Recent Publications

A deep learning-based model for screening and staging pneumoconiosisZhang, L., Rong, R., Li, Q., Yang, D. M., Yao, B., Luo, D., Zhang, X., Zhu, X., Luo, J., Liu, Y., Yang, X., Ji, X., Liu, Z., Xie, Y., Sha, Y., Li, Z. & Xiao, G., Dec 2021, In: Scientific reports. 11, 1, 2201.Research output: Contribution to […]

Assessing consistency across functional screening datasets in cancer cellsCai, L., Liu, H., Minna, J. D., Deberardinis, R. J., Xiao, G. & Xie, Y., Dec 1 2021, In: Bioinformatics. 37, 23, p. 4540-4547 8 p.Research output: Contribution to journal › Article › peer-review

Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancerCai, L., Liu, H., Huang, F., Fujimoto, J., Girard, L., Chen, J., Li, Y., Zhang, Y. A., Deb, D., Stastny, V., Pozo, K., Kuo, C. S., Jia, G., Yang, C., Zou, W., Alomar, A., Huffman, K., Papari-Zareei, M., Yang, L. & […]

Bayesian modeling of spatial molecular profiling data via Gaussian processLi, Q., Zhang, M., Xie, Y. & Xiao, G., Nov 15 2021, In: Bioinformatics. 37, 22, p. 4129-4136 8 p.Research output: Contribution to journal › Article › peer-review

Association of healthcare access with intensive care unit utilization and mortality in patients of hispanic ethnicity hospitalized with COVID-19Velasco, F., Yang, D. M., Zhang, M., Nelson, T., Sheffield, T., Keller, T., Wang, Y., Walker, C., Katterapalli, C., Zimmerman, K., Masica, A., Lehmann, C. U., Xie, Y. & Hollingsworth, J. W., Nov 2021, In: Journal of […]

Upfront Brain Treatments Followed by Lung Surgery Improves Survival for Stage IV Non-small Cell Lung Cancer Patients With Brain Metastases: A Large Cohort AnalysisHe, X., Yin, S., Liu, H., Lu, R., Kernstine, K., Gerber, D. E., Xie, Y. & Yang, D. M., Oct 13 2021, In: Frontiers in Surgery. 8, 649531.Research output: Contribution to journal […]

Association between body mass index, dosing strategy, and efficacy of immune checkpoint inhibitorsAhmed, M., Von Itzstein, M. S., Sheffield, T., Khan, S., Fattah, F., Park, J. Y., Popat, V., Saltarski, J. M., Gloria-Mccutchen, Y., Hsiehchen, D., Ostmeyer, J., Khan, S. A., Sultana, N., Xie, Y., Li, Q. Z., Wakeland, E. K. & Gerber, D. E., […]

Experience, perceptions, and recommendations concerning COVID-19-related clinical research adjustmentsGerber, D. E., Sheffield, T. Y., Beg, M. S., Williams, E. L., Clark, V. L., Xie, Y., Holbein, M. E. B., Skinner, C. S. & Lee, S. J. C., May 2021, In: JNCCN Journal of the National Comprehensive Cancer Network. 19, 5, p. 505-512 8 p.Research output: […]

Spatial molecular profiling: Platforms, applications and analysis toolsZhang, M., Sheffield, T., Zhan, X., Li, Q., Yang, D. M., Wang, Y., Wang, S., Xie, Y., Wang, T. & Xiao, G., May 1 2021, In: Briefings in Bioinformatics. 22, 3, bbaa145.Research output: Contribution to journal › Review article › peer-review

MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing dataKim, J., Jiang, S., Yiqing, W., Xiao, G., Xie, Y., Liu, D. J., Li, Q., Koh, A. & Zhan, X., Apr 2021, In: G3: Genes, Genomes, Genetics. 11, 4, jkab046.Research output: Contribution to journal › Article › peer-review

SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded SamplesYin, S., Zhan, X., Yao, B., Xiao, G., Wang, X. & Xie, Y., Mar 24 2021, In: Frontiers in Genetics. 12, 650795.Research output: Contribution to journal › Article › peer-review

Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherinWijshake, T., Zou, Z., Chen, B., Zhong, L., Xiao, G., Xie, Y., Doench, J. G., Bennett, L. & Levine, B., Feb 2 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 5, e2020478118.Research output: Contribution to journal › […]

MB-GAN: Microbiome Simulation via Generative Adversarial NetworkRong, R., Jiang, S., Xu, L., Xiao, G., Xie, Y., Liu, D. J., Li, Q. & Zhan, X., Feb 1 2021, In: GigaScience. 10, 2, giab005.Research output: Contribution to journal › Article › peer-review

Evaluating short-Term forecasting of COVID-19 cases among different epidemiological models under a Bayesian frameworkLi, Q., Bedi, T., Lehmann, C. U., Xiao, G. & Xie, Y., Feb 1 2021, In: GigaScience. 10, 2, giab009.Research output: Contribution to journal › Article › peer-review

Sorting nexin 5 mediates virus-induced autophagy and immunityDong, X., Yang, Y., Zou, Z., Zhao, Y., Ci, B., Zhong, L., Bhave, M., Wang, L., Kuo, Y. C., Zang, X., Zhong, R., Aguilera, E. R., Richardson, R. B., Simonetti, B., Schoggins, J. W., Pfeiffer, J. K., Yu, L., Zhang, X., Xie, Y. & Schmid, S. L. & […]

Developing and using a data commons for understanding the molecular characteristics of germ cell tumorsCi, B., Lin, S. Y., Yao, B., Luo, D., Xu, L., Krailo, M., Murray, M. J., Amatruda, J. F., Frazier, A. L. & Xie, Y., 2021, Methods in Molecular Biology. Humana Press Inc., p. 263-275 13 p. (Methods in Molecular Biology; […]

A Multipronged Approach Establishes Covalent Modification of β-Tubulin as the Mode of Action of Benzamide Anti-cancer ToxinsPovedano, J. M., Rallabandi, R., Bai, X., Ye, X., Liou, J., Chen, H., Kim, J., Xie, Y., Posner, B., Rice, L., De Brabander, J. K. & McFadden, D. G., Nov 25 2020, In: Journal of Medicinal Chemistry. 63, 22, […]

Statin Intolerance, Anti-HMGCR Antibodies, and Immune Checkpoint Inhibitor-Associated Myositis: A “Two-Hit” Autoimmune Toxicity or Clinical Predisposition?von Itzstein, M. S., Khan, S., Popat, V., Lu, R., Khan, S. A., Fattah, F. J., Park, J. Y., Bermas, B. L., Karp, D. R., Ahmed, M., Saltarski, J. M., Gloria-McCutchen, Y., Xie, Y., Li, Q. Z., Wakeland, E. K. […]

Molecular differences across invasive lung adenocarcinoma morphological subgroupsCi, B., Yang, D. M., Cai, L., Yang, L., Girard, L., Fujimoto, J., Wistuba, I. I., Xie, Y., Minna, J. D., Travis, W. & Xiao, G., Aug 2020, In: Translational Lung Cancer Research. 9, 4, p. 1029-1040 12 p.Research output: Contribution to journal › Article › peer-review

Biomarkers for RBM39 degradation in acute myeloid leukemiaHsiehchen, D., Goralski, M., Kim, J., Xie, Y. & Nijhawan, D., Jul 1 2020, In: Leukemia. 34, 7, p. 1924-1928 5 p.Research output: Contribution to journal › Article › peer-review