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, Integrative Genomics, Biostatistics & Bioinformatics 2019
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 2018 - 2019
- Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2014 - 2018
Research
Selected Grants
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2020
- Identification and validation of plasma-based protein biomarkers for cediranib and olaparib 2019 - 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 2019
- Duke CTSA (UL1) awarded by National Institutes of Health 2013 - 2018
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Sung AD, Jauhari S, Siamakpour-Reihani S, Rao AV, Staats J, Chan C, et al. Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects. Am J Hematol. 2020 Jun;95(6):662–71.
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  - Elsamadicy AA, Ashraf B, Ren X, Sergesketter AR, Charalambous L, Kemeny H, et al. Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach With Neurostimulation. Neuromodulation. 2019 Dec;22(8):960–9.
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  - Wang X, Liu H, Xu Y, Xie J, Zhu D, Amos CI, et al. Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival. Carcinogenesis. 2019 Apr 29;40(2):279–88.
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  - Elsamadicy AA, Ren X, Kemeny H, Charalambous L, Sergesketter AR, Rahimpour S, et al. Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery: A National Trend Analysis of 144 123 Patients. Neurosurgery. 2019 Mar 1;84(3):758–67.
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  - Xu Y, Liu H, Liu S, Wang Y, Xie J, Stinchcombe TE, et al. Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer. Int J Cancer. 2018 Nov 15;143(10):2400–8.
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  - Xie J, Li R. False discovery rate control for high dimensional networks of quantile associations conditioning on covariates. J R Stat Soc Series B Stat Methodol. 2018 Nov;80(5):1015–34.
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  - Lin J, Gresham J, Wang T, Kim SY, Alvarez J, Damrauer JS, et al. bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. Bioinformatics. 2018 Oct 15;34(20):3581–3.
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  - Zeng Y, Nie C, Min J, Chen H, Liu X, Ye R, et al. Sex Differences in Genetic Associations With Longevity. Jama Netw Open. 2018 Aug;1(4):e181670.
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  - Elsamadicy AA, Yang S, Sergesketter AR, Ashraf B, Charalambous L, Kemeny H, et al. Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation. Neuromodulation. 2018 Jul;21(5):423–30.
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  - Lad SP, Yang S, Xie J, Farjat A, Pagadala P, Parente B. Down the Rabbit Hole: Specialty Influence on SCS Outcomes. Neuromodulation. 2018 Jun;21(4):417–20.
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  - Duan B, Hu J, Liu H, Wang Y, Li H, Liu S, et al. Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk. Int J Cancer. 2018 Apr 1;142(7):1322–31.
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  - Charalambous LT, Premji A, Tybout C, Hunt A, Cutshaw D, Elsamadicy AA, et al. Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States. J Med Microbiol. 2018 Feb;67(2):215–27.
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  - Feng Y, Wang Y, Liu H, Liu Z, Mills C, Owzar K, et al. Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer. Mol Carcinog. 2018 Feb;57(2):216–24.
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  - Elsamadicy AA, Sergesketter A, Ren X, Mohammed Qasim Hussaini S, Laarakker A, Rahimpour S, et al. Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation. Neuromodulation. 2018 Jan;21(1):87–92.
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  - Farber SH, Han JL, Elsamadicy AA, Hussaini Q, Yang S, Pagadala P, et al. Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome. Pain Physician. 2017 Sep;20(6):E797–805.
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  - Farber SH, Han JL, Elsamadicy AA, Hussaini Q, Yang S, Pagadala P, et al. Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome. Pain Physician. 2017 Sep 1;20(6):E796–804.
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  - Farber SH, Han JL, Petraglia FW, Gramer R, Yang S, Pagadala P, et al. Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation. Pain Physician. 2017 Sep 1;20(6):E968–76.
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  - Farber SH, Han JL, Petraglia Iii FW, Gramer R, Yang S, Pagadala P, et al. Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation. Pain Physician. 2017 Sep;20(6):E969–77.
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  - Elsamadicy AA, Farber SH, Yang S, Hussaini SMQ, Murphy KR, Sergesketter A, et al. Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients. Neuromodulation. 2017 Jun;20(4):354–60.
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  - Han JL, Murphy KR, Hussaini SMQ, Yang S, Parente B, Xie J, et al. Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation. Neuromodulation. 2017 Jun;20(4):331–9.
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  - Hussaini SMQ, Murphy KR, Han JL, Elsamadicy AA, Yang S, Premji A, et al. Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain. Neuromodulation. 2017 Jun;20(4):340–7.
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  - Murphy KR, Han JL, Hussaini SMQ, Yang S, Parente B, Xie J, et al. The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation. Neuromodulation. 2017 Apr;20(3):256–62.
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  - Xie J, Kang J. High-dimensional tests for functional networks of brain anatomic regions. J Multivar Anal. 2017 Apr;156:70–88.
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  - Farber SH, Murphy KR, Suryadevara CM, Babu R, Yang S, Feng L, et al. Comparing outcomes of early, late, and non-surgical management of intraspinal abscess. J Clin Neurosci. 2017 Feb;36:64–71.
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  - Murphy KR, Han JL, Yang S, Hussaini SMQ, Elsamadicy AA, Parente B, et al. Prevalence of Specific Types of Pain Diagnoses in a Sample of United States Adults. Pain Physician. 2017 Feb;20(2):E257–68.
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  - Krucoff MO, Cook S, Adogwa O, Moreno J, Yang S, Xie J, et al. Racial, Socioeconomic, and Gender Disparities in the Presentation, Treatment, and Outcomes of Adult Chiari I Malformations. World Neurosurg. 2017 Jan;97:431–7.
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  - Cai TT, Li H, Liu W, Xie J. Joint Estimation of Multiple High-dimensional Precision Matrices. Stat Sin. 2016 Apr;26(2):445–64.
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  - Farber SH, Hatef J, Han JL, Marky AH, Xie J, Huang K, et al. Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures. Neuromodulation. 2016 Apr;19(3):319–28.
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  - Ha MJ, Sun W, Xie J. PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs. Biometrics. 2016 Mar;72(1):146–55.
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  - Xie J, Cai TT, Li H. Correction to the paper "Optimal false discovery rate control for dependent data" [Statistics and Its Interface, 4 (2011) 417-430]. Statistics and Its Interface. 2016 Jan 1;9(1):33–5.
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  - Napoli A, Xie J, Obeid I. Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis. Bmc Neurosci. 2014 Jan 21;15:17.
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  - Cai TT, Li H, Liu W, Xie J. Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics. Biometrika. 2013 Mar;100(1):139–56.
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  - John Daye Z, Xie J, Li H. A sparse structured shrinkage estimator for nonparametric varying-coefficient model with an application in genomics. Journal of Computational and Graphical Statistics. 2012 Apr 23;21(1):110–33.
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  - Xie J, Cai TT, Li H. Sample size and power analysis for sparse signal recovery in genome-wide association studies. Biometrika. 2011 Jun;98(2):273–90.
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  - Chen J, Xie J, Li H. A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis. Biometrics. 2011 Mar;67(1):299–308.
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  - Xie J, Cai TT, Maris J, Li H. Optimal False Discovery Rate Control for Dependent Data. Stat Interface. 2011;4(4):417–30.
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  - Cotch MF, Peet J, Shults J, Stambolian D, Xie J. Quasi-least squares with mixed linear correlation structures. Statistics and Its Interface. 2010;3(2):223–33.
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  - Pura J, Chan C, Xie J. Multiple Testing Embedded in an Aggregation Tree to Identify where Two Distributions Differ.
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- Conference Papers
  - Ramalingam S, Siamakpour-Reihani S, Bohannon L, Ren Y, Sibley A, Nixon A, et al. Phase II Trial of Pasireotide to Prevent GI Toxicity and Acute Gvhd in Allogeneic HSCT. In: Biology of Blood and Marrow Transplantation. ELSEVIER SCIENCE INC; 2020. p. S48–9.
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  - Elsamadicy AA, Ren X, Kemeny H, Charalambous L, Rahimpour S, Williamson T, et al. 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. Oxford University Press (OUP); 2018. p. 100–100.
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Teaching & Mentoring
Recent Courses
- BIOSTAT 906: Statistical Inference 2020

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Conference Papers

Recent Courses