Publication

2024

• Gao, Q; Ji, J; Wang, L; Owzar, K; Li Q; Chan, C; Xie, J. SifiNet: A robust and accurate method to identify feature gene sets and annotate cells. Nucleic Acids Research (2024): 52(9): e46.

• Li, X; Pura, J; Allen, A; Owzar, K; Lu, J, Harms, M.; and Xie, J. DYNATE: Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree. Genetic Epidemiology (2024): 48(1), 42-55.

2023

• Li, X; Sung, A; and Xie, J. DART: Distance Assisted Recursive Testing. Journal of Machine Learning Research (2023): 24(169), 1−41.

• Pura, J; Li, X; Chan, C; and Xie, J. TEAM: A Multiple Testing Algorithm on the Aggregation Tree for Flow Cytometry Analysis. Annals of Applied Statistics (2023): 17(1), 621-640.

• Hou, L; Ji, Z; Wang, J; and Xie, J. Editorial: Statistical and computational methods for single-cell sequencing analysis. Frontiers in Genetics (2023): Sec. Statistical Genetics and Methodology, Volume 14. https://doi.org/10.3389/fgene.2023.1235174

• Poe, J; Fang, J; Zhang, D; Lee, MR; DiCioccio, R; Su, H; Qin, X; Zhang, JY; Visentin, J; Bracken, SJ; Ho, VT; Wang, KS; Rose, JJ; Hakim, FT; Jia, W; Suthers, AN; Curry-Chisolm, TM; Horwitz, ME; Rizzierri, DA; McManigle, WC; Chao, NJ; Cardones, AR; Xie, J; Owzar, K; and Sarantopoulos, S. Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD. JCI Insights (2023). https://doi.org/10.1172/jci.insight.169732

• Murdoch, DM; Barfield, R; Chan, C; Towe, SL; Bell, RP; Volkheimer, A; Choe, J; Hall, SA; Berger, M; Xie, J; Meade, CS. Neuroimaging and immunological features of neurocognitive function related to substance use in people with HIV. Journal of NeuroVirology (2023): 29(1), 78-93.

• Moris, D; Barfield, R; Chan, C; Chasse, S; Stempora, L; Xie, J; Plichta, JK; Thacker, J; Harpole, DH; Purves, T; Lagoo-Deenadayalan, S; Hwang, ES; Kirk, AD. Immune Phenotype and Postoperative Complications following Elective Surgery. Annals of Surgery (2023): 278(6), 873-882.

2022

• Fang, J; Chan, C; Owzar, K; Wang, L; Qin, D; Li Q; and Xie, J. Clustering Deviation Index (CDI): A robust and accurate internal measure for evaluating scRNA-seq data clustering. Genome Biology (2022) 23: 269. https://doi.org/10.1186/s13059-022-02825-5.

• NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. (Listed as a consortium coauthor) Nature aging (2022): 2(12), 1090-1100.

• DiMarco, AV; Qin, X; McKinney, BJ; Garcia, NMG; Van Alsten, SC; Mendes, EA; Force, J; Hanks, BA; Troester, MA; Owzar, K; Xie, J; Alvarez, JV. APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. Cancer Immunol Res (2022): 10(1), 70–86.

2020

• Siamakpour-Reihani, S; Cao, F; Lyu, J; Ren, Y; Nixon, AB; Xie, J; Bush, AT; Starr, MD; Bain, JR; Muehlbauer, MJ; Ilkayeva, O; Byers Kraus, V; Huebner, JL; Chao, NJ; Sung, AD. Evaluating immune response and metabolic related biomarkers pre-allogenic hematopoietic stem cell transplant in acute myeloid leukemia. Plos One (2020): 17(6), e0268963

• Sung, AD; Jauhari, S; Siamakpour-Reihani, S; Rao, AV; Staats, J; Chan, C; Meyer, E; Gadi, VK; Nixon, AB; Lyu, J; Xie, J; Bohannon, L; Li, Z; Hourigan, CS; Dillon, LW; Wong, HY; Shelby, R; Diehl, L; de Castro, C; LeBlanc, T; Brander, D; Erba, H; Galal, A; Stefanovic, A; Chao, N; Rizzieri, DA. Microtransplantation in older patients with AML: A pilot study of safety, efficacy and immunologic effects. American Journal of Hematology (2020): 95(6), 662–671.

• Mathews, AM, Wysham, NG, Xie, J, Qin, X, Giovacchini, CX, Ekström, M, & MacIntyre, NR. Hypercapnia in Advanced Chronic Obstructive Pulmonary Disease: A Secondary Analysis of the National Emphysema Treatment Trial. Chronic Obstructive Pulmonary Diseases (2020): 7(4).

2019

• Elsamadicy, AA; Ashraf, B; Ren, X; Sergesketter, AR; Charalambous, L; Kemeny, H; Ejikeme, T; Yang, S; Pagadala, P; Parente, B; Xie, J; Pappas, TN; Lad, SP. Prevalence and Cost Analysis of Chronic Pain After Hernia Repair: A Potential Alternative Approach with Neurostimulation. Neuromodulation (2019): 22(8), 960–9

• 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 (2019): 40(2), 279–88. PMID: 30596980; PMCID: PMC6487681

• 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 (2019): 1, 84(3), 758–67. PMID: 29893899

2018

• 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) (2018); 80(5): 1015-1034. PMID: 31057329, PMCID: PMC6497089

• 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 (2018). 15; 34(20): 3581-3583. doi: 10.1093/bioinformatics/bty402. PMID: 29790906

• 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 (2018): 2400–2408. PMID: 29978465; PMCID: PMC6205899

• 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 (2018): 1(4). PMID: 30294719; PMCID: PMC6173523

• 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 (2018). PMID: 29978465

• 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 (2018): 423-430. PMID: 28961359

• 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 Patients. Neurosurgery (2018). PMID: 29893899

• 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 (2018): 417-420. PMID: 29975008

• 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 142-7 (2018): 1322-1331. PMID: 29168174

• 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 (2018): 57(2), 216–24. PMID: 29071797

2017

• Xie, J, and Kang, J. High-dimensional tests for functional networks of brain anatomic regions. Journal of Multivariate Analysis 156 (2017): 70-88. PMID: 28413234, PMCID: PMC5391152

• Charalambous, LT, Premji, A, Ty, 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, 67-2 (2017): 215-227. PMID: 29244019

• 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 (2017). PMID: 28961362

• 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 (2017): E797-E805. PMID: 28934786

• 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 (2017): E969-E977. PMID: 28934801

• 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 (2017): 354-360. PMID: 28322477, PMCID: PMC5482408

• 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 (2017): 331-339. PMID: 28205332, PMCID: PMC5464976

• 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 (2017): 340-347. PMID: 28370989, PMCID: PMC5464972

• 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 (2017): 256-262. PMID: 27696607, PMCID: PMC5378689

• 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 (2017): 64-71. PMID: 27836393

• 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 (2017): E257-E268. PMID: 28158163

• 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 (2017): 431-437. PMID: 27751919

Before 2017

• 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. PMID: 26406114, PMCID: PMC4808501

• Cai, TT, Li, H, Liu, W, and Xie, J. Joint Estimation of Multiple High-dimensional Precision Matrices. Statistica Sinica 26, no. 2 (2016): 445-464. PMID: 28316451, PMCID: PMC5351783

• 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 (2016): 319-328. PMID: 26857099

• Napoli, A, Xie, J, and Obeid, I. Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis. BMC neuroscience 15 (2014): 17. PMID: 24443925, PMCID: PMC3902005

• Cai, TT, Li, H, Liu, W, and Xie, J. Covariate-adjusted precision matrix estimation with an application in genetical genomics. Biometrika 100, no. 1 (2013): 139-156. PMID: 28316337, PMCID: PMC5351557

• Daye, ZJ, 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 (2012): 110-133. PMID: 22904608, PMCID: PMC3419598
  [Xie, J, Cai, TT, and Li, H. Correction to the paper “Optimal false discovery rate control for dependent data”. Statistics and its Interface 9, no. 1 (2016): 33-35.]

• Xie, J, Cai, TT, Maris, J, and Li, H. Optimal False Discovery Rate Control for Dependent Data. Statistics and its interface 4, no. 4 (2011): 417-430. PMID: 23378870, PMCID: PMC3559028

• 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 (2011): 273-290. PMID: 23049128, PMCID: PMC3419390

• 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 (2011): 299-308. PMID: 20374241, PMCID: PMC2902622

• 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. PMID: 22518205, PMCID: PMC3328409