Jichun Xie | Scholars@Duke

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

3 Genome Ct, 1243 MSRB III, Durham, NC 27705
Duke Box 103854, Durham, NC 27710
jichun.xie@duke.edu (919) 684-6465
Xie Group Website

Background
Education, Training, & Certifications
- Ph.D., University of Pennsylvania 2011
Duke Appointment History
- 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
Selected Grants
- 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
External Relationships
- 10x Genomics Inc.
Publications & Artistic Works
Selected Publications
- Academic Articles
  - 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.7.4.2020.0176
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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.25781
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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 : Journal of the International Neuromodulation Society, 22(8), 960–969. https://doi.org/10.1111/ner.12871
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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/bgy188
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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/nyy215
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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.31660
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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.12288
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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/bty402
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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.2018.1670
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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.12691
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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.12789
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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.31171
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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.0.000656
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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.22748
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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.12689
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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.
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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.
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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.
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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.
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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.12584
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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.12567
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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.12582
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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 : Journal of the International Neuromodulation Society, 20(3), 256–262. https://doi.org/10.1111/ner.12526
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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.2017.01.011
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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.2016.10.035
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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.
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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.2016.10.026
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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.2014.256
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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.12393
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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.12415
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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.e1
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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/10.1186/1471-2202-15-17
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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/ass058
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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.2011.10102
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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/asr003
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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.x
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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.a1
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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.a9
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  - Li, X., Sung, A., & Xie, J. (n.d.). Distance Assisted Recursive Testing.
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- Conference Papers
  - 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).
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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.
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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 Poster Session Abstracts. American Association for Cancer Research. https://doi.org/10.1158/1538-7445.sabcs19-p1-06-02
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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-2019-130928
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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: A National Trend Analysis of 144 123 Patients. In Neurosurgery (Vol. 65, pp. 100–100). Oxford University Press (OUP). https://doi.org/10.1093/neuros/nyy303.156
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Teaching & Mentoring
Recent Courses

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

External Relationships

Selected Publications

Academic Articles

Conference Papers

Recent Courses