Yuan Ji

Biosciences Graduate Program Association
Awards & Honors
  • 2015 - Mitchell Prize ISBA
  • 2020 - Elected Fellow The American Statistical Association
  1. Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma. Commun Med (Lond). 2023 Mar 03; 3(1):35. View in: PubMed

  2. Differences in Molecular Subtype Reference Standards Impact AI-based Breast Cancer Classification with Dynamic Contrast-enhanced MRI. Radiology. 2023 Jan 03; 220984. View in: PubMed

  3. Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease. Transl Stroke Res. 2022 Jun 17. View in: PubMed

  4. Impact of continuous learning on diagnostic breast MRI AI: evaluation on an independent clinical dataset. J Med Imaging (Bellingham). 2022 May; 9(3):034502. View in: PubMed

  5. Bayesian Adaptive Design for Finding the Maximum Tolerated Sequence of Doses in Multicycle Dose-Finding Clinical Trials. JCO Precis Oncol. 2018 Nov; 2:1-19. View in: PubMed

  6. Practical Impact of Modern Dose-Finding Designs When Compared With the 3 + 3 Design: An Editorial. JCO Precis Oncol. 2021 11; 5:1584-1587. View in: PubMed

  7. Multi-Stage Harmonization for Robust AI across Breast MR Databases. Cancers (Basel). 2021 Sep 26; 13(19). View in: PubMed

  8. Perfusion and Permeability MRI Predicts Future Cavernous Angioma Hemorrhage and Growth. J Magn Reson Imaging. 2022 05; 55(5):1440-1449. View in: PubMed

  9. Improved Classification of Benign and Malignant Breast Lesions Using Deep Feature Maximum Intensity Projection MRI in Breast Cancer Diagnosis Using Dynamic Contrast-enhanced MRI. Radiol Artif Intell. 2021 May; 3(3):e200159. View in: PubMed

  10. Comparison of Breast MRI Tumor Classification Using Human-Engineered Radiomics, Transfer Learning From Deep Convolutional Neural Networks, and Fusion Methods. Proc IEEE Inst Electr Electron Eng. 2020 Jan; 108(1):163-177. View in: PubMed

  11. Perfusion and permeability as diagnostic biomarkers of cavernous angioma with symptomatic hemorrhage. J Cereb Blood Flow Metab. 2021 11; 41(11):2944-2956. View in: PubMed

  12. A Roadmap for Developing Plasma Diagnostic and Prognostic Biomarkers of Cerebral Cavernous Angioma With Symptomatic Hemorrhage (CASH). Neurosurgery. 2021 02 16; 88(3):686-697. View in: PubMed

  13. Personalized Antibodies for Gastroesophageal Adenocarcinoma (PANGEA): A Phase II Study Evaluating an Individualized Treatment Strategy for Metastatic Disease. Cancer Discov. 2021 02; 11(2):308-325. View in: PubMed

  14. Harmonization of radiomic features of breast lesions across international DCE-MRI datasets. J Med Imaging (Bellingham). 2020 Jan; 7(1):012707. View in: PubMed

  15. RoBoT: a robust Bayesian hypothesis testing method for basket trials. Biostatistics. 2021 10 13; 22(4):897-912. View in: PubMed

  16. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. View in: PubMed

  17. Heterogeneity of human prostate carcinoma-associated fibroblasts implicates a role for subpopulations in myeloid cell recruitment. Prostate. 2020 02; 80(2):173-185. View in: PubMed

  18. Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling. Cancer Imaging. 2019 Jul 15; 19(1):48. View in: PubMed

  19. The i3+3 design for phase I clinical trials. J Biopharm Stat. 2020 03; 30(2):294-304. View in: PubMed

  20. Anatomic extent of lymph node metastases as an independent prognosticator in node-positive major salivary gland carcinoma: A?study of the US SEER database and a Chinese multicenter cohort. Eur J Surg Oncol. 2019 Nov; 45(11):2143-2150. View in: PubMed

  21. AAA: triple adaptive Bayesian designs for the identification of optimal dose combinations in dual-agent dose finding trials. J R Stat Soc Ser C Appl Stat. 2019 Feb; 68(2):385-410. View in: PubMed

  22. An Oncolytic Adenovirus Targeting Transforming Growth Factor ? 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

  23. Variants in STAT4 Associated With Cure of Chronic HBV Infection in HBeAg-positive Patients Treated With Pegylated Interferon-alpha. Clin Gastroenterol Hepatol. 2020 01; 18(1):196-204.e8. View in: PubMed

  24. Hyperglycemia and T Cell infiltration are associated with stromal and epithelial prostatic hyperplasia in the nonobese diabetic mouse. Prostate. 2019 06; 79(9):980-993. View in: PubMed

  25. [Protective effect of raspberry extract on ConA-induced acute liver injuryin mice]. Zhongguo Zhong Yao Za Zhi. 2019 Feb; 44(4):774-780. View in: PubMed

  26. Discussion of "A hybrid phase I-II/III clinical trial design allowing dose re-optimization in phase III" by Andrew G. Chapple and Peter F. Thall. Biometrics. 2019 06; 75(2):385-388. View in: PubMed

  27. A Bayesian random partition model for sequential refinement and coagulation. Biometrics. 2019 09; 75(3):988-999. View in: PubMed

  28. 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

  29. 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

  30. Design and implementation of pragmatic clinical trials using the electronic medical record and an adaptive design. JAMIA Open. 2018 Jul; 1(1):99-106. View in: PubMed

  31. 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

  32. [Study on the Apoptotic Mechanisms of Human Liver Cancer HepG-2 Cells Induced by Total Saponins of Ornithogalum caudatum]. Zhong Yao Cai. 2016 Apr; 39(4):867-71. View in: PubMed

  33. [Trace phenolic compounds from Red Yeast Rice]. Zhongguo Zhong Yao Za Zhi. 2018 Feb; 43(4):755-759. View in: PubMed

  34. Bayesian graphical models for computational network biology. BMC Bioinformatics. 2018 03 21; 19(Suppl 3):63. View in: PubMed

  35. Validation of the novel susceptibility loci for prostate cancer in a Chinese population. Oncol Lett. 2018 Feb; 15(2):2567-2573. View in: PubMed

  36. TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data. Bioinformatics. 2018 05 01; 34(9):1615-1617. View in: PubMed

  37. Heterogeneous reciprocal graphical models. Biometrics. 2018 06; 74(2):606-615. View in: PubMed

  38. Clustering distributions with the marginalized nested Dirichlet process. Biometrics. 2018 06; 74(2):584-594. View in: PubMed

  39. 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

  40. A Bayesian interval dose-finding design addressingOckham's?razor:?mTPI-2. Contemp Clin Trials. 2017 07; 58:23-33. View in: PubMed

  41. 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

  42. 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

  43. A subgroup cluster-based Bayesian adaptive design for precision medicine. Biometrics. 2017 06; 73(2):367-377. View in: PubMed

  44. 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

  45. Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials. Stat Biosci. 2016 Jun; 8(1):159-180. View in: PubMed

  46. 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

  47. 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


  49. 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

  50. Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma. Sci Rep. 2015 Dec 07; 5:17787. View in: PubMed

  51. Characterizing Cancer-Specific Networks by Integrating TCGA Data. Cancer Inform. 2014; 13(Suppl 2):125-31. View in: PubMed

  52. 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

  53. A decision-theoretic phase I-II design for ordinal outcomes in two cycles. Biostatistics. 2016 Apr; 17(2):304-19. View in: PubMed

  54. 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

  55. A Nonparametric Bayesian Model for Nested Clustering. Methods Mol Biol. 2016; 1362:129-41. View in: PubMed

  56. 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

  57. An integrated dose-finding tool for phase I trials in oncology. Contemp Clin Trials. 2015 Nov; 45(Pt B):426-434. View in: PubMed

  58. 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


  60. Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data. Bayesian Anal. 2013 Dec; 8(4):759-780. View in: PubMed

  61. Propriety conditions for the Bayesian autologistic model - Inference for histone modifications. J Stat Theory Pract. 2013; 7(2):248-258. View in: PubMed

  62. A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments. J Appl Stat. 2014; 41(11):2483-2492. View in: PubMed

  63. Modeling Protein Expression and Protein Signaling Pathways. J Am Stat Assoc. 2011; 107(500):1372-1384. View in: PubMed

  64. Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data. Stat Biosci. 2015 May 01; 7(1):48-67. View in: PubMed

  65. 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

  66. Targeted gene capture and massively parallel sequencing identify TMC1 as the causative gene in a six-generation Chinese family with autosomal dominant hearing loss. Am J Med Genet A. 2015 Oct; 167A(10):2357-65. View in: PubMed

  67. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. J Natl Cancer Inst. 2015 Aug; 107(8). View in: PubMed

  68. 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

  69. Sparse Bayesian Graphical Models for RPPA Time Course Data. IEEE Int Workshop Genomic Signal Process Stat. 2012 Dec; 2012:113-117. View in: PubMed

  70. Ethanol but not aqueous extracts of tubers of Sauromatum Giganteum(Engl.) Cusimano and Hett inhibit cancer cell proliferation. Asian Pac J Cancer Prev. 2014; 15(24):10613-9. View in: PubMed

  71. Bayclone: Bayesian nonparametric inference of tumor subclones using NGS data. Pac Symp Biocomput. 2015; 467-78. View in: PubMed

  72. Bayesian hierarchical models for protein networks in single-cell mass cytometry. Cancer Inform. 2014; 13(Suppl 4):79-89. View in: PubMed

  73. Detecting differential patterns of interaction in molecular pathways. Biostatistics. 2015 Apr; 16(2):240-51. View in: PubMed

  74. Alkaloids from beach spider lily (Hymenocallis littoralis) induce apoptosis of HepG-2 cells by the fas-signaling pathway. Asian Pac J Cancer Prev. 2014; 15(21):9319-25. View in: PubMed

  75. Bayesian disease classification using copy number data. Cancer Inform. 2014; 13(Suppl 2):83-91. View in: PubMed

  76. Downregulation of Cdk1 and cyclinB1 expression contributes to oridonin-induced cell cycle arrest at G2/M phase and growth inhibition in SGC-7901 gastric cancer cells. Asian Pac J Cancer Prev. 2014; 15(15):6437-41. View in: PubMed

  77. TCGA-assembler: open-source software for retrieving and processing TCGA data. Nat Methods. 2014 Jun; 11(6):599-600. View in: PubMed

  78. Schedule-dependent effects of kappa-selenocarrageenan in combination with epirubicin on hepatocellular carcinoma. Asian Pac J Cancer Prev. 2014; 15(8):3651-7. View in: PubMed

  79. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nat Med. 2014 Jun; 20(6):596-8. View in: PubMed

  80. Laminarin-induced apoptosis in human colon cancer LoVo cells. Oncol Lett. 2014 May; 7(5):1728-1732. View in: PubMed

  81. 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

  82. Identification of thresholds for dichotomizing DNA methylation data. EURASIP J Bioinform Syst Biol. 2013 Jun 06; 2013(1):8. View in: PubMed

  83. [Research progress of transgenic Drosophila model of Alzheimer disease]. Yao Xue Xue Bao. 2013 Mar; 48(3):333-6. View in: PubMed

  84. Modified toxicity probability interval design: a safer and more reliable method than the 3 + 3 design for practical phase I trials. J Clin Oncol. 2013 May 10; 31(14):1785-91. View in: PubMed

  85. BM-BC: a Bayesian method of base calling for Solexa sequence data. BMC Bioinformatics. 2012; 13 Suppl 13:S6. View in: PubMed

  86. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics. 2012; 13 Suppl 13:S5. View in: PubMed

  87. Bayesian continual reassessment method for dose-finding trials infusing T cells with limited sample size. J Biopharm Stat. 2012; 22(6):1206-19. View in: PubMed

  88. The pan-deacetylase inhibitor panobinostat induces cell death and synergizes with everolimus in Hodgkin lymphoma cell lines. Blood. 2012 Apr 26; 119(17):4017-25. View in: PubMed

  89. Mocetinostat for relapsed classical Hodgkin's lymphoma: an open-label, single-arm, phase 2 trial. Lancet Oncol. 2011 Dec; 12(13):1222-8. View in: PubMed

  90. On differential gene expression using RNA-Seq data. Cancer Inform. 2011; 10:205-15. View in: PubMed

  91. The histone deacetylase inhibitor entinostat (SNDX-275) induces apoptosis in?Hodgkin lymphoma cells and synergizes with Bcl-2 family inhibitors. Exp Hematol. 2011 Oct; 39(10):1007-1017.e1. View in: PubMed

  92. BM-map: Bayesian mapping of multireads for next-generation sequencing data. Biometrics. 2011 Dec; 67(4):1215-24. View in: PubMed

  93. Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data. J Am Stat Assoc. 2010 12; 105(492):1358-1375. View in: PubMed

  94. A modified toxicity probability interval method for dose-finding trials. Clin Trials. 2010 Dec; 7(6):653-63. View in: PubMed

  95. Incidence and risk factors of venous thromboembolic events in lymphoma. Am J Med. 2010 Oct; 123(10):935-41. View in: PubMed

  96. Screening mutations of OTOF gene in Chinese patients with auditory neuropathy, including a familial case of temperature-sensitive auditory neuropathy. BMC Med Genet. 2010 May 26; 11:79. View in: PubMed

  97. Tumor invasion after treatment of glioblastoma with bevacizumab: radiographic and pathologic correlation in humans and mice. Neuro Oncol. 2010 Mar; 12(3):233-42. View in: PubMed

  98. Phase II study of yttrium-90-ibritumomab tiuxetan in patients with relapsed or refractory mantle cell lymphoma. J Clin Oncol. 2009 Nov 01; 27(31):5213-8. View in: PubMed

  99. Risk-group-specific dose finding based on an average toxicity score. Biometrics. 2010 Jun; 66(2):541-8. View in: PubMed

  100. Mechanism of Fas signaling regulation by human herpesvirus 8 K1 oncoprotein. J Natl Cancer Inst. 2009 Mar 18; 101(6):399-411. View in: PubMed

  101. Adaptive randomization for multiarm comparative clinical trials based on joint efficacy/toxicity outcomes. Biometrics. 2009 Sep; 65(3):876-84. View in: PubMed

  102. [Effects of CPUY013, a novel Topo I inhibitor, on human gastric adenocarcinoma BGC823 cells in vitro and in vivo]. Yao Xue Xue Bao. 2008 Aug; 43(8):811-8. View in: PubMed

  103. [Studies of betuionic acid on cell cycle and related protein expressions on mice of bearing H22 tumor cells]. Zhongguo Zhong Yao Za Zhi. 2008 Jul; 33(14):1739-43. View in: PubMed

  104. Dose--schedule finding in phase I/II clinical trials using a Bayesian isotonic transformation. Stat Med. 2008 Oct 30; 27(24):4895-913. View in: PubMed

  105. Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells. Mol Cancer Ther. 2008 Mar; 7(3):464-73. View in: PubMed

  106. Bayesian models based on test statistics for multiple hypothesis testing problems. Bioinformatics. 2008 Apr 01; 24(7):943-9. View in: PubMed

  107. Monitoring late-onset toxicities in phase I trials using predicted risks. Biostatistics. 2008 Jul; 9(3):442-57. View in: PubMed

  108. Extracting three-way gene interactions from microarray data. Bioinformatics. 2007 Nov 01; 23(21):2903-9. View in: PubMed

  109. Dose-finding in phase I clinical trials based on toxicity probability intervals. Clin Trials. 2007; 4(3):235-44. View in: PubMed

  110. Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain. Mamm Genome. 2007 Aug; 18(8):584-95. View in: PubMed

  111. [Identification of metabolites of environmental hormone butylbenzyl phthalate in mice urine by liquid chromatography/ion trap mass spectrometry]. Huan Jing Ke Xue. 2007 Mar; 28(3):627-32. View in: PubMed

  112. Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratios. Biometrics. 2006 Sep; 62(3):777-84. View in: PubMed

  113. [Effect of Sudan I, III and IV on proliferation of HepG-2 and SGC-7901]. Huan Jing Ke Xue. 2006 Jun; 27(6):1201-7. View in: PubMed

  114. RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms. Appl Bioinformatics. 2006; 5(2):89-98. View in: PubMed

  115. Preparation of enteric microsphere of oleanolic acid dihemiphthalate sodium by salting-out action using spherical crystallization technique. Yao Xue Xue Bao. 2005 Mar; 40(3):267-73. View in: PubMed

  116. Applications of beta-mixture models in bioinformatics. Bioinformatics. 2005 May 01; 21(9):2118-22. View in: PubMed

  117. Delta24-hyCD adenovirus suppresses glioma growth in vivo by combining oncolysis and chemosensitization. Cancer Gene Ther. 2005 Mar; 12(3):284-94. View in: PubMed

  118. A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples. Bioinformatics. 2005 Apr 01; 21(7):1055-61. View in: PubMed