Jichun Xie | Scholars@Duke

Jichun Xie
Associate Professor of Biostatistics & Bioinformatics

My research focuses on identifying rare events and inferring complex dependence structures of high dimensional data, and their application in translational biomedical research.

Current Research Interests

Methodology: Large-scale multiple-testing; high dimensional inference; deep learning.
Data: High-throughput sequencing (DNA-seq, RNA-seq, scRNA-seq); flow cytometry; EHR data.

Current Appointments & Affiliations

Associate Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2018

Contact Information

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

Background
Education, Training, & Certifications
- Ph.D., University of Pennsylvania 2011
Duke Appointment History
- Assistant Professor of Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2014 - 2018
Research
Selected Grants
- Race-related alternative splicing: novel targets in prostate cancer awarded by National Institutes of Health 2017 - 2022
- Mechanisms that Direct Airway Remodeling in Obese Asthma awarded by National Institutes of Health 2017 - 2021
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2019
- Duke CTSA (UL1) awarded by National Institutes of Health 2013 - 2018
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Wang, X, Liu, H, Xu, Y, Xie, J, Zhu, D, Amos, CI, Fang, S, Lee, JE, Li, X, Nan, H, Song, Y, and Wei, Q. "Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival." Carcinogenesis (December 29, 2018). Full Text
  - Xie, J, and Li, R. "False discovery rate control for high dimensional networks of quantile associations conditioning on covariates." Journal of the Royal Statistical Society: Series B (Statistical Methodology) 80, no. 5 (November 2018): 1015-1034. Full Text Open Access Copy
  - Xu, Y, Liu, H, Liu, S, Wang, Y, Xie, J, Stinchcombe, TE, Su, L, Zhang, R, Christiani, DC, Li, W, and Wei, Q. "Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer." International Journal of Cancer 143, no. 10 (November 2018): 2400-2408. Full Text
  - Elsamadicy, AA, Ashraf, B, Ren, X, Sergesketter, AR, Charalambous, L, Kemeny, H, Ejikeme, T, Yang, S, Pagadala, P, Parente, B, Xie, J, Pappas, TN, and Lad, SP. "Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach With Neurostimulation." Neuromodulation : Journal of the International Neuromodulation Society (October 15, 2018). Full Text
  - Lin, J, Gresham, J, Wang, T, Kim, SY, Alvarez, J, Damrauer, JS, Floyd, S, Granek, J, Allen, A, Chan, C, Xie, J, and Owzar, K. "bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens." Bioinformatics (Oxford, England) 34, no. 20 (October 2018): 3581-3583. Full Text
  - Zeng, Y, Nie, C, Min, J, Chen, H, Liu, X, Ye, R, Chen, Z, Bai, C, Xie, E, Yin, Z, Lv, Y, Lu, J, Li, J, Ni, T, Bolund, L, Land, KC, Yashin, A, O'Rand, AM, Sun, L, Yang, Z, Tao, W, Gurinovich, A, Franceschi, C, Xie, J, Gu, J, Hou, Y, Liu, X, Xu, X, Robine, J-M, Deelen, J, Sebastiani, P, Slagboom, E, Perls, T, Hauser, E, Gottschalk, W, Tan, Q, Christensen, K, Shi, X, Lutz, M, Tian, X-L, Yang, H, and Vaupel, J. "Sex Differences in Genetic Associations With Longevity." Jama Network Open 1, no. 4 (August 24, 2018). Full Text
  - Elsamadicy, AA, Yang, S, Sergesketter, AR, Ashraf, B, Charalambous, L, Kemeny, H, Ejikeme, T, Ren, X, Pagadala, P, Parente, B, Xie, J, and Lad, SP. "Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation." Neuromodulation : Journal of the International Neuromodulation Society 21, no. 5 (July 2018): 423-430. (Review) Full Text
  - Elsamadicy, AA, Ren, X, Kemeny, H, Charalambous, L, Sergesketter, AR, Rahimpour, S, Williamson, T, Goodwin, CR, Abd-El-Barr, MM, Gottfried, ON, Xie, J, and Lad, SP. "Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery: A National Trend Analysis of 144 123 Patients." Neurosurgery (June 11, 2018). Full Text
  - Lad, SP, Yang, S, Xie, J, Farjat, A, Pagadala, P, and Parente, B. "Down the Rabbit Hole: Specialty Influence on SCS Outcomes." Neuromodulation : Journal of the International Neuromodulation Society 21, no. 4 (June 2018): 417-420. (Letter) Full Text
  - Duan, B, Hu, J, Liu, H, Wang, Y, Li, H, Liu, S, Xie, J, Owzar, K, Abbruzzese, J, Hurwitz, H, Gao, H, and Wei, Q. "Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk." International Journal of Cancer 142, no. 7 (April 2018): 1322-1331. Full Text
  - Charalambous, LT, Premji, A, Tybout, C, Hunt, A, Cutshaw, D, Elsamadicy, AA, Yang, S, Xie, J, Giamberardino, C, Pagadala, P, Perfect, JR, and Lad, SP. "Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States." Journal of Medical Microbiology 67, no. 2 (February 2018): 215-227. Full Text
  - Feng, Y, Wang, Y, Liu, H, Liu, Z, Mills, C, Owzar, K, Xie, J, Han, Y, Qian, DC, Hung Rj, RJ, Brhane, Y, McLaughlin, J, Brennan, P, Bickeböller, H, Rosenberger, A, Houlston, RS, Caporaso, N, Landi, MT, Brüske, I, Risch, A, Ye, Y, Wu, X, Christiani, DC, Amos, CI, and Wei, Q. "Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer." Molecular Carcinogenesis 57, no. 2 (February 2018): 216-224. Full Text
  - Elsamadicy, AA, Sergesketter, A, Ren, X, Mohammed Qasim Hussaini, S, Laarakker, A, Rahimpour, S, Ejikeme, T, Yang, S, Pagadala, P, Parente, B, Xie, J, and Lad, SP. "Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation." Neuromodulation : Journal of the International Neuromodulation Society 21, no. 1 (January 2018): 87-92. Full Text
  - Farber, SH, Han, JL, Elsamadicy, AA, Hussaini, Q, Yang, S, Pagadala, P, Parente, B, Xie, J, and Lad, SP. "Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome." Pain Physician 20, no. 6 (September 2017): E797-E805.
  - Farber, SH, Han, JL, Elsamadicy, AA, Hussaini, Q, Yang, S, Pagadala, P, Parente, B, Xie, J, and Lad, SP. "Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome." Pain Physician 20, no. 6 (September 1, 2017): E796-E804. (Review) Link to Item
  - Farber, SH, Han, JL, Petraglia Iii, FW, Gramer, R, Yang, S, Pagadala, P, Parente, B, Xie, J, Petrella, JR, and Lad, SP. "Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation." Pain Physician 20, no. 6 (September 2017): E969-E977.
  - Farber, SH, Han, JL, Petraglia, FW, Gramer, R, Yang, S, Pagadala, P, Parente, B, Xie, J, Petrella, JR, and Lad, SP. "Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation." Pain Physician 20, no. 6 (September 1, 2017): E968-E976. (Academic Article) Link to Item
  - Elsamadicy, AA, Farber, SH, Yang, S, Hussaini, SMQ, Murphy, KR, Sergesketter, A, Suryadevara, CM, Pagadala, P, Parente, B, Xie, J, and Lad, SP. "Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients." Neuromodulation : Journal of the International Neuromodulation Society 20, no. 4 (June 2017): 354-360. Full Text
  - Han, JL, Murphy, KR, Hussaini, SMQ, Yang, S, Parente, B, Xie, J, Pagadala, P, and Lad, SP. "Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation." Neuromodulation : Journal of the International Neuromodulation Society 20, no. 4 (June 2017): 331-339. Full Text
  - Hussaini, SMQ, Murphy, KR, Han, JL, Elsamadicy, AA, Yang, S, Premji, A, Parente, B, Xie, J, Pagadala, P, and Lad, SP. "Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain." Neuromodulation : Journal of the International Neuromodulation Society 20, no. 4 (June 2017): 340-347. Full Text
  - Murphy, KR, Han, JL, Hussaini, SMQ, Yang, S, Parente, B, Xie, J, and Lad, SP. "The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation." Neuromodulation : Journal of the International Neuromodulation Society 20, no. 3 (April 2017): 256-262. Full Text
  - Xie, J, and Kang, J. "High-dimensional tests for functional networks of brain anatomic regions." Journal of Multivariate Analysis 156 (April 2017): 70-88. Full Text
  - Farber, SH, Murphy, KR, Suryadevara, CM, Babu, R, Yang, S, Feng, L, Xie, J, Perfect, JR, and Lad, SP. "Comparing outcomes of early, late, and non-surgical management of intraspinal abscess." Journal of Clinical Neuroscience : Official Journal of the Neurosurgical Society of Australasia 36 (February 2017): 64-71. Full Text
  - Murphy, KR, Han, JL, Yang, S, Hussaini, SMQ, Elsamadicy, AA, Parente, B, Xie, J, Pagadala, P, and Lad, SP. "Prevalence of Specific Types of Pain Diagnoses in a Sample of United States Adults." Pain Physician 20, no. 2 (February 2017): E257-E268.
  - Krucoff, MO, Cook, S, Adogwa, O, Moreno, J, Yang, S, Xie, J, Firempong, AO, Lad, N, and Bagley, CA. "Racial, Socioeconomic, and Gender Disparities in the Presentation, Treatment, and Outcomes of Adult Chiari I Malformations." World Neurosurgery 97 (January 2017): 431-437. Full Text
  - Cai, TT, Li, H, Liu, W, and Xie, J. "Joint Estimation of Multiple High-dimensional Precision Matrices." Statistica Sinica 26, no. 2 (April 2016): 445-464. Full Text Open Access Copy
  - Farber, SH, Hatef, J, Han, JL, Marky, AH, Xie, J, Huang, K, Verla, T, Lokhnygina, Y, Collins, TA, and Lad, SP. "Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures." Neuromodulation : Journal of the International Neuromodulation Society 19, no. 3 (April 2016): 319-328. Full Text
  - Ha, MJ, Sun, W, and Xie, J. "PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs." Biometrics 72, no. 1 (March 2016): 146-155. Full Text Open Access Copy
  - Xie, J, Cai, TT, and 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 9, no. 1 (January 1, 2016): 33-35. Full Text
  - Napoli, A, Xie, J, and Obeid, I. "Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis." Bmc Neuroscience 15 (January 21, 2014): 17-null. Full Text
  - Cai, TT, Li, H, Liu, W, and Xie, J. "Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics." Biometrika 100, no. 1 (March 2013): 139-156. Full Text
  - John Daye, Z, Xie, J, and Li, H. "A sparse structured shrinkage estimator for nonparametric varying-coefficient model with an application in genomics." Journal of Computational and Graphical Statistics 21, no. 1 (April 23, 2012): 110-133. Full Text
  - Xie, J, Cai, TT, and Li, H. "Sample size and power analysis for sparse signal recovery in genome-wide association studies." Biometrika 98, no. 2 (June 2011): 273-290. Full Text
  - Chen, J, Xie, J, and Li, H. "A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis." Biometrics 67, no. 1 (March 2011): 299-308. Full Text
  - Xie, J, Cai, TT, Maris, J, and Li, H. "Optimal False Discovery Rate Control for Dependent Data." Statistics and Its Interface 4, no. 4 (January 2011): 417-430. Full Text
  - Cotch, MF, Peet, J, Shults, J, Stambolian, D, and Xie, J. "Quasi-least squares with mixed linear correlation structures." Statistics and Its Interface 3, no. 2 (2010): 223-233. Full Text
Teaching & Mentoring
Recent Courses
- BIOSTAT 906: Statistical Inference 2018

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Recent Courses