Publications of Jichun Xie    :chronological  alphabetical  combined  bibtex listing:

Papers Published

1. Gao, Q; Ji, Z; Wang, L; Owzar, K; Li, Q-J; Chan, C; Xie, J, SifiNet: a robust and accurate method to identify feature gene sets and annotate cells., Nucleic Acids Res, vol. 52 no. 9 (May, 2024), pp. e46 [doi]  [abs]
2. Gao, Q; Ji, Z; Wang, L; Owzar, K; Li, Q-J; Chan, C; Xie, J, SifiNet: A robust and accurate method to identify feature gene sets and annotate cells., bioRxiv (April, 2024) [doi]  [abs]
3. Li, X; Pura, J; Allen, A; Owzar, K; Lu, J; Harms, M; Xie, J, DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree., Genet Epidemiol, vol. 48 no. 1 (February, 2024), pp. 42-55 [doi]  [abs]
4. Moris, D; Barfield, R; Chan, C; Chasse, S; Stempora, L; Xie, J; Plichta, JK; Thacker, J; Harpole, DH; Purves, T; Lagoo-Deenadayalan, S; Hwang, E-SS; Kirk, AD, Immune Phenotype and Postoperative Complications After Elective Surgery., Ann Surg, vol. 278 no. 6 (December, 2023), pp. 873-882 [doi]  [abs]
5. Poe, JC; Fang, J; Zhang, D; Lee, MR; DiCioccio, RA; Su, H; Qin, X; Zhang, JY; Visentin, J; Bracken, SJ; Ho, VT; Wang, KS; Rose, JJ; Pavletic, SZ; Hakim, FT; Jia, W; Suthers, AN; Curry-Chisolm, IM; Horwitz, ME; Rizzieri, DA; McManigle, WC; Chao, NJ; Cardones, AR; Xie, J; Owzar, K; Sarantopoulos, S, Single-cell landscape analysis unravels molecular programming of the human B cell compartment in chronic GVHD., JCI Insight, vol. 8 no. 11 (June, 2023), pp. e169732 [doi]  [abs]
6. Li, X; Sung, A; Xie, J, DART: Distance Assisted Recursive Testing, Journal of Machine Learning Research, vol. 24 no. 169 (April, 2023)  [abs]
7. Pura, JA; Li, X; Chan, C; Xie, J, TEAM: A MULTIPLE TESTING ALGORITHM ON THE AGGREGATION TREE FOR FLOW CYTOMETRY ANALYSIS., Ann Appl Stat, vol. 17 no. 1 (March, 2023), pp. 621-640 [doi]  [abs]
8. 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., J Neurovirol, vol. 29 no. 1 (February, 2023), pp. 78-93 [doi]  [abs]
9. Hou, L; Ji, Z; Wang, J; Xie, J, Editorial: Statistical and computational methods for single-cell sequencing analysis., Front Genet, vol. 14 (2023), pp. 1235174 [doi]
10. Li, X; Sung, AD; Xie, J, DART: Distance Assisted Recursive Testing., J Mach Learn Res, vol. 24 (2023)  [abs]
11. Fang, J; Chan, C; Owzar, K; Wang, L; Qin, D; Li, Q-J; Xie, J, Clustering Deviation Index (CDI): a robust and accurate internal measure for evaluating scRNA-seq data clustering., Genome Biol, vol. 23 no. 1 (December, 2022), pp. 269 [doi]  [abs]
12. SenNet Consortium, NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health., Nat Aging, vol. 2 no. 12 (December, 2022), pp. 1090-1100 [doi]  [abs]
13. 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, vol. 10 no. 1 (January, 2022), pp. 70-86 [doi]  [abs]
14. 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, vol. 17 no. 6 (2022), pp. e0268963 [doi]  [abs]
15. DiMarco, AV; Qin, X; McKinney, B; Lupo, R; Xie, J; Owzar, K; Alvarez, J, 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., CANCER IMMUNOLOGY RESEARCH, vol. 9 no. 2 (2021)
16. 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 Obstr Pulm Dis, vol. 7 no. 4 (October, 2020), pp. 336-345 [doi]  [abs]
17. 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., Am J Hematol, vol. 95 no. 6 (June, 2020), pp. 662-671 [doi]  [abs]
18. Ramalingam, S; Siamakpour-Reihani, S; Bohannon, L; Ren, Y; Sibley, A; Nixon, A; Lyu, J; Xie, J; Choi, T; Gasparetto, C; Horwitz, ME; Long, GD; Lopez, R; Rizzieri, DA; Sarantopoulos, S; Chao, NJ; Sung, AD, Phase II Trial of Pasireotide to Prevent GI Toxicity and Acute Gvhd in Allogeneic HSCT, BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION, vol. 26 no. 3 (March, 2020), pp. S48-S49, ELSEVIER SCIENCE INC
19. Force, J; Qin, X; Zhang, D; Marcom, PK; Marks, J; Taylor, ML; Anders, C; Owzar, K; Xie, J, 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, Cancer Research, vol. 80 no. 4_Supplement (February, 2020), American Association for Cancer Research (AACR) [doi]  [abs]
20. 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, vol. 22 no. 8 (December, 2019), pp. 960-969 [doi]  [abs]
21. Poe, JC; Zhang, D; Xie, J; DiCioccio, RA; Qin, X; Fang, J; Ho, VT; Rose, JJ; Pavletic, SZ; Hakim, FT; Jia, W; Suthers, AN; Horwitz, ME; Rizzieri, DA; McManigle, WC; Chao, NJ; Owzar, K; Sarantopoulos, S, Single-Cell RNA-Seq Identifies Potentially Pathogenic B Cell Populations That Uniquely Circulate in Patients with Chronic Gvhd, Blood, vol. 134 no. Supplement_1 (November, 2019), pp. 874-874, American Society of Hematology [doi]  [abs]
22. Wang, X; Liu, H; Xu, Y; Xie, J; Zhu, D; Amos, CI; Fang, S; Lee, JE; Li, X; Nan, H; Song, Y; Wei, Q, Genetic variants in the calcium signaling pathway genes are associated with cutaneous melanoma-specific survival., Carcinogenesis, vol. 40 no. 2 (April, 2019), pp. 279-288 [doi]  [abs]
23. Elsamadicy, AA; Ren, X; Kemeny, H; Charalambous, L; Sergesketter, AR; Rahimpour, S; Williamson, T; Goodwin, CR; Abd-El-Barr, MM; Gottfried, ON; Xie, J; 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, vol. 84 no. 3 (March, 2019), pp. 758-767 [doi]  [abs]
24. Xu, Y; Liu, H; Liu, S; Wang, Y; Xie, J; Stinchcombe, TE; Su, L; Zhang, R; Christiani, DC; Li, W; Wei, Q, Genetic variant of IRAK2 in the toll-like receptor signaling pathway and survival of non-small cell lung cancer., Int J Cancer, vol. 143 no. 10 (November, 2018), pp. 2400-2408 [doi]  [abs]
25. 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, vol. 80 no. 5 (November, 2018), pp. 1015-1034 [doi]  [abs]
26. Lin, J; Gresham, J; Wang, T; Kim, SY; Alvarez, J; Damrauer, JS; Floyd, S; Granek, J; Allen, A; Chan, C; Xie, J; Owzar, K, bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens., Bioinformatics, vol. 34 no. 20 (October, 2018), pp. 3581-3583 [doi]  [abs]
27. Elsamadicy, AA; Ren, X; Kemeny, H; Charalambous, L; Rahimpour, S; Williamson, T; Goodwin, CR; Abd-El-Barr, MM; Gottfried, ON; Xie, J; Lad, N, 156 Independent Associations With 30- and 90-Day Unplanned Readmissions After Elective Lumbar Spine Surgery, Neurosurgery, vol. 65 no. CN_suppl_1 (September, 2018), pp. 100-100, Ovid Technologies (Wolters Kluwer Health) [doi]
28. 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; Vaupel, J, Sex Differences in Genetic Associations With Longevity., JAMA Netw Open, vol. 1 no. 4 (August, 2018), pp. e181670 [doi]  [abs]
29. Elsamadicy, AA; Yang, S; Sergesketter, AR; Ashraf, B; Charalambous, L; Kemeny, H; Ejikeme, T; Ren, X; Pagadala, P; Parente, B; Xie, J; Lad, SP, Prevalence and Cost Analysis of Complex Regional Pain Syndrome (CRPS): A Role for Neuromodulation., Neuromodulation, vol. 21 no. 5 (July, 2018), pp. 423-430 [doi]  [abs]
30. Lad, SP; Yang, S; Xie, J; Farjat, A; Pagadala, P; Parente, B, Down the Rabbit Hole: Specialty Influence on SCS Outcomes., Neuromodulation, vol. 21 no. 4 (June, 2018), pp. 417-420 [doi]
31. Duan, B; Hu, J; Liu, H; Wang, Y; Li, H; Liu, S; Xie, J; Owzar, K; Abbruzzese, J; Hurwitz, H; Gao, H; Wei, Q, Genetic variants in the platelet-derived growth factor subunit B gene associated with pancreatic cancer risk., Int J Cancer, vol. 142 no. 7 (April, 2018), pp. 1322-1331 [doi]  [abs]
32. 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; Wei, Q, Novel genetic variants in the P38MAPK pathway gene ZAK and susceptibility to lung cancer., Mol Carcinog, vol. 57 no. 2 (February, 2018), pp. 216-224 [doi]  [abs]
33. Charalambous, LT; Premji, A; Tybout, C; Hunt, A; Cutshaw, D; Elsamadicy, AA; Yang, S; Xie, J; Giamberardino, C; Pagadala, P; Perfect, JR; Lad, SP, Prevalence, healthcare resource utilization and overall burden of fungal meningitis in the United States., J Med Microbiol, vol. 67 no. 2 (February, 2018), pp. 215-227 [doi]  [abs]
34. Elsamadicy, AA; Sergesketter, A; Ren, X; Mohammed Qasim Hussaini, S; Laarakker, A; Rahimpour, S; Ejikeme, T; Yang, S; Pagadala, P; Parente, B; Xie, J; Lad, SP, Drivers and Risk Factors of Unplanned 30-Day Readmission Following Spinal Cord Stimulator Implantation., Neuromodulation, vol. 21 no. 1 (January, 2018), pp. 87-92 [doi]  [abs]
35. Farber, SH; Han, JL; Elsamadicy, AA; Hussaini, Q; Yang, S; Pagadala, P; Parente, B; Xie, J; Lad, SP, Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome, PAIN PHYSICIAN, vol. 20 no. 6 (September, 2017), pp. E796-E804, AM SOC INTERVENTIONAL PAIN PHYSICIANS
36. Farber, SH; Han, JL; Petraglia, FW; Gramer, R; Yang, S; Pagadala, P; Parente, B; Xie, J; Petrella, JR; Lad, SP, Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation, PAIN PHYSICIAN, vol. 20 no. 6 (September, 2017), pp. E968-E976, AM SOC INTERVENTIONAL PAIN PHYSICIANS
37. Farber, SH; Han, JL; Petraglia Iii, FW; Gramer, R; Yang, S; Pagadala, P; Parente, B; Xie, J; Petrella, JR; Lad, SP, Increasing Rates of Imaging in Failed Back Surgery Syndrome Patients: Implications for Spinal Cord Stimulation., Pain Physician, vol. 20 no. 6 (September, 2017), pp. E969-E977  [abs]
38. Farber, SH; Han, JL; Elsamadicy, AA; Hussaini, Q; Yang, S; Pagadala, P; Parente, B; Xie, J; Lad, SP, Long-term Cost Utility of Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome., Pain Physician, vol. 20 no. 6 (September, 2017), pp. E797-E805  [abs]
39. Han, JL; Murphy, KR; Hussaini, SMQ; Yang, S; Parente, B; Xie, J; Pagadala, P; Lad, SP, Explantation Rates and Healthcare Resource Utilization in Spinal Cord Stimulation., Neuromodulation, vol. 20 no. 4 (June, 2017), pp. 331-339 [doi]  [abs]
40. Elsamadicy, AA; Farber, SH; Yang, S; Hussaini, SMQ; Murphy, KR; Sergesketter, A; Suryadevara, CM; Pagadala, P; Parente, B; Xie, J; Lad, SP, Impact of Insurance Provider on Overall Costs in Failed Back Surgery Syndrome: A Cost Study of 122,827 Patients., Neuromodulation, vol. 20 no. 4 (June, 2017), pp. 354-360 [doi]  [abs]
41. Hussaini, SMQ; Murphy, KR; Han, JL; Elsamadicy, AA; Yang, S; Premji, A; Parente, B; Xie, J; Pagadala, P; Lad, SP, Specialty-Based Variations in Spinal Cord Stimulation Success Rates for Treatment of Chronic Pain., Neuromodulation, vol. 20 no. 4 (June, 2017), pp. 340-347 [doi]  [abs]
42. Murphy, KR; Han, JL; Hussaini, SMQ; Yang, S; Parente, B; Xie, J; Lad, SP, The Volume-Outcome Effect: Impact on Trial-to-Permanent Conversion Rates in Spinal Cord Stimulation., Neuromodulation, vol. 20 no. 3 (April, 2017), pp. 256-262 [doi]  [abs]
43. Xie, J; Kang, J, High-dimensional tests for functional networks of brain anatomic regions., J Multivar Anal, vol. 156 (April, 2017), pp. 70-88 [doi]  [abs]
44. Farber, SH; Murphy, KR; Suryadevara, CM; Babu, R; Yang, S; Feng, L; Xie, J; Perfect, JR; Lad, SP, Comparing outcomes of early, late, and non-surgical management of intraspinal abscess., J Clin Neurosci, vol. 36 (February, 2017), pp. 64-71 [doi]  [abs]
45. Murphy, KR; Han, JL; Yang, S; Hussaini, SMQ; Elsamadicy, AA; Parente, B; Xie, J; Pagadala, P; Lad, SP, Prevalence of Specific Types of Pain Diagnoses in a Sample of United States Adults., Pain Physician, vol. 20 no. 2 (February, 2017), pp. E257-E268  [abs]
46. Krucoff, MO; Cook, S; Adogwa, O; Moreno, J; Yang, S; Xie, J; Firempong, AO; Lad, N; Bagley, CA, Racial, Socioeconomic, and Gender Disparities in the Presentation, Treatment, and Outcomes of Adult Chiari I Malformations., World Neurosurg, vol. 97 (January, 2017), pp. 431-437 [doi]  [abs]
47. Cai, TT; Li, H; Liu, W; Xie, J, Joint Estimation of Multiple High-dimensional Precision Matrices., Stat Sin, vol. 26 no. 2 (April, 2016), pp. 445-464 [doi]  [abs]
48. Farber, SH; Hatef, J; Han, JL; Marky, AH; Xie, J; Huang, K; Verla, T; Lokhnygina, Y; Collins, TA; Lad, SP, Implantable Neurostimulation for Headache Disorders: Effect on Healthcare Utilization and Expenditures., Neuromodulation, vol. 19 no. 3 (April, 2016), pp. 319-328 [doi]  [abs]
49. Ha, MJ; Sun, W; Xie, J, PenPC: A two-step approach to estimate the skeletons of high-dimensional directed acyclic graphs., Biometrics, vol. 72 no. 1 (March, 2016), pp. 146-155 [doi]  [abs]
50. Xie, J; Cai, TT; Li, H, Correction to the paper “Optimal False Discovery Rate Control for Dependent Data”, Statistics and its Interface, vol. 9 no. 1 (January, 2016), pp. 33-35 [doi]  [abs]
51. Napoli, A; Xie, J; Obeid, I, Understanding the temporal evolution of neuronal connectivity in cultured networks using statistical analysis., BMC Neurosci, vol. 15 (January, 2014), pp. 17 [doi]  [abs]
52. Cai, TT; Li, H; Liu, W; Xie, J, Covariate-Adjusted Precision Matrix Estimation with an Application in Genetical Genomics., Biometrika, vol. 100 no. 1 (March, 2013), pp. 139-156 [doi]  [abs]
53. 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, vol. 21 no. 1 (April, 2012), pp. 110-133 [doi]  [abs]
54. Xie, J; Cai, TT; Li, H, Sample size and power analysis for sparse signal recovery in genome-wide association studies., Biometrika, vol. 98 no. 2 (June, 2011), pp. 273-290 [doi]  [abs]
55. Chen, J; Xie, J; Li, H, A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis., Biometrics, vol. 67 no. 1 (March, 2011), pp. 299-308 [doi]  [abs]
56. Xie, J; Cai, TT; Maris, J; Li, H, Optimal False Discovery Rate Control for Dependent Data., Stat Interface, vol. 4 no. 4 (2011), pp. 417-430 [doi]  [abs]
57. Cotch, MF; Peet, J; Shults, J; Stambolian, D; Xie, J, Quasi-least squares with mixed linear correlation structures, Statistics and Its Interface, vol. 3 no. 2 (2010), pp. 223-233, International Press of Boston [doi]