Jichun Xie
Associate Professor of Biostatistics & Bioinformatics
Current Research Interests
My research is focused on the development of computational and statistical methods for extracting meaningful information from the high-throughput sequencing data in cancer and/or immunology. I am interested in understanding the complicated structure and the biological background of the data, and adaptively developing new methods to utilize the data structure and biological background to increase the analysis power. Thus, my research sits at the intersection of Statistics, Machine Learning, Bioinformatics, and Genetics and Genomics/Cancer/Immunology. I enjoy collaborating with both biomedical and quantitative investigators, and involving students in those projects.
Aside from high-throughput sequencing data, I have also collaborated actively in analyzing EHR data and developing longitudinal models to compare health utilities and treatment outcomes.
Current Appointments & Affiliations
- Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2020
- Associate Professor of Mathematics, Mathematics, Trinity College of Arts & Sciences 2020
- Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 2019
Contact Information
- Duke Box 103854, Durham, NC 27710
- Hock Plaza 10048, 2424 Erwin Rd, Durham, NC 27705, Durham, NC 27705
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jichun.xie@duke.edu
(919) 684-6465
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Xie Group Website
- Background
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Education, Training, & Certifications
- Ph.D., University of Pennsylvania 2011
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Previous Appointments & Affiliations
- Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2019 - 2020
- Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2018 - 2019
- Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2014 - 2018
- Research
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Selected Grants
- New computational methods to dynamically pinpointing the subregions carrying disease-associated rare variants awarded by National Institutes of Health 2022 - 2026
- Race-related differential RNA splicing: novel targets for precision oncology in non-small cell lung cancer awarded by National Institutes of Health 2020 - 2025
- Training Program in Bioinformatics at the Intersection of Cancer Immunology and Microbiome awarded by National Institutes of Health 2020 - 2025
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Identification and validation of plasma-based protein biomarkers for cediranib and olaparib awarded by Leidos Biomedical Research, Inc. 2019 - 2020
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- Statistical/Computational Methods for Pharmacogenomics and Individualized Therapy awarded by University of North Carolina - Chapel Hill 2015 - 2020
- Identification and validation of plasma-based protein biomarkers for cediranib and olaparib awarded by Leidos Biomedical Research, Inc. 2019
- Duke CTSA (UL1) awarded by National Institutes of Health 2013 - 2018
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Fang, J., Chan, C., Owzar, K., Wang, L., Qin, D., Li, Q.-J., & Xie, J. (2022). Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering. Genome Biol, 23(1), 269. https://doi.org/10.1186/s13059-022-02825-5Full Text Link to Item
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Murdoch, D. M., Barfield, R., Chan, C., Towe, S. L., Bell, R. P., Volkheimer, A., … Meade, C. S. (2022). Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV. J Neurovirol. https://doi.org/10.1007/s13365-022-01102-2Full Text Link to Item
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DiMarco, A. V., Qin, X., McKinney, B. J., Garcia, N. M. G., Van Alsten, S. C., Mendes, E. A., … Alvarez, J. V. (2022). APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. Cancer Immunol Res, 10(1), 70–86. https://doi.org/10.1158/2326-6066.CIR-21-0146Full Text Link to Item
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Siamakpour-Reihani, S., Cao, F., Lyu, J., Ren, Y., Nixon, A. B., Xie, J., … Sung, A. D. (2022). Evaluating immune response and metabolic related biomarkers pre-allogenic hematopoietic stem cell transplant in acute myeloid leukemia. Plos One, 17(6), e0268963. https://doi.org/10.1371/journal.pone.0268963Full Text Link to Item
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Li, X., Sung, A., & Xie, J. (2021). Distance Assisted Recursive Testing.Link to Item
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Mathews, A. M., Wysham, N. G., Xie, J., Qin, X., Giovacchini, C. X., Ekström, M., & MacIntyre, N. R. (2020). Hypercapnia in Advanced Chronic Obstructive Pulmonary Disease: A Secondary Analysis of the National Emphysema Treatment Trial. Chronic Obstr Pulm Dis, 7(4), 336–345. https://doi.org/10.15326/jcopdf.7.4.2020.0176Full Text Link to Item
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Sung, A. D., Jauhari, S., Siamakpour-Reihani, S., Rao, A. V., Staats, J., Chan, C., … Rizzieri, D. A. (2020). Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects. Am J Hematol, 95(6), 662–671. https://doi.org/10.1002/ajh.25781Full Text Link to Item
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Elsamadicy, A. A., Ashraf, B., Ren, X., Sergesketter, A. R., Charalambous, L., Kemeny, H., … Lad, S. P. (2019). Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach With Neurostimulation. Neuromodulation, 22(8), 960–969. https://doi.org/10.1111/ner.12871Full Text Link to Item
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Wang, X., Liu, H., Xu, Y., Xie, J., Zhu, D., Amos, C. I., … Wei, Q. (2019). Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival. Carcinogenesis, 40(2), 279–288. https://doi.org/10.1093/carcin/bgy188Full Text Open Access Copy Link to Item
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Elsamadicy, A. A., Ren, X., Kemeny, H., Charalambous, L., Sergesketter, A. R., Rahimpour, S., … Lad, S. P. (2019). Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery: A National Trend Analysis of 144 123 Patients. Neurosurgery, 84(3), 758–767. https://doi.org/10.1093/neuros/nyy215Full Text Link to Item
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Xu, Y., Liu, H., Liu, S., Wang, Y., Xie, J., Stinchcombe, T. E., … Wei, Q. (2018). Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer. Int J Cancer, 143(10), 2400–2408. https://doi.org/10.1002/ijc.31660Full Text Open Access Copy Link to Item
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Xie, J., & Li, R. (2018). False discovery rate control for high dimensional networks of quantile associations conditioning on covariates. J R Stat Soc Series B Stat Methodol, 80(5), 1015–1034. https://doi.org/10.1111/rssb.12288Full Text Open Access Copy Link to Item
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Lin, J., Gresham, J., Wang, T., Kim, S. Y., Alvarez, J., Damrauer, J. S., … Owzar, K. (2018). bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. Bioinformatics, 34(20), 3581–3583. https://doi.org/10.1093/bioinformatics/bty402Full Text Link to Item
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Zeng, Y., Nie, C., Min, J., Chen, H., Liu, X., Ye, R., … Vaupel, J. (2018). Sex Differences in Genetic Associations With Longevity. Jama Netw Open, 1(4), e181670. https://doi.org/10.1001/jamanetworkopen.2018.1670Full Text Link to Item
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Elsamadicy, A. A., Yang, S., Sergesketter, A. R., Ashraf, B., Charalambous, L., Kemeny, H., … Lad, S. P. (2018). Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation. Neuromodulation, 21(5), 423–430. https://doi.org/10.1111/ner.12691Full Text Link to Item
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Lad, S. P., Yang, S., Xie, J., Farjat, A., Pagadala, P., & Parente, B. (2018). Down the Rabbit Hole: Specialty Influence on SCS Outcomes. Neuromodulation, 21(4), 417–420. https://doi.org/10.1111/ner.12789Full Text Link to Item
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Duan, B., Hu, J., Liu, H., Wang, Y., Li, H., Liu, S., … Wei, Q. (2018). Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk. Int J Cancer, 142(7), 1322–1331. https://doi.org/10.1002/ijc.31171Full Text Open Access Copy Link to Item
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Charalambous, L. T., Premji, A., Tybout, C., Hunt, A., Cutshaw, D., Elsamadicy, A. A., … Lad, S. P. (2018). Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States. J Med Microbiol, 67(2), 215–227. https://doi.org/10.1099/jmm.0.000656Full Text Link to Item
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Feng, Y., Wang, Y., Liu, H., Liu, Z., Mills, C., Owzar, K., … Wei, Q. (2018). Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog, 57(2), 216–224. https://doi.org/10.1002/mc.22748Full Text Open Access Copy Link to Item
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Elsamadicy, A. A., Sergesketter, A., Ren, X., Mohammed Qasim Hussaini, S., Laarakker, A., Rahimpour, S., … Lad, S. P. (2018). Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation. Neuromodulation, 21(1), 87–92. https://doi.org/10.1111/ner.12689Full Text Link to Item
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Farber, S. H., Han, J. L., Elsamadicy, A. A., Hussaini, Q., Yang, S., Pagadala, P., … Lad, S. P. (2017). Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome. Pain Physician, 20(6), E797–E805.Link to Item
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Farber, S. H., Han, J. L., Elsamadicy, A. A., Hussaini, Q., Yang, S., Pagadala, P., … Lad, S. P. (2017). Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome. Pain Physician, 20(6), E796–E804.Link to Item
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Farber, S. H., Han, J. L., Petraglia Iii, F. W., Gramer, R., Yang, S., Pagadala, P., … Lad, S. P. (2017). Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation. Pain Physician, 20(6), E969–E977.Link to Item
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Farber, S. H., Han, J. L., Petraglia, F. W., Gramer, R., Yang, S., Pagadala, P., … Lad, S. P. (2017). Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation. Pain Physician, 20(6), E968–E976.Link to Item
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Elsamadicy, A. A., Farber, S. H., Yang, S., Hussaini, S. M. Q., Murphy, K. R., Sergesketter, A., … Lad, S. P. (2017). Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients. Neuromodulation, 20(4), 354–360. https://doi.org/10.1111/ner.12584Full Text Link to Item
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Han, J. L., Murphy, K. R., Hussaini, S. M. Q., Yang, S., Parente, B., Xie, J., … Lad, S. P. (2017). Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation. Neuromodulation, 20(4), 331–339. https://doi.org/10.1111/ner.12567Full Text Link to Item
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Hussaini, S. M. Q., Murphy, K. R., Han, J. L., Elsamadicy, A. A., Yang, S., Premji, A., … Lad, S. P. (2017). Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain. Neuromodulation, 20(4), 340–347. https://doi.org/10.1111/ner.12582Full Text Link to Item
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Murphy, K. R., Han, J. L., Hussaini, S. M. Q., Yang, S., Parente, B., Xie, J., & Lad, S. P. (2017). The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation. Neuromodulation, 20(3), 256–262. https://doi.org/10.1111/ner.12526Full Text Link to Item
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Xie, J., & Kang, J. (2017). High-dimensional tests for functional networks of brain anatomic regions. J Multivar Anal, 156, 70–88. https://doi.org/10.1016/j.jmva.2017.01.011Full Text Link to Item
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Farber, S. H., Murphy, K. R., Suryadevara, C. M., Babu, R., Yang, S., Feng, L., … Lad, S. P. (2017). Comparing outcomes of early, late, and non-surgical management of intraspinal abscess. J Clin Neurosci, 36, 64–71. https://doi.org/10.1016/j.jocn.2016.10.035Full Text Link to Item
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Murphy, K. R., Han, J. L., Yang, S., Hussaini, S. M. Q., Elsamadicy, A. A., Parente, B., … Lad, S. P. (2017). Prevalence of Specific Types of Pain Diagnoses in a Sample of United States Adults. Pain Physician, 20(2), E257–E268.Link to Item
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Krucoff, M. O., Cook, S., Adogwa, O., Moreno, J., Yang, S., Xie, J., … Bagley, C. A. (2017). Racial, Socioeconomic, and Gender Disparities in the Presentation, Treatment, and Outcomes of Adult Chiari I Malformations. World Neurosurg, 97, 431–437. https://doi.org/10.1016/j.wneu.2016.10.026Full Text Link to Item
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Cai, T. T., Li, H., Liu, W., & Xie, J. (2016). Joint Estimation of Multiple High-dimensional Precision Matrices. Stat Sin, 26(2), 445–464. https://doi.org/10.5705/ss.2014.256Full Text Open Access Copy Link to Item
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Farber, S. H., Hatef, J., Han, J. L., Marky, A. H., Xie, J., Huang, K., … Lad, S. P. (2016). Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures. Neuromodulation, 19(3), 319–328. https://doi.org/10.1111/ner.12393Full Text Link to Item
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Ha, M. J., Sun, W., & Xie, J. (2016). PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs. Biometrics, 72(1), 146–155. https://doi.org/10.1111/biom.12415Full Text Open Access Copy Link to Item
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Xie, J., Cai, T. T., & Li, H. (2016). Correction to the paper "Optimal false discovery rate control for dependent data" [Statistics and Its Interface, 4 (2011) 417-430]. Statistics and Its Interface, 9(1), 33–35. https://doi.org/10.4310/SII.2016.v9.n1.e1Full Text
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Xie, J., Cai, T. T., & Li, H. (2016). Correction to the paper “Optimal False Discovery Rate Control for Dependent Data”. Statistics and Its Interface, 9(1), 33–35. https://doi.org/10.4310/SII.2016.V9.N1.E3Full Text
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Napoli, A., Xie, J., & Obeid, I. (2014). Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis. Bmc Neurosci, 15, 17. https://doi.org/10.1186/1471-2202-15-17Full Text Link to Item
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Cai, T. T., Li, H., Liu, W., & Xie, J. (2013). Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics. Biometrika, 100(1), 139–156. https://doi.org/10.1093/biomet/ass058Full Text Link to Item
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John Daye, Z., Xie, J., & Li, H. (2012). A sparse structured shrinkage estimator for nonparametric varying-coefficient model with an application in genomics. Journal of Computational and Graphical Statistics, 21(1), 110–133. https://doi.org/10.1198/jcgs.2011.10102Full Text
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Xie, J., Cai, T. T., & Li, H. (2011). Sample size and power analysis for sparse signal recovery in genome-wide association studies. Biometrika, 98(2), 273–290. https://doi.org/10.1093/biomet/asr003Full Text Link to Item
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Chen, J., Xie, J., & Li, H. (2011). A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis. Biometrics, 67(1), 299–308. https://doi.org/10.1111/j.1541-0420.2010.01413.xFull Text Link to Item
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Xie, J., Cai, T. T., Maris, J., & Li, H. (2011). Optimal False Discovery Rate Control for Dependent Data. Stat Interface, 4(4), 417–430. https://doi.org/10.4310/sii.2011.v4.n4.a1Full Text Link to Item
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Cotch, M. F., Peet, J., Shults, J., Stambolian, D., & Xie, J. (2010). Quasi-least squares with mixed linear correlation structures. Statistics and Its Interface, 3(2), 223–233. https://doi.org/10.4310/sii.2010.v3.n2.a9Full Text
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Conference Papers
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DiMarco, A. V., Qin, X., McKinney, B., Lupo, R., Xie, J., Owzar, K., & Alvarez, J. (2021). APOBEC mutagenesis as a driver of tumor evolution by promoting tumor recurrence and modulating tumor-immune system interactions in a syngeneic murine model of breast cancer. In Cancer Immunology Research (Vol. 9).Link to Item
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Ramalingam, S., Siamakpour-Reihani, S., Bohannon, L., Ren, Y., Sibley, A., Nixon, A., … Sung, A. D. (2020). Phase II Trial of Pasireotide to Prevent GI Toxicity and Acute Gvhd in Allogeneic HSCT. In Biology of Blood and Marrow Transplantation (Vol. 26, pp. S48–S49). Orlando, FL: ELSEVIER SCIENCE INC.Link to Item
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Force, J., Qin, X., Zhang, D., Marcom, P. K., Marks, J., Taylor, M. L., … Xie, J. (2020). Abstract P1-06-02: Characterization of gene- and sample-level APOBEC mutagenesis enrichment with respect to intrinsic subtypes, tumor mutational burden, and immune composition in breast cancer. In Cancer Research (Vol. 80). American Association for Cancer Research (AACR). https://doi.org/10.1158/1538-7445.sabcs19-p1-06-02Full Text
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Poe, J. C., Zhang, D., Xie, J., DiCioccio, R. A., Qin, X., Fang, J., … Sarantopoulos, S. (2019). Single-Cell RNA-Seq Identifies Potentially Pathogenic B Cell Populations That Uniquely Circulate in Patients with Chronic Gvhd. In Blood (Vol. 134, pp. 874–874). American Society of Hematology. https://doi.org/10.1182/blood-2019-130928Full Text
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Elsamadicy, A. A., Ren, X., Kemeny, H., Charalambous, L., Rahimpour, S., Williamson, T., … Lad, N. (2018). 156 Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery. In Neurosurgery (Vol. 65, pp. 100–100). Ovid Technologies (Wolters Kluwer Health). https://doi.org/10.1093/neuros/nyy303.156Full Text
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- Teaching & Mentoring
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Recent Courses
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