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Yuan Ji

InstitutionUniversity of Chicago
DepartmentPublic Health Sciences
AddressChicago IL 60637
Phone+1 (773) 8340214
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    Collapse Overview 

    Collapse Biography 
    Collapse awards and honors
    2015Mitchell Prize, ISBA
    2020Elected Fellow, The American Statistical Association

    Collapse Research 
    Collapse research activities and funding
    R01CA132897     (JI, YUAN)Sep 15, 2008 - Apr 30, 2021
    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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Jiang Z, Mi G, Lin J, Lorenzato C, Ji Y. A Multi-Arm Two-Stage (MATS) design for proof-of-concept and dose optimization in early-phase oncology trials. Contemp Clin Trials. 2023 09; 132:107278. PMID: 37419308.
      Citations: 1     Fields:    Translation:Humans
    2. Srinath A, Xie B, Li Y, Sone JY, Romanos S, Chen C, Sharma A, Polster S, Dorrestein PC, Weldon KC, DeBiasse D, Moore T, Lightle R, Zhang D, Stadnik A, Piedad K, Hagan M, Shkoukani A, Bi D, Shen L, Shenkar R, Ji Y, Sidebottom A, Pamer E, Gilbert JA, Kahn ML, D'Souza M, Sulakhe D, Awad IA, Girard R, Koskimäki J, Carrión-Penagos J. Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma. Commun Med (Lond). 2023 Mar 03; 3(1):35. PMID: 36869161; PMCID: PMC9984539.
    3. Romanos SG, Srinath A, Li Y, Xie B, Chen C, Li Y, Moore T, Bi D, Sone JY, Lightle R, Hobson N, Zhang D, Shen L, McCurdy S, Lai CC, Stadnik A, Piedad K, Shkoukani A, Snellings D, Shenkar R, Sulakhe D, Ji Y, Lopez-Ramirez MA, Kahn ML, Marchuk DA, Ginsberg MH, Girard R, Awad IA, Koskimäki J, Carrión-Penagos J. Circulating Plasma miRNA Homologs in Mice and Humans Reflect Familial Cerebral Cavernous Malformation Disease. Transl Stroke Res. 2023 08; 14(4):513-529. PMID: 35715588; PMCID: PMC9758276.
      Citations:    Fields:    Translation:HumansAnimals
    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. PMID: 34994645.
      Citations:    Fields:    
    5. Zhou T, Ji Y. RoBoT: a robust Bayesian hypothesis testing method for basket trials. Biostatistics. 2021 10 13; 22(4):897-912. PMID: 32061093.
      Citations: 4     Fields:    Translation:Humans
    6. Sone JY, Li Y, Hobson N, Romanos SG, Srinath A, Shkoukani A, Stadnik A, Piedad K, Lightle R, Moore T, Li Y, Bi D, Shenkar R, Carroll T, Ji Y, Girard R, Awad IA, Lyne SB, Carrión-Penagos J. Perfusion and permeability as diagnostic biomarkers of cavernous angioma with symptomatic hemorrhage. J Cereb Blood Flow Metab. 2021 11; 41(11):2944-2956. PMID: 34039038; PMCID: PMC8756480.
      Citations: 4     Fields:    Translation:Humans
    7. 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; PMCID: PMC7884145.
      Citations: 12     Fields:    Translation:HumansCells
    8. 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; PMCID: PMC7858231.
      Citations: 31     Fields:    Translation:HumansCTClinical Trials
    9. 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, 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, PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P, PCAWG Consortium, Vázquez-García I. The evolutionary history of 2,658 cancers. Nature. 2020 02; 578(7793):122-128. PMID: 32025013; PMCID: PMC7054212.
      Citations: 363     Fields:    Translation:HumansCells
    10. 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.
      Citations: 36     Fields:    Translation:HumansCells
    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.
      Citations: 7     Fields:    Translation:Humans
    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; PMCID: PMC6628478.
      Citations: 27     Fields:    Translation:Humans
    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; PMCID: PMC6761593.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 3     Fields:    Translation:Humans
    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.
      Citations: 8     Fields:    Translation:Humans
    16. 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. PMID: 30999385; PMCID: PMC6591734.
      Citations: 9     Fields:    Translation:AnimalsCells
    17. Zanini CTP, Ji Y, Müller P, Quintana FA. A Bayesian random partition model for sequential refinement and coagulation. Biometrics. 2019 09; 75(3):988-999. PMID: 30820945.
      Citations:    Fields:    Translation:Humans
    18. 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.
      Citations:    Fields:    
    19. 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.
      Citations: 2     Fields:    Translation:Humans
    20. 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; PMCID: PMC6874020.
      Citations: 28     Fields:    Translation:Humans
    21. 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.
      Citations: 2     Fields:    Translation:Animals
    22. 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. PMID: 35135150.
      Citations: 3     Fields:    
    23. 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.
      Citations: 20     Fields:    Translation:HumansCells
    24. 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; PMCID: PMC6561465.
      Citations: 3     
    25. 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; PMCID: PMC6207187.
      Citations: 4     
    26. 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; PMCID: PMC5925773.
      Citations: 98     Fields:    
    27. Ni Y, Wei L, Ji Y, Müller P. Bayesian graphical models for computational network biology. BMC Bioinformatics. 2018 03 21; 19(Suppl 3):63. PMID: 29589555; PMCID: PMC5872517.
      Citations: 5     Fields:    Translation:HumansCells
    28. 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.
      Citations: 1     Fields:    Translation:Animals
    29. 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; PMCID: PMC5777361.
      Citations: 2     
    30. Ni Y, Zhu Y, Ji Y, Müller P. Heterogeneous reciprocal graphical models. Biometrics. 2018 06; 74(2):606-615. PMID: 29023632.
      Citations: 6     Fields:    Translation:Humans
    31. Zhu Y, Yang S, Ji Y, Zuanetti DA, Müller P. Clustering distributions with the marginalized nested Dirichlet process. Biometrics. 2018 06; 74(2):584-594. PMID: 28960246.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    32. 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.
      Citations: 24     Fields:    Translation:Humans
    33. 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; PMCID: PMC5245120.
      Citations: 14     Fields:    Translation:Humans
    34. 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; PMCID: PMC5923898.
      Citations: 9     Fields:    Translation:Humans
    35. 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.
      Citations: 13     Fields:    Translation:Humans
    36. 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; PMCID: PMC5108580.
      Citations: 167     
    37. 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; PMCID: PMC5069147.
      Citations: 227     Fields:    Translation:Humans
    38. 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.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    39. Lee J, Sengupta S, Gulukota K, Ji Y, Müller P. 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; PMCID: PMC5408274.
      Citations: 6     
    40. Sengupta S, Zhou T, Ji Y, Müeller P. A BAYESIAN NONPARAMETRIC MODEL FOR RECONSTRUCTING TUMOR SUBCLONES BASED ON MUTATION PAIRS. Pac Symp Biocomput. 2016; 21:393-404. PMID: 26776203.
      Citations:    Fields:    Translation:Humans
    41. Lee J, Zhu Y, Ji Y, Müller P. A Nonparametric Bayesian Model for Nested Clustering. Methods Mol Biol. 2016; 1362:129-41. PMID: 26519174.
      Citations:    Fields:    
    42. 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; PMCID: PMC4671006.
      Citations: 79     Fields:    Translation:HumansCells
    43. 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; PMCID: PMC4764425.
      Citations: 34     Fields:    Translation:Humans
    44. Xu Y, Zhu Y, Mitra R, Ji Y, Müller P. Characterizing Cancer-Specific Networks by Integrating TCGA Data. Cancer Inform. 2014; 13(Suppl 2):125-31. PMID: 26628858; PMCID: PMC4657757.
      Citations: 4     
    45. 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; PMCID: PMC4834949.
      Citations: 3     Fields:    Translation:Humans
    46. 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; PMCID: PMC4756850.
      Citations: 9     Fields:    Translation:Humans
    47. 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.
      Citations: 4     Fields:    Translation:CTClinical Trials
    48. Guo W, Li H, Zhu Y, Lan L, Yang S, Drukker K, Morris E, Burnside E, Whitman G, Giger ML, Ji Y, Tcga Breast Phenotype Research Group. 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; PMCID: PMC4718467.
      Citations: 80     
    49. 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; PMCID: PMC4627719.
      Citations: 4     
    50. 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. PMID: 26079994; PMCID: PMC4567392.
      Citations: 9     Fields:    Translation:HumansCells
    51. 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; PMCID: PMC4562700.
      Citations: 19     
    52. Zhu Y, Xu Y, Helseth DL, Gulukota K, Yang S, Pesce LL, Mitra R, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y, Müller P. Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. J Natl Cancer Inst. 2015 Aug; 107(8). PMID: 25956356; PMCID: PMC4554190.
      Citations: 14     Fields:    Translation:Humans
    53. 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; PMCID: PMC4504699.
    54. Xu Y, Yuan Y, Gulukota K, Ji Y, Müller P. MAD Bayes for Tumor Heterogeneity - Feature Allocation with Exponential Family Sampling. J Am Stat Assoc. 2015 Mar 01; 110(510):503-514. PMID: 26170513; PMCID: PMC4498588.
      Citations: 11     
    55. Sengupta S, Wang J, Lee J, Gulukota K, Banerjee A, Ji Y, Müller P. Bayclone: Bayesian nonparametric inference of tumor subclones using NGS data. Pac Symp Biocomput. 2015; 467-78. PMID: 25592605.
      Citations: 14     Fields:    Translation:Humans
    56. 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; PMCID: PMC4441103.
      Citations: 7     Fields:    Translation:HumansCells
    57. Mitra R, Qiu P, Ji Y, Müller P. Bayesian hierarchical models for protein networks in single-cell mass cytometry. Cancer Inform. 2014; 13(Suppl 4):79-89. PMID: 25574129; PMCID: PMC4266200.
      Citations: 3     
    58. Guha S, Ji Y, Baladandayuthapani V. Bayesian disease classification using copy number data. Cancer Inform. 2014; 13(Suppl 2):83-91. PMID: 25336897; PMCID: PMC4196891.
      Citations: 1     
    59. Xu Y, Trippa L, Ji Y, Müller P. Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials. Stat Biosci. 2016 Jun; 8(1):159-180. PMID: 27617041; PMCID: PMC5014435.
      Citations: 13     
    60. 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; PMCID: PMC4387197.
      Citations: 218     Fields:    
    61. 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. PMID: 24859531; PMCID: PMC4048332.
      Citations: 77     Fields:    Translation:HumansCells
    62. Ji CF, Ji YB. Laminarin-induced apoptosis in human colon cancer LoVo cells. Oncol Lett. 2014 May; 7(5):1728-1732. PMID: 24765209; PMCID: PMC3997718.
      Citations: 20     
    63. 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.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    64. 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.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    65. 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.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    66. 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.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    67. 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; PMCID: PMC4523298.
      Citations: 13     
    68. 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; PMCID: PMC3913186.
      Citations: 33     
    69. Mitra R, Ji Y, Zhu Y, Mills G, Lu Y, Müller P. A Bayesian hierarchical model for inference across related reverse phase protein arrays experiments. J Appl Stat. 2014; 41(11):2483-2492. PMID: 26246652; PMCID: PMC4523276.
    70. Xu Y, Lee J, Yuan Y, Mitra R, Liang S, Ji Y, Müller P. Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data. Bayesian Anal. 2013 Dec; 8(4):759-780. PMID: 26246865; PMCID: PMC4523245.
      Citations: 6     
    71. 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. PMID: 23742247; PMCID: PMC3680080.
      Citations: 7     
    72. 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; PMCID: PMC3641699.
      Citations: 66     Fields:    Translation:Humans
    73. 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.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    74. Mitra R, Ji Y, Müller P. Propriety conditions for the Bayesian autologistic model - Inference for histone modifications. J Stat Theory Pract. 2013; 7(2):248-258. PMID: 26246801; PMCID: PMC4523243.
    75. Xu Y, Zhang J, Yuan Y, Mitra R, Ji Y, Müller P. A Bayesian Graphical Model for Integrative Analysis of TCGA Data. IEEE Int Workshop Genomic Signal Process Stat. 2012 Dec; 2012:135-138. PMID: 25859418; PMCID: PMC4387199.
      Citations: 5     
    76. 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. PMID: 25859417; PMCID: PMC4387196.
      Citations: 1     
    77. 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; PMCID: PMC4697941.
      Citations: 1     
    78. Cai G, Li H, Lu Y, Huang X, Lee J, Ji Y, Liang S, Müller P. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics. 2012; 13 Suppl 13:S5. PMID: 23320920; PMCID: PMC3426807.
      Citations: 13     Fields:    
    79. 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; PMCID: PMC3426806.
      Citations: 2     Fields:    
    80. 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; PMCID: PMC3350366.
      Citations: 43     Fields:    Translation:HumansCells
    81. 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. PMID: 23075018; PMCID: PMC3501341.
      Citations: 3     Fields:    Translation:HumansCells
    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; PMCID: PMC5042214.
      Citations: 73     Fields:    Translation:HumansCTClinical Trials
    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; PMCID: PMC3153162.
      Citations: 11     
    84. Khaskhely N, Buglio D, Shafer JA, Derenzini E, Bollard CM, Medeiros LJ, Ji Y, Younes A, Jóna A, Illés 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; PMCID: PMC3177003.
      Citations: 21     Fields:    Translation:HumansCells
    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; PMCID: PMC3190637.
      Citations: 16     Fields:    Translation:Cells
    86. Telesca D, Kornblau SM, Suchard MA, Ji Y, Müller P. Modeling Protein Expression and Protein Signaling Pathways. J Am Stat Assoc. 2011; 107(500):1372-1384. PMID: 26246646; PMCID: PMC4523312.
      Citations: 9     
    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; PMCID: PMC3079218.
      Citations: 23     
    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; PMCID: PMC5038924.
      Citations: 74     Fields:    Translation:Humans
    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.
      Citations: 15     Fields:    Translation:Humans
    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; PMCID: PMC2901213.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    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; PMCID: PMC2940588.
      Citations: 280     Fields:    Translation:HumansAnimals
    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.
      Citations: 25     Fields:    Translation:HumansCTClinical Trials
    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; PMCID: PMC4570736.
      Citations: 7     Fields:    Translation:Humans
    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; PMCID: PMC2720696.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 5     Fields:    Translation:Humans
    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; PMCID: PMC4562497.
      Citations: 18     Fields:    
    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.
      Citations:    Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 1     Fields:    Translation:AnimalsCells
    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. Mol Cancer Ther. 2008 Mar; 7(3):464-73. PMID: 18347134.
      Citations: 158     Fields:    Translation:HumansCells
    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.
      Citations: 2     Fields:    
    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; PMCID: PMC3294317.
      Citations: 20     Fields:    Translation:Humans
    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.
      Citations: 22     Fields:    Translation:HumansAnimalsCells
    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; PMCID: PMC2647748.
      Citations: 10     Fields:    Translation:AnimalsCells
    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.
      Citations:    Fields:    Translation:Animals
    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.
      Citations: 48     Fields:    Translation:Humans
    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.
      Citations: 65     Fields:    Translation:Humans
    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.
      Citations:    Fields:    Translation:HumansCells
    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.
      Citations: 3     Fields:    Translation:HumansCells
    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.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    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.
      Citations:    Fields:    Translation:Animals
    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.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 2     Fields:    Translation:HumansCells
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