Yuan Ji

Publications
  1. Yeh AC, Li H, Zhu Y, Zhang J, Khramtsova G, Drukker K, Edwards A, McGregor S, Yoshimatsu T, Zheng Y, Niu Q, Abe H, Mueller J, Conzen S, Ji Y, Giger ML, Olopade OI. Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling. Cancer Imaging. 2019 Jul 15; 19(1):48. View in: PubMed

  2. Liu M, Wang SJ, Ji Y. The i3+3 design for phase I clinical trials. J Biopharm Stat. 2019 Jul 15; 1-11. View in: PubMed

  3. Yang Y, Xu W, Peng D, Wang H, Zhang X, Wang H, Xiao F, Zhu Y, Ji Y, Gulukota K, Helseth DL, Mangold KA, Sullivan M, Kaul K, Wang E, Prabhakar BS, Li J, Wu X, Wang L, Seth P. An Oncolytic Adenovirus Targeting Transforming Growth Factor ß Inhibits Protumorigenic Signals and Produces Immune Activation: A Novel Approach to Enhance Anti-PD-1 and Anti-CTLA-4 Therapy. Hum Gene Ther. 2019 09; 30(9):1117-1132. View in: PubMed

  4. Guo W, Ji Y, Li D. R-TPI: rolling toxicity probability interval design to shorten the duration and maintain safety of phase I trials. J Biopharm Stat. 2019; 29(3):411-424. View in: PubMed

  5. Zhu Y, Mohamed ASR, Lai SY, Yang S, Kanwar A, Wei L, Kamal M, Sengupta S, Elhalawani H, Skinner H, Mackin DS, Shiao J, Messer J, Wong A, Ding Y, Zhang L, Court L, Ji Y, Fuller CD. Imaging-Genomic Study of Head and Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes and Genomic Mechanisms via Integration of The Cancer Genome Atlas and The Cancer Imaging Archive. JCO Clin Cancer Inform. 2019 02; 3:1-9. View in: PubMed

  6. Shen X, Wu D, Tang M, Sun H, Ji Y, Huang C, Zeng M. Liver computed tomographic perfusion for monitoring the early therapeutic response to sorafenib in advanced hepatocellular carcinoma patients. J Cancer Res Ther. 2018; 14(7):1556-1562. View in: PubMed

  7. Jin K, Wang H, Zeng M, Rao S, Yan L, Ji Y, Fu C, Sheng R. A comparative study of MR extracellular volume fraction measurement and two-dimensional shear-wave elastography in assessment of liver fibrosis with chronic hepatitis B. Abdom Radiol (NY). 2019 Apr; 44(4):1407-1414. View in: PubMed

  8. Zheng BH, Liu LZ, Zhang ZZ, Shi JY, Dong LQ, Tian LY, Ding ZB, Ji Y, Rao SX, Zhou J, Fan J, Wang XY, Gao Q. Radiomics score: a potential prognostic imaging feature for postoperative survival of solitary HCC patients. BMC Cancer. 2018 Nov 21; 18(1):1148. View in: PubMed

  9. Cheng X, Yu S, Wang Y, Cui Y, Li W, Yu Y, Tang C, Jiang H, Ji Y, Sun Y, Wang X, Shen Z, Liu F, Liu TS. The role of oxaliplatin in the adjuvant setting of different Lauren's type of gastric adenocarcinoma after D2 gastrectomy: a real-world study. Gastric Cancer. 2019 05; 22(3):587-597. View in: PubMed

  10. Zhou J, Sun HC, Wang Z, Cong WM, Wang JH, Zeng MS, Yang JM, Bie P, Liu LX, Wen TF, Han GH, Wang MQ, Liu RB, Lu LG, Ren ZG, Chen MS, Zeng ZC, Liang P, Liang CH, Chen M, Yan FH, Wang WP, Ji Y, Cheng WW, Dai CL, Jia WD, Li YM, Li YX, Liang J, Liu TS, Lv GY, Mao YL, Ren WX, Shi HC, Wang WT, Wang XY, Xing BC, Xu JM, Yang JY, Yang YF, Ye SL, Yin ZY, Zhang BH, Zhang SJ, Zhou WP, Zhu JY, Liu R, Shi YH, Xiao YS, Dai Z, Teng GJ, Cai JQ, Wang WL, Dong JH, Li Q, Shen F, Qin SK, Fan J. Guidelines for Diagnosis and Treatment of Primary Liver Cancer in China (2017 Edition). Liver Cancer. 2018 Sep; 7(3):235-260. View in: PubMed

  11. Chen XX, Yin Y, Cheng JW, Huang A, Hu B, Zhang X, Sun YF, Wang J, Wang YP, Ji Y, Qiu SJ, Fan J, Zhou J, Yang XR. BAP1 acts as a tumor suppressor in intrahepatic cholangiocarcinoma by modulating the ERK1/2 and JNK/c-Jun pathways. Cell Death Dis. 2018 10 10; 9(10):1036. View in: PubMed

  12. Gillard M, Javier R, Ji Y, Zheng SL, Xu J, Brendler CB, Crawford SE, Pierce BL, Griend DJV, Franco OE. Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men. Cancer Res. 2018 11 01; 78(21):6134-6145. View in: PubMed

  13. Sheng RF, Jin KP, Yang L, Wang HQ, Liu H, Ji Y, Fu CX, Zeng MS. Histogram Analysis of Diffusion Kurtosis Magnetic Resonance Imaging for Diagnosis of Hepatic Fibrosis. Korean J Radiol. 2018 Sep-Oct; 19(5):916-922. View in: PubMed

  14. Xiao Q, Sun Y, Dobi A, Srivastava S, Wang W, Srivastava S, Ji Y, Hou J, Zhao GP, Li Y, Li H. Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer. Sci Rep. 2018 08 27; 8(1):12868. View in: PubMed

  15. Cheng J, Wei D, Ji Y, Chen L, Yang L, Li G, Wu L, Hou T, Xie L, Ding G, Li H, Li Y. Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers. Genome Med. 2018 05 30; 10(1):42. View in: PubMed

  16. Wang WT, Zhu S, Ding Y, Yang L, Chen CZ, Ye QH, Ji Y, Zeng MS, Rao SX. T1 mapping on gadoxetic acid-enhanced MR imaging predicts recurrence of hepatocellular carcinoma after hepatectomy. Eur J Radiol. 2018 Jun; 103:25-31. View in: PubMed

  17. Ni Y, Müller P, Wei L, Ji Y. Bayesian graphical models for computational network biology. BMC Bioinformatics. 2018 03 21; 19(Suppl 3):63. View in: PubMed

  18. Wang H, Yang C, Rao S, Ji Y, Han J, Sheng R, Zeng M. MR imaging of hepatocellular adenomas on genotype-phenotype classification: A report from China. Eur J Radiol. 2018 Mar; 100:135-141. View in: PubMed

  19. Hu B, Ding GY, Fu PY, Zhu XD, Ji Y, Shi GM, Shen YH, Cai JB, Yang Z, Zhou J, Fan J, Sun HC, Kuang M, Huang C. NOD-like receptor X1 functions as a tumor suppressor by inhibiting epithelial-mesenchymal transition and inducing aging in hepatocellular carcinoma cells. J Hematol Oncol. 2018 02 26; 11(1):28. View in: PubMed

  20. Yang C, Wang H, Tang Y, Rao S, Sheng R, Ji Y, Zeng M. ADC similarity predicts microvascular invasion of bifocal hepatocellular carcinoma. Abdom Radiol (NY). 2018 09; 43(9):2295-2302. View in: PubMed

  21. Sheng RF, Zhai CW, Ji Y, Chen CZ, Yang L, Zeng MS. Role of MR in the differentiation of IgG4-related from non-IgG4-related hepatic inflammatory pseudotumor. Hepatobiliary Pancreat Dis Int. 2017 Dec 15; 16(6):631-637. View in: PubMed

  22. Wei L, Jin Z, Yang S, Xu Y, Zhu Y, Ji Y. TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data. Bioinformatics. 2018 05 01; 34(9):1615-1617. View in: PubMed

  23. Sun X, Wang SC, Wei Y, Luo X, Jia Y, Li L, Gopal P, Zhu M, Nassour I, Chuang JC, Maples T, Celen C, Nguyen LH, Wu L, Fu S, Li W, Hui L, Tian F, Ji Y, Zhang S, Sorouri M, Hwang TH, Letzig L, James L, Wang Z, Yopp AC, Singal AG, Zhu H. Arid1a Has Context-Dependent Oncogenic and Tumor Suppressor Functions in Liver Cancer. Cancer Cell. 2017 11 13; 32(5):574-589.e6. View in: PubMed

  24. Hu C, Li W, Tian F, Jiang K, Liu X, Cen J, He Q, Qiu Z, Kienast Y, Wang Z, Zhang H, Ji Y, Hu J, Hui L. Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma. J Hepatol. 2018 03; 68(3):465-475. View in: PubMed

  25. Sun YF, Guo W, Xu Y, Shi YH, Gong ZJ, Ji Y, Du M, Zhang X, Hu B, Huang A, Chen GG, Lai PBS, Cao Y, Qiu SJ, Zhou J, Yang XR, Fan J. Circulating Tumor Cells from Different Vascular Sites Exhibit Spatial Heterogeneity in Epithelial and Mesenchymal Composition and Distinct Clinical Significance in Hepatocellular Carcinoma. Clin Cancer Res. 2018 02 01; 24(3):547-559. View in: PubMed

  26. Ni Y, Müller P, Zhu Y, Ji Y. Heterogeneous reciprocal graphical models. Biometrics. 2018 06; 74(2):606-615. View in: PubMed

  27. Zuanetti DA, Müller P, Zhu Y, Yang S, Ji Y. Clustering distributions with the marginalized nested Dirichlet process. Biometrics. 2018 06; 74(2):584-594. View in: PubMed

  28. Xu Y, Zhao G, Pu N, Nuerxiati A, Ji Y, Zhang L, Rong Y, Lou W, Wang D, Kuang T, Xu X, Wu W. One Hundred Twenty-One Resected Solid Pseudopapillary Tumors of the Pancreas: An 8-Year Single-Institution Experience at Zhongshan Hospital, Shanghai, China. Pancreas. 2017 09; 46(8):1023-1028. View in: PubMed

  29. Wang ZC, Wang C, Ding Y, Ji Y, Zeng MS, Rao SX. CT volumetry can potentially predict the local stage for gastric cancer after chemotherapy. Diagn Interv Radiol. 2017 Jul-Aug; 23(4):257-262. View in: PubMed

  30. Sheng RF, Wang HQ, Jin KP, Yang L, Liu H, Ji Y, Fu CX, Zeng MS. Histogram analyses of diffusion kurtosis indices and apparent diffusion coefficient in assessing liver regeneration after ALPPS and a comparative study with portal vein ligation. J Magn Reson Imaging. 2018 03; 47(3):729-736. View in: PubMed

  31. Chen T, Ji Y, Yao LQ, Xu MD, Zhou PH. Colonic polypoid mucosa-associated lymphoid tissue lymphoma. Clin Res Hepatol Gastroenterol. 2018 04; 42(2):101-102. View in: PubMed

  32. Manching H, Sengupta S, Hopper KR, Polson SW, Ji Y, Wisser RJ. Phased Genotyping-by-Sequencing Enhances Analysis of Genetic Diversity and Reveals Divergent Copy Number Variants in Maize. G3 (Bethesda). 2017 07 05; 7(7):2161-2170. View in: PubMed

  33. Lee J, Müller P, Sengupta S, Gulukota K, Ji Y. Bayesian inference for intratumour heterogeneity in mutations and copy number variation. J R Stat Soc Ser C Appl Stat. 2016 08; 65(4):547-563. View in: PubMed

  34. Guo W, Wang SJ, Yang S, Lynn H, Ji Y. A Bayesian interval dose-finding design addressingOckham's razor: mTPI-2. Contemp Clin Trials. 2017 07; 58:23-33. View in: PubMed

  35. Huang C, Zhu XD, Ji Y, Ding GY, Shi GM, Shen YH, Zhou J, Fan J, Sun HC. Microvascular invasion has limited clinical values in hepatocellular carcinoma patients at Barcelona Clinic Liver Cancer (BCLC) stages 0 or B. BMC Cancer. 2017 01 17; 17(1):58. View in: PubMed

  36. Chen T, Zhou PH, Chu Y, Zhang YQ, Chen WF, Ji Y, Yao LQ, Xu MD. Long-term Outcomes of Submucosal Tunneling Endoscopic Resection for Upper Gastrointestinal Submucosal Tumors. Ann Surg. 2017 02; 265(2):363-369. View in: PubMed

  37. Narayanan J, Dobrin S, Choi J, Rubin S, Pham A, Patel V, Frigerio R, Maurer D, Gupta P, Link L, Walters S, Wang C, Ji Y, Maraganore DM. Structured clinical documentation in the electronic medical record to improve quality and to support practice-based research in epilepsy. Epilepsia. 2017 01; 58(1):68-76. View in: PubMed

  38. Hu XX, Yang ZX, Liang HY, Ding Y, Grimm R, Fu CX, Liu H, Yan X, Ji Y, Zeng MS, Rao SX. Whole-tumor MRI histogram analyses of hepatocellular carcinoma: Correlations with Ki-67 labeling index. J Magn Reson Imaging. 2017 08; 46(2):383-392. View in: PubMed

  39. Li H, Zhu Y, Burnside ES, Huang E, Drukker K, Hoadley KA, Fan C, Conzen SD, Zuley M, Net JM, Sutton E, Whitman GJ, Morris E, Perou CM, Ji Y, Giger ML. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set. NPJ Breast Cancer. 2016; 2. View in: PubMed

  40. Yang C, Wang H, Sheng R, Ji Y, Rao S, Zeng M. Microvascular invasion in hepatocellular carcinoma: is it predictable with a new, preoperative application of diffusion-weighted imaging? Clin Imaging. 2017 Jan - Feb; 41:101-105. View in: PubMed

  41. Guo W, Ji Y, Catenacci DVT. A subgroup cluster-based Bayesian adaptive design for precision medicine. Biometrics. 2017 06; 73(2):367-377. View in: PubMed

  42. Li DH, Whitmore JB, Guo W, Ji Y. Toxicity and Efficacy Probability Interval Design for Phase I Adoptive Cell Therapy Dose-Finding Clinical Trials. Clin Cancer Res. 2017 Jan 01; 23(1):13-20. View in: PubMed

  43. Xu Y, Trippa L, Müller P, Ji Y. Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials. Stat Biosci. 2016 Jun; 8(1):159-180. View in: PubMed

  44. Li L, Li D, Tian F, Cen J, Chen X, Ji Y, Hui L. Hepatic Loss of Borealin Impairs Postnatal Liver Development, Regeneration, and Hepatocarcinogenesis. J Biol Chem. 2016 Sep 30; 291(40):21137-21147. View in: PubMed

  45. Zhang L, Shao Y, Li L, Tian F, Cen J, Chen X, Hu D, Zhou Y, Xie W, Zheng Y, Ji Y, Liu M, Li D, Hui L. Efficient liver repopulation of transplanted hepatocyte prevents cirrhosis in a rat model of hereditary tyrosinemia type I. Sci Rep. 2016 08 11; 6:31460. View in: PubMed

  46. Lin C, Zhao GC, Xu YD, Wang DS, Jin DY, Ji Y, Lou WH, Wu WC. Increased expression of aTubulin is associated with poor prognosis in patients with pancreatic cancer after surgical resection. Oncotarget. 2016 Sep 13; 7(37):60657-60664. View in: PubMed

  47. Ma Y, Ji Y, You M, Wang S, Dong Y, Jin G, Lin M, Wang Q, Li A, Zhang X, Xu F. Labeling and long-term tracking of bone marrow mesenchymal stem cells in vitro using NaYF4:Yb(3+),Er(3+) upconversion nanoparticles. Acta Biomater. 2016 09 15; 42:199-208. View in: PubMed

  48. Sheng RF, Xie YH, Ji Y, Chen CZ, Yang L, Jin KP, Zeng MS. MR comparative study of combined hepatocellular-cholangiocarcinoma in normal, fibrotic, and cirrhotic livers. Abdom Radiol (NY). 2016 11; 41(11):2102-2114. View in: PubMed

  49. Li D, Fu J, Du M, Zhang H, Li L, Cen J, Li W, Chen X, Lin Y, Conway EM, Pikarsky E, Wang H, Pan G, Ji Y, Wang HY, Hui L. Hepatocellular carcinoma repression by TNFa-mediated synergistic lethal effect of mitosis defect-induced senescence and cell death sensitization. Hepatology. 2016 10; 64(4):1105-20. View in: PubMed

  50. Li H, Zhu Y, Burnside ES, Drukker K, Hoadley KA, Fan C, Conzen SD, Whitman GJ, Sutton EJ, Net JM, Ganott M, Huang E, Morris EA, Perou CM, Ji Y, Giger ML. MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays. Radiology. 2016 Nov; 281(2):382-391. View in: PubMed

  51. Luo R, Zhao J, Tan Y, Sujie A, Zeng H, Ji Y. [Hepatic angiomyolipoma: a clinicopathologic features and prognosis analysis of 182 cases]. Zhonghua Bing Li Xue Za Zhi. 2016 Mar; 45(3):165-9. View in: PubMed

  52. Guo W, Li H, Zhu Y, Lan L, Yang S, Drukker K, Morris E, Burnside E, Whitman G, Giger ML, Ji Y. Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data. J Med Imaging (Bellingham). 2015 10; 2(4):041007. View in: PubMed

  53. Chen T, Zhou PH, Chu Y, Zhang YQ, Chen WF, Ji Y, Yao LQ, Xu MD. Long-term Outcomes of Submucosal Tunneling Endoscopic Resection for Upper Gastrointestinal Submucosal Tumors. Ann Surg. 2016 Jan 19. View in: PubMed

  54. Sengupta S, Zhou T, Müeller P, Ji Y. A BAYESIAN NONPARAMETRIC MODEL FOR RECONSTRUCTING TUMOR SUBCLONES BASED ON MUTATION PAIRS. Pac Symp Biocomput. 2016; 21:393-404. View in: PubMed

  55. Xu Y, Zheng X, Yuan Y, Estecio MR, Issa JP, Ji Y, Liang S. A Bayesian Model for SNP Discovery Based on Next-Generation Sequencing Data. IEEE Int Workshop Genomic Signal Process Stat. 2012 Dec; 2012:42-45. View in: PubMed

  56. Ge X, Wang H, Xu C, Liu Y, Ji Y, Tan Y, Hou Y, Qin J. Heterogeneous Her2/Neu expression in gastric and gastroesophageal cancer-reply. Hum Pathol. 2016 Feb; 48:174-5. View in: PubMed

  57. Ma Y, Ji Y, Huang G, Ling K, Zhang X, Xu F. Bioprinting 3D cell-laden hydrogel microarray for screening human periodontal ligament stem cell response to extracellular matrix. Biofabrication. 2015 Dec 22; 7(4):044105. View in: PubMed

  58. Zhu Y, Li H, Guo W, Drukker K, Lan L, Giger ML, Ji Y. Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma. Sci Rep. 2015 Dec 07; 5:17787. View in: PubMed

  59. Xu Y, Zhu Y, Müller P, Mitra R, Ji Y. Characterizing Cancer-Specific Networks by Integrating TCGA Data. Cancer Inform. 2014; 13(Suppl 2):125-31. View in: PubMed

  60. Burnside ES, Drukker K, Li H, Bonaccio E, Zuley M, Ganott M, Net JM, Sutton EJ, Brandt KR, Whitman GJ, Conzen SD, Lan L, Ji Y, Zhu Y, Jaffe CC, Huang EP, Freymann JB, Kirby JS, Morris EA, Giger ML. Using computer-extracted image phenotypes from tumors on breast magnetic resonance imaging to predict breast cancer pathologic stage. Cancer. 2016 Mar 01; 122(5):748-57. View in: PubMed

  61. Lee J, Thall PF, Ji Y, Müller P. A decision-theoretic phase I-II design for ordinal outcomes in two cycles. Biostatistics. 2016 Apr; 17(2):304-19. View in: PubMed

  62. Guo W, Ni Y, Ji Y. TEAMS: Toxicity- and Efficacy-based Dose Insertion Design with Adaptive Model Selection for Phase I/II Dose-Escalation Trials in Oncology. Stat Biosci. 2015 Oct; 7(2):432-459. View in: PubMed

  63. Lee J, Müller P, Zhu Y, Ji Y. A Nonparametric Bayesian Model for Nested Clustering. Methods Mol Biol. 2016; 1362:129-41. View in: PubMed

  64. Zhang J, Fan S, Mao Y, Ji Y, Jin L, Lu J, Chen X. Cardiovascular protective effect of polysaccharide from Ophiopogon japonicus in diabetic rats. Int J Biol Macromol. 2016 Jan; 82:505-13. View in: PubMed

  65. Sengupta S, Gulukota K, Zhu Y, Ober C, Naughton K, Wentworth-Sheilds W, Ji Y. Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples. Nucleic Acids Res. 2016 Feb 18; 44(3):e25. View in: PubMed

  66. Yang S, Wang SJ, Ji Y. An integrated dose-finding tool for phase I trials in oncology. Contemp Clin Trials. 2015 Nov; 45(Pt B):426-434. View in: PubMed

  67. Lee J, Thall PF, Ji Y, Müller P. Bayesian Dose-Finding in Two Treatment Cycles Based on the Joint Utility of Efficacy and Toxicity. J Am Stat Assoc. 2015 Jun 01; 110(510):711-722. View in: PubMed

  68. Xu Y, Zheng X, Yuan Y, Estecio MR, Issa JP, Qiu P, Ji Y, Liang S. BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data. IEEE/ACM Trans Comput Biol Bioinform. 2014 Nov-Dec; 11(6):1038-44. View in: PubMed

  69. Yang LX, Gao Q, Shi JY, Wang ZC, Zhang Y, Gao PT, Wang XY, Shi YH, Ke AW, Shi GM, Cai JB, Liu WR, Duan M, Zhao YJ, Ji Y, Gao DM, Zhu K, Zhou J, Qiu SJ, Cao Y, Tang QQ, Fan J. Mitogen-activated protein kinase kinase kinase 4 deficiency in intrahepatic cholangiocarcinoma leads to invasive growth and epithelial-mesenchymal transition. Hepatology. 2015 Dec; 62(6):1804-16. View in: PubMed

  70. Sheng RF, Zeng MS, Ji Y, Yang L, Chen CZ, Rao SX. MR features of small hepatocellular carcinoma in normal, fibrotic, and cirrhotic livers: a comparative study. Abdom Imaging. 2015 Oct; 40(8):3062-9. View in: PubMed

  71. Chen T, Yao LQ, Xu MD, Zhang YQ, Chen WF, Shi Q, Cai SL, Chen YY, Xie YH, Ji Y, Chen SY, Zhou PH, Zhong YS. Efficacy and Safety of Endoscopic Submucosal Dissection for Colorectal Carcinoids. Clin Gastroenterol Hepatol. 2016 Apr; 14(4):575-81. View in: PubMed

  72. Xu Y, Lee J, Yuan Y, Mitra R, Liang S, Müller P, Ji Y. Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data. Bayesian Anal. 2013 Dec; 8(4):759-780. View in: PubMed

  73. Mitra R, Müller P, Ji Y. Propriety conditions for the Bayesian autologistic model - Inference for histone modifications. J Stat Theory Pract. 2013; 7(2):248-258. View in: PubMed

  74. Mitra R, Müller P, Ji Y, Zhu Y, Mills G, Lu Y. A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments. J Appl Stat. 2014; 41(11):2483-2492. View in: PubMed

  75. Telesca D, Müller P, Kornblau SM, Suchard MA, Ji Y. Modeling Protein Expression and Protein Signaling Pathways. J Am Stat Assoc. 2011; 107(500):1372-1384. View in: PubMed

  76. Lee J, Ji Y, Liang S, Cai G, Müller P. Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data. Stat Biosci. 2015 May 01; 7(1):48-67. View in: PubMed

  77. Xu Y, Müller P, Yuan Y, Gulukota K, Ji Y. MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling. J Am Stat Assoc. 2015 Mar 01; 110(510):503-514. View in: PubMed

  78. Xu X, Han X, Liu L, Ji Y, Li J, Lou W. Clinical Analysis and Comprehensive Treatment of Nonfunctional Pancreatic Neuroendocrine Tumor With Liver Metastases: A Retrospective Single-Center Study. Pancreas. 2015 Aug; 44(6):995-6. View in: PubMed

  79. Qian Y, Zeng ZC, Ji Y, Xiao YP. Microinvasion of liver metastases from colorectal cancer: predictive factors and application for determining clinical target volume. Radiat Oncol. 2015 Jun 04; 10:125. View in: PubMed

  80. Huang J, Luo RK, Du M, Zeng HY, Chen LL, Ji Y. Clear cell sarcoma of the pancreas: a case report and review of literature. Int J Clin Exp Pathol. 2015; 8(2):2171-5. View in: PubMed

  81. Zhu Y, Xu Y, Helseth DL, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. J Natl Cancer Inst. 2015 Aug; 107(8). View in: PubMed

  82. Sheng R, Xie Y, Zeng M, Ji Y, Rao S, Chen C. MR imaging of primary hepatic neuroendocrine neoplasm and metastatic hepatic neuroendocrine neoplasm: a comparative study. Radiol Med. 2015 Nov; 120(11):1012-20. View in: PubMed

  83. Ge X, Wang H, Zeng H, Jin X, Sujie A, Xu C, Liu Y, Huang J, Ji Y, Tan Y, Liu T, Hou Y, Qin J, Sun Y, Qin X. Clinical significance of assessing Her2/neu expression in gastric cancer with dual tumor tissue paraffin blocks. Hum Pathol. 2015 Jun; 46(6):850-7. View in: PubMed

  84. Xu Y, Zhang J, Yuan Y, Mitra R, Müller P, Ji Y. A Bayesian Graphical Model for Integrative Analysis of TCGA Data. IEEE Int Workshop Genomic Signal Process Stat. 2012 Dec; 2012:135-138. View in: PubMed

  85. Mitra R, Mueller P, Ji Y, Mills G, Lu Y. Sparse Bayesian Graphical Models for RPPA Time Course Data. IEEE Int Workshop Genomic Signal Process Stat. 2012 Dec; 2012:113-117. View in: PubMed

  86. Han X, Zhang C, Tang M, Xu X, Liu L, Ji Y, Pan B, Lou W. The value of serum chromogranin A as a predictor of tumor burden, therapeutic response, and nomogram-based survival in well-moderate nonfunctional pancreatic neuroendocrine tumors with liver metastases. Eur J Gastroenterol Hepatol. 2015 May; 27(5):527-35. View in: PubMed

  87. Ge XW, Zeng HY, Su-Jie A, Du M, Ji Y, Tan YS, Hou YY, Xu JF. Hepatocellular carcinoma with concomitant hepatic angiomyolipoma and cavernous hemangioma in one patient. World J Gastroenterol. 2015 Mar 21; 21(11):3414-9. View in: PubMed

  88. Gao SY, Gong YF, Sun QJ, Bai J, Wang L, Fan ZQ, Sun Y, Su YJ, Gang J, Ji YB. Screening antitumor bioactive fraction from Sauromatum giganteum (Engl.) Cusimano & Hett and sensitive cell lines with the serum pharmacology method and identification by UPLC-TOF-MS. Molecules. 2015 Mar 06; 20(3):4290-306. View in: PubMed

  89. Sengupta S, Wang J, Lee J, Müller P, Gulukota K, Banerjee A, Ji Y. Bayclone: Bayesian nonparametric inference of tumor subclones using NGS data. Pac Symp Biocomput. 2015; 467-78. View in: PubMed

  90. Mitra R, Müller P, Qiu P, Ji Y. Bayesian hierarchical models for protein networks in single-cell mass cytometry. Cancer Inform. 2014; 13(Suppl 4):79-89. View in: PubMed

  91. Yajima M, Telesca D, Ji Y, Müller P. Detecting differential patterns of interaction in molecular pathways. Biostatistics. 2015 Apr; 16(2):240-51. View in: PubMed

  92. Wu D, Tan M, Zhou M, Sun H, Ji Y, Chen L, Chen G, Zeng M. Liver computed tomographic perfusion in the assessment of microvascular invasion in patients with small hepatocellular carcinoma. Invest Radiol. 2015 Apr; 50(4):188-94. View in: PubMed

  93. Chen L, Tan Y, Zeng H, Hou Y, Xu J, Zhao J, Ji Y. [Dysplastic nodule of liver versus early hepatocellular carcinoma: a clinicopathologic and prognostic study]. Zhonghua Bing Li Xue Za Zhi. 2014 May; 43(5):301-6. View in: PubMed

  94. Zhu Y, Qiu P, Ji Y. TCGA-assembler: open-source software for retrieving and processing TCGA data. Nat Methods. 2014 Jun; 11(6):599-600. View in: PubMed

  95. Liu C, Karam R, Zhou Y, Su F, Ji Y, Li G, Xu G, Lu L, Wang C, Song M, Zhu J, Wang Y, Zhao Y, Foo WC, Zuo M, Valasek MA, Javle M, Wilkinson MF, Lu Y. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nat Med. 2014 Jun; 20(6):596-8. View in: PubMed

  96. Wang Y, Yu YY, Li W, Feng Y, Hou J, Ji Y, Sun YH, Shen KT, Shen ZB, Qin XY, Liu TS. A phase II trial of Xeloda and oxaliplatin (XELOX) neo-adjuvant chemotherapy followed by surgery for advanced gastric cancer patients with para-aortic lymph node metastasis. Cancer Chemother Pharmacol. 2014 Jun; 73(6):1155-61. View in: PubMed

  97. Yang B, Tan Y, Sun H, Fan J, Tang Z, Ji Y. Higher intratumor than peritumor expression of DUSP6/MKP-3 is associated with recurrence after curative resection of hepatocellular carcinoma. Chin Med J (Engl). 2014; 127(7):1211-7. View in: PubMed

  98. Yu Y, Dou XM, Wei B, Zha GW, Shang XJ, Wang L, Su D, Xu JX, Wang HY, Ni HQ, Sun BQ, Ji Y, Han XD, Niu ZC. Self-assembled quantum dot structures in a hexagonal nanowire for quantum photonics. Adv Mater. 2014 May; 26(17):2710-7, 2616. View in: PubMed

  99. Han X, Xu X, Jin D, Wang D, Ji Y, Lou W. Clinicopathological characteristics and prognosis-related factors of resectable pancreatic neuroendocrine tumors: a retrospective study of 104 cases in a single Chinese center. Pancreas. 2014 May; 43(4):526-31. View in: PubMed

  100. Sheng RF, Zeng MS, Rao SX, Ji Y, Chen LL. MRI of small intrahepatic mass-forming cholangiocarcinoma and atypical small hepatocellular carcinoma (=3 cm) with cirrhosis and chronic viral hepatitis: a comparative study. Clin Imaging. 2014 May-Jun; 38(3):265-72. View in: PubMed

  101. Cai C, Yuan Y, Ji Y. A Bayesian Dose-finding Design for Oncology Clinical Trials of Combinational Biological Agents. J R Stat Soc Ser C Appl Stat. 2014 01 01; 63(1):159-173. View in: PubMed

  102. Lee J, Müller P, Zhu Y, Ji Y. A Nonparametric Bayesian Model for Local Clustering with Application to Proteomics. J Am Stat Assoc. 2013 01 01; 108(503). View in: PubMed

  103. Pan J, Chen L, Fan J, Zhou J, Qin L, Tan Y, Ji Y, Huang X. Retrospective study of hepatocellular adenomas based on the phenotypic classification system: A report from China. Histol Histopathol. 2014 02; 29(2):243-9. View in: PubMed

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