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Yuan Ji

TitleProfessor
InstitutionUniversity of Chicago
DepartmentPublic Health Sciences
AddressChicago IL 60637
Phone+1 (773) 8340214
Email
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    Collapse Biography 
    Collapse awards and honors
    2015Mitchell Prize, ISBA
    2020Elected Fellow, The American Statistical Association

    Collapse ORNG Applications 
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    Collapse Research 
    Collapse research activities and funding
    R01CA132897     (JI, YUAN)Sep 1, 2007 - Apr 30, 2020
    NIH
    Bayesian Inference for Tumor Heterogeneity with Next-Generation Sequencing Data
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Zhou T, Ji Y. RoBoT: a robust Bayesian hypothesis testing method for basket trials. Biostatistics. 2021 Oct 13; 22(4):897-912. PMID: 32061093.
      View in: PubMed
    2. 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). PMID: 34638294.
      View in: PubMed
    3. 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. 2021 Sep 24. PMID: 34558140.
      View in: PubMed
    4. 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 Nov; 41(11):2944-2956. PMID: 34039038.
      View in: PubMed
    5. 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. PMID: 33469662.
      View in: PubMed
    6. 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. PMID: 33234578.
      View in: PubMed
    7. 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. PMID: 32206682.
      View in: PubMed
    8. 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. PMID: 32025013.
      View in: PubMed
    9. 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. PMID: 31763714.
      View in: PubMed
    10. 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. PMID: 34045769.
      View in: PubMed
    11. Liu M, Wang SJ, Ji Y. The i3+3 design for phase I clinical trials. J Biopharm Stat. 2020 03; 30(2):294-304. PMID: 31304864.
      View in: PubMed
    12. 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. PMID: 31307537.
      View in: PubMed
    13. 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. PMID: 31126191.
      View in: PubMed
    14. 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. PMID: 31253544.
      View in: PubMed
    15. 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. PMID: 31042581.
      View in: PubMed
    16. 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. PMID: 30820945.
      View in: PubMed
    17. 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. PMID: 30945260.
      View in: PubMed
    18. 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. PMID: 30744484.
      View in: PubMed
    19. 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. PMID: 30730765.
      View in: PubMed
    20. 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. PMID: 30989891.
      View in: PubMed
    21. 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. PMID: 30181178.
      View in: PubMed
    22. 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. PMID: 31190687.
      View in: PubMed
    23. 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. PMID: 30386852.
      View in: PubMed
    24. 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. PMID: 29272348.
      View in: PubMed
    25. Ni Y, Müller P, Wei L, Ji Y. Bayesian graphical models for computational network biology. BMC Bioinformatics. 2018 03 21; 19(Suppl 3):63. PMID: 29589555.
      View in: PubMed
    26. 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. PMID: 29600651.
      View in: PubMed
    27. 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. PMID: 29434975.
      View in: PubMed
    28. Ni Y, Müller P, Zhu Y, Ji Y. Heterogeneous reciprocal graphical models. Biometrics. 2018 06; 74(2):606-615. PMID: 29023632.
      View in: PubMed
    29. 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. PMID: 28960246.
      View in: PubMed
    30. 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. PMID: 28458054.
      View in: PubMed
    31. 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. PMID: 27864833.
      View in: PubMed
    32. Guo W, Ji Y, Catenacci DVT. A subgroup cluster-based Bayesian adaptive design for precision medicine. Biometrics. 2017 06; 73(2):367-377. PMID: 27775814.
      View in: PubMed
    33. 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. PMID: 27742793.
      View in: PubMed
    34. 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. PMID: 27853751.
      View in: PubMed
    35. 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. PMID: 27144536.
      View in: PubMed
    36. 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. PMID: 30132597.
      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. PMID: 28461708.
      View in: PubMed
    38. Lee J, Müller P, Zhu Y, Ji Y. A Nonparametric Bayesian Model for Nested Clustering. Methods Mol Biol. 2016; 1362:129-41. PMID: 26519174.
      View in: PubMed
    39. 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. PMID: 26639025.
      View in: PubMed
    40. 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. PMID: 26619259.
      View in: PubMed
    41. 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. PMID: 26628858.
      View in: PubMed
    42. 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. PMID: 26553915.
      View in: PubMed
    43. 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. PMID: 26420835.
      View in: PubMed
    44. 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. PMID: 26419937.
      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. PMID: 26835491.
      View in: PubMed
    46. 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. PMID: 26528377.
      View in: PubMed
    47. 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. . 2015 Oct; 167A(10):2357-65. PMID: 26079994.
      View in: PubMed
    48. 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. PMID: 26366026.
      View in: PubMed
    49. 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). PMID: 25956356.
      View in: PubMed
    50. 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. PMID: 26191087.
      View in: PubMed
    51. 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. PMID: 26170513.
      View in: PubMed
    52. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 25859417.
      View in: PubMed
    53. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 23742247.
      View in: PubMed
    54. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 23320920.
      View in: PubMed
    55. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 26776203.
      View in: PubMed
    56. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 25592605.
      View in: PubMed
    57. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 24859531.
      View in: PubMed
    58. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 34235439.
      View in: PubMed
    59. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 30999385.
      View in: PubMed
    60. Kaucikas M, Fitzpatrick A, Bryan E, Struve A, Henning R, Kosheleva I, Srajer V, Groenhof G, Van Thor JJ. Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa. Proteins. 2015 Mar; 83(3):397-402. PMID: 23075018.
      View in: PubMed
    61. Yajima M, Telesca D, Ji Y, Müller P. Detecting differential patterns of interaction in molecular pathways. Biostatistics. 2015 Apr; 16(2):240-51. PMID: 25519431.
      View in: PubMed
    62. 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. PMID: 25574129.
      View in: PubMed
    63. Guha S, Ji Y, Baladandayuthapani V. Bayesian disease classification using copy number data. Cancer Inform. 2014; 13(Suppl 2):83-91. PMID: 25336897.
      View in: PubMed
    64. 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. PMID: 27617041.
      View in: PubMed
    65. 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. PMID: 24874569.
      View in: PubMed
    66. Ji CF, Ji YB. Laminarin-induced apoptosis in human colon cancer LoVo cells. Oncol Lett. 2014 May; 7(5):1728-1732. PMID: 24765209.
      View in: PubMed
    67. 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. PMID: 24870773.
      View in: PubMed
    68. 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. PMID: 25422219.
      View in: PubMed
    69. 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. PMID: 26246866.
      View in: PubMed
    70. 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. PMID: 25124639.
      View in: PubMed
    71. 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. PMID: 25605148.
      View in: PubMed
    72. 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. PMID: 26246652.
      View in: PubMed
    73. 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. PMID: 24511160.
      View in: PubMed
    74. 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. PMID: 26246865.
      View in: PubMed
    75. 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. PMID: 23569307.
      View in: PubMed
    76. 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. PMID: 23724643.
      View in: PubMed
    77. 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. PMID: 26246801.
      View in: PubMed
    78. 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. PMID: 25859418.
      View in: PubMed
    79. 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. PMID: 26726304.
      View in: PubMed
    80. 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. PMID: 23320938.
      View in: PubMed
    81. 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. PMID: 22408261.
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    82. 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. PMID: 22033282.
      View in: PubMed
    83. Lee J, Ji Y, Liang S, Cai G, Müller P. On differential gene expression using RNA-Seq data. Cancer Inform. 2011; 10:205-15. PMID: 21863128.
      View in: PubMed
    84. 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. PMID: 21767511.
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    85. 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. PMID: 21517792.
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    86. 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. PMID: 26246646.
      View in: PubMed
    87. 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. PMID: 21512611.
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    88. 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. PMID: 20935021.
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    89. 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. PMID: 20920696.
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    90. 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. PMID: 20504331.
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    91. 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. PMID: 20167811.
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    92. 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. PMID: 19770379.
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    93. Bekele BN, Li Y, Ji Y. Risk-group-specific dose finding based on an average toxicity score. Biometrics. 2010 Jun; 66(2):541-8. PMID: 19645698.
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    94. 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. PMID: 19276446.
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    95. Ji Y, Bekele BN. Adaptive randomization for multiarm comparative clinical trials based on joint efficacy/toxicity outcomes. Biometrics. 2009 Sep; 65(3):876-84. PMID: 19173694.
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    96. 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. PMID: 18563789.
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    97. 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. PMID: 18956773.
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    98. 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. PMID: 18841782.
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    99. 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. . 2008 Mar; 7(3):464-73. PMID: 18347134.
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    100. 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. PMID: 18245123.
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    101. 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. PMID: 18084008.
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    102. Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics. 2007 Nov 01; 23(21):2903-9. PMID: 17921496.
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    103. 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. PMID: 17671812.
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    104. 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. PMID: 17633646.
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    105. 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. PMID: 17715248.
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    106. 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. PMID: 16984320.
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    107. 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. PMID: 16921962.
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    108. 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. PMID: 16722773.
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    109. 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. PMID: 15650766.
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    110. 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. PMID: 15952602.
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    111. 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. PMID: 15713737.
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    112. 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. PMID: 15514000.
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