., Houghton, O.M., & Say, E.A. Ultra-widefield fundus autofluorescence in age-related macular degeneration. PLOS ONE, 12(6), e0177207 (2017). https://doi.org/10.1371/journal.pone.0177207

Kreimer, A., Zeng, H., Edwards, M.D., Guo, Y., Tian, K., Shin, S., Welch,R., Wainberg, M., Mohan, R., Sinnott-Armstrong, N.A., Li, Y., Eraslan, G., Amin, T.B., Tewhey, R., Sabeti, P.C., Goke, J., Mueller, N.S., Kellis, M., Kundaje, A., Beer, M.A., Keles, S., Gifford, D.K., & Yosef, N. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation, 38(9):1240-1250 (2017). https://doi.org/10.1002/humu.23197

Shin, S., Fine, J.P., & Liu, Y. Adaptive estimation with partially overlapping models. Statistica Sinica, 26(1), 235-253 (2016). https://doi.org/10.5705/ss.2014.233

Zuo, C., Shin, S., & Keles, S. atSNP: transcription factor binding affinity testing for regulatory SNP detection. Bioinformatics, 31(20), 3353-3355 (2015). https://doi.org/10.1093/bioinformatics/btv328