Biosciences Graduate Program Association
Awards & Honors
  • 2015 - Mitchell Prize ISBA
  • 2020 - Elected Fellow The American Statistical Association
  1. Romanos SG, Srinath A, Li Y, Xie B, Chen C, Li Y, Moore T, Bi D, Sone JY, Lightle R, Hobson N, Zhang D, Koskimäki J, Shen L, McCurdy S, Lai CC, Stadnik A, Piedad K, Carrión-Penagos J, Shkoukani A, Snellings D, Shenkar R, Sulakhe D, Ji Y, Lopez-Ramirez MA, Kahn ML, Marchuk DA, Ginsberg MH, Girard R, Awad IA. Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease. Transl Stroke Res. 2022 Jun 17. View in: PubMed

  2. Li H, Whitney HM, Ji Y, Edwards A, Papaioannou J, Liu P, Giger ML. 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

  3. Lyu J, Curran E, Ji Y. 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

  4. Ji Y, Yuan S. 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

  5. Whitney HM, Li H, Ji Y, Liu P, Giger ML. Multi-Stage Harmonization for Robust AI across Breast MR Databases. Cancers (Basel). 2021 Sep 26; 13(19). View in: PubMed

  6. Sone JY, Hobson N, Srinath A, Romanos SG, Li Y, Carrión-Penagos J, Shkoukani A, Stadnik A, Piedad K, Lightle R, Moore T, DeBiasse D, Bi D, Shenkar R, Carroll T, Ji Y, Girard R, Awad IA. Perfusion and Permeability MRI Predicts Future Cavernous Angioma Hemorrhage and Growth. J Magn Reson Imaging. 2022 05; 55(5):1440-1449. View in: PubMed

  7. Hu Q, Whitney HM, Li H, Ji Y, Liu P, Giger ML. 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

  8. Whitney HM, Li H, Ji Y, Liu P, Giger ML. 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

  9. Sone JY, Li Y, Hobson N, Romanos SG, Srinath A, Lyne SB, Shkoukani A, Carrión-Penagos J, Stadnik A, Piedad K, Lightle R, Moore T, Li Y, Bi D, Shenkar R, Carroll T, Ji Y, Girard R, Awad IA. 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

  10. Girard R, Li Y, Stadnik A, Shenkar R, Hobson N, Romanos S, Srinath A, Moore T, Lightle R, Shkoukani A, Akers A, Carroll T, Christoforidis GA, Koenig JI, Lee C, Piedad K, Greenberg SM, Kim H, Flemming KD, Ji Y, Awad IA. 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

  11. Catenacci DVT, Moya S, Lomnicki S, Chase LM, Peterson BF, Reizine N, Alpert L, Setia N, Xiao SY, Hart J, Siddiqui UD, Hogarth DK, Eng OS, Turaga K, Roggin K, Posner MC, Chang P, Narula S, Rampurwala M, Ji Y, Karrison T, Liao CY, Polite BN, Kindler HL. 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

  12. Whitney HM, Li H, Ji Y, Liu P, Giger ML. Harmonization of radiomic features of breast lesions across international DCE-MRI datasets. J Med Imaging (Bellingham). 2020 Jan; 7(1):012707. View in: PubMed

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

  14. Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. View in: PubMed

  15. Vickman RE, Broman MM, Lanman NA, Franco OE, Sudyanti PAG, Ni Y, Ji Y, Helfand BT, Petkewicz J, Paterakos MC, Crawford SE, Ratliff TL, Hayward SW. 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

  16. 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

  17. Liu M, Wang SJ, Ji Y. The i3+3 design for phase I clinical trials. J Biopharm Stat. 2020 03; 30(2):294-304. View in: PubMed

  18. Shi X, Liu XK, An CM, Wei WJ, Tao Y, Ji Y, Zhang Y, Han W, Xue JC, Huang NS, Ma B, Zhang CP, Yang X, Wang KJ, Liu QJ, Liu Y, Wang Y, Lei BW, Yu PC, Hu JQ, Lu ZW, Hu WP, Tian YX, Wang YL, Ji QH. 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

  19. Lyu J, Ji Y, Zhao N, Catenacci DVT. 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

  20. 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

  21. Chen H, Sun J, Zhou B, Xie Q, Liang X, Fan R, Conran C, Xu J, Ji Y, Zhang X, Sun L, Jia J, Wang G, Hou J, Jiang DK. 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

  22. Aaron-Brooks LM, Sasaki T, Vickman RE, Wei L, Franco OE, Ji Y, Crawford SE, Hayward SW. 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

  23. Ji YB, Bao XW, Shan Y, Yang SX, Zhang LM, Hou SY, Li LY, Cao L. [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

  24. Zhou T, Ji Y. 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

  25. Zanini CTP, Müller P, Ji Y, Quintana FA. A Bayesian random partition model for sequential refinement and coagulation. Biometrics. 2019 09; 75(3):988-999. View in: PubMed

  26. 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

  27. 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

  28. Simon KC, Tideman S, Hillman L, Lai R, Jathar R, Ji Y, Bergman-Bock S, Castle J, Franada T, Freedom T, Marcus R, Mark A, Meyers S, Rubin S, Semenov I, Yucus C, Pham A, Garduno L, Szela M, Frigerio R, Maraganore DM. 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

  29. 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

  30. Qu ZY, Shi X, Zou X, Ji YB. [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

  31. Ji YB, Xu F, Liu BY, Wei Q, Guo YZ, Dong Y, Sun Y, Hu YC. [Trace phenolic compounds from Red Yeast Rice]. Zhongguo Zhong Yao Za Zhi. 2018 Feb; 43(4):755-759. View in: PubMed

  32. 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

  33. Wu Y, Chen H, Ji Y, Na R, Mo Z, Ye D, Wang M, Qi J, Lin X, Ding Q, Xu J, Zheng SL, Sun Y, Meng W. Validation of the novel susceptibility loci for prostate cancer in a Chinese population. Oncol Lett. 2018 Feb; 15(2):2567-2573. View in: PubMed

  34. 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

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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  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 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

  45. 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

  46. 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

  47. 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

  48. 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

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. Baladandayuthapani V, Talluri R, Ji Y, Coombes KR, Lu Y, Hennessy BT, Davies MA, Mallick BK. BAYESIAN SPARSE GRAPHICAL MODELS FOR CLASSIFICATION WITH APPLICATION TO PROTEIN EXPRESSION DATA. Ann Appl Stat. 2014; 8(3):1443-1468. View in: PubMed

  58. 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

  59. 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

  60. 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

  61. 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

  62. 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

  63. 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

  64. Gao X, Huang SS, Yuan YY, Wang GJ, Xu JC, Ji YB, Han MY, Yu F, Kang DY, Lin X, Dai P. 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

  65. 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

  66. 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

  67. 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

  68. Gao SY, Li J, Wang L, Sun QJ, Gong YF, Gang J, Su YJ, Ji YB. 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

  69. 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

  70. 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

  71. 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

  72. Ji YB, Chen N, Zhu HW, Ling N, Li WL, Song DX, Gao SY, Zhang WC, Ma NN. 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

  73. Guha S, Ji Y, Baladandayuthapani V. Bayesian disease classification using copy number data. Cancer Inform. 2014; 13(Suppl 2):83-91. View in: PubMed

  74. Gao SY, Li J, Qu XY, Zhu N, Ji YB. 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

  75. 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

  76. Ji YB, Ling N, Zhou XJ, Mao YX, Li WL, Chen N. 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

  77. 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

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

  79. 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

  80. Liu Y, Ji Y, Qiu P. Identification of thresholds for dichotomizing DNA methylation data. EURASIP J Bioinform Syst Biol. 2013 Jun 06; 2013(1):8. View in: PubMed

  81. Tan Y, Ji YB, Zhao J. [Research progress of transgenic Drosophila model of Alzheimer disease]. Yao Xue Xue Bao. 2013 Mar; 48(3):333-6. View in: PubMed

  82. Ji Y, Wang SJ. 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

  83. Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S. BM-BC: a Bayesian method of base calling for Solexa sequence data. BMC Bioinformatics. 2012; 13 Suppl 13:S6. View in: PubMed

  84. Cai G, Li H, Lu Y, Huang X, Lee J, Müller P, Ji Y, Liang S. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics. 2012; 13 Suppl 13:S5. View in: PubMed

  85. Ji Y, Feng L, Liu P, Shpall EJ, Kebriaei P, Champlin R, Berry D, Cooper LJ. 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

  86. Lemoine M, Derenzini E, Buglio D, Medeiros LJ, Davis RE, Zhang J, Ji Y, Younes A. 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

  87. Younes A, Oki Y, Bociek RG, Kuruvilla J, Fanale M, Neelapu S, Copeland A, Buglio D, Galal A, Besterman J, Li Z, Drouin M, Patterson T, Ward MR, Paulus JK, Ji Y, Medeiros LJ, Martell RE. 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

  88. Lee J, Ji Y, Liang S, Cai G, Müller P. On differential gene expression using RNA-Seq data. Cancer Inform. 2011; 10:205-15. View in: PubMed

  89. Jóna A, Khaskhely N, Buglio D, Shafer JA, Derenzini E, Bollard CM, Medeiros LJ, Illés A, Ji Y, Younes A. 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

  90. Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C, Liang S, Liang H. BM-map: Bayesian mapping of multireads for next-generation sequencing data. Biometrics. 2011 Dec; 67(4):1215-24. View in: PubMed

  91. Baladandayuthapani V, Ji Y, Talluri R, Nieto-Barajas LE, Morris JS. 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

  92. Ji Y, Liu P, Li Y, Bekele BN. A modified toxicity probability interval method for dose-finding trials. Clin Trials. 2010 Dec; 7(6):653-63. View in: PubMed

  93. Zhou X, Teegala S, Huen A, Ji Y, Fayad L, Hagemeister FB, Gladish G, Vadhan-Raj S. Incidence and risk factors of venous thromboembolic events in lymphoma. Am J Med. 2010 Oct; 123(10):935-41. View in: PubMed

  94. Wang DY, Wang YC, Weil D, Zhao YL, Rao SQ, Zong L, Ji YB, Liu Q, Li JQ, Yang HM, Shen Y, Benedict-Alderfer C, Zheng QY, Petit C, Wang QJ. 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

  95. de Groot JF, Fuller G, Kumar AJ, Piao Y, Eterovic K, Ji Y, Conrad CA. 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

  96. Wang M, Oki Y, Pro B, Romaguera JE, Rodriguez MA, Samaniego F, McLaughlin P, Hagemeister F, Neelapu S, Copeland A, Samuels BI, Loyer EM, Ji Y, Younes A. 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

  97. Bekele BN, Li Y, Ji Y. Risk-group-specific dose finding based on an average toxicity score. Biometrics. 2010 Jun; 66(2):541-8. View in: PubMed

  98. Berkova Z, Wang S, Wise JF, Maeng H, Ji Y, Samaniego F. 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

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

  100. Ji YB, Zhou JH, Zuo MX, You QD. [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

  101. Zhang XJ, Han L, Ji YB, Fang GZ. [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

  102. Li Y, Bekele BN, Ji Y, Cook JD. 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

  103. Sun M, Estrov Z, Ji Y, Coombes KR, Harris DH, Kurzrock R. 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

  104. Ji Y, Lu Y, Mills GB. Bayesian models based on test statistics for multiple hypothesis testing problems. Bioinformatics. 2008 Apr 01; 24(7):943-9. View in: PubMed

  105. Bekele BN, Ji Y, Shen Y, Thall PF. Monitoring late-onset toxicities in phase I trials using predicted risks. Biostatistics. 2008 Jul; 9(3):442-57. View in: PubMed

  106. Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics. 2007 Nov 01; 23(21):2903-9. View in: PubMed

  107. Ji Y, Li Y, Nebiyou Bekele B. Dose-finding in phase I clinical trials based on toxicity probability intervals. Clin Trials. 2007; 4(3):235-44. View in: PubMed

  108. Zhu R, Ji Y, Xiao L, Matin A. 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

  109. Li WL, Ji YB, Zhang DL, Fan YQ. [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

  110. Yin G, Li Y, Ji Y. 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

  111. Ji YB, Ji CF, Gao SY, Lang L, Yu L. [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

  112. Ji Y, Coombes K, Zhang J, Wen S, Mitchell J, Pusztai L, Symmans WF, Wang J. 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

  113. Fan YL, Cui FD, Yang MS, Ji YB. 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

  114. Ji Y, Wu C, Liu P, Wang J, Coombes KR. Applications of beta-mixture models in bioinformatics. Bioinformatics. 2005 May 01; 21(9):2118-22. View in: PubMed

  115. Conrad C, Miller CR, Ji Y, Gomez-Manzano C, Bharara S, McMurray JS, Lang FF, Wong F, Sawaya R, Yung WK, Fueyo J. 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

  116. Ji Y, Tsui KW, Kim K. 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