Yuan Ji

Summary

Affiliation: The University of Texas
Country: USA

Publications

  1. doi A modified toxicity probability interval method for dose-finding trials
    Yuan Ji
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, Houston, TX, USA
    Clin Trials 7:653-63. 2010
  2. ncbi A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
    Yuan Ji
    Department of Biostatistics and Applied Mathematics, The University of Texas M D Anderson Cancer Center Houston, TX 77030, USA
    Bioinformatics 21:1055-61. 2005
  3. doi Bayesian models based on test statistics for multiple hypothesis testing problems
    Yuan Ji
    Department of Bioinformatics and Computational Biology, The University of Texas, M D Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 24:943-9. 2008
  4. ncbi Dose-finding in phase I clinical trials based on toxicity probability intervals
    Yuan Ji
    Department of Bioinformatics and Computational Biology, University of Texas, M D Anderson Cancer Center, Houston, TX, USA
    Clin Trials 4:235-44. 2007
  5. pmc On Differential Gene Expression Using RNA-Seq Data
    JuHee Lee
    Department of Biostatistics, UT M D Anderson Cancer Center Houston, Texas, USA
    Cancer Inform 10:205-15. 2011
  6. pmc The pan-deacetylase inhibitor panobinostat induces cell death and synergizes with everolimus in Hodgkin lymphoma cell lines
    Manuela Lemoine
    Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Blood 119:4017-25. 2012
  7. pmc BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data
    Yuan Yuan
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S9. 2012
  8. pmc Risk-group-specific dose finding based on an average toxicity score
    B Nebiyou Bekele
    Department of Biostatistics, Division of Quantitative Sciences, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
    Biometrics 66:541-8. 2010
  9. ncbi Extracting three-way gene interactions from microarray data
    Jiexin Zhang
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030 4009, USA
    Bioinformatics 23:2903-9. 2007
  10. pmc Dose--schedule finding in phase I/II clinical trials using a Bayesian isotonic transformation
    Yisheng Li
    Department of Biostatistics, Division of Quantitative Sciences, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Unit 447, Houston, TX 77030, USA
    Stat Med 27:4895-913. 2008

Collaborators

Detail Information

Publications35

  1. doi A modified toxicity probability interval method for dose-finding trials
    Yuan Ji
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, Houston, TX, USA
    Clin Trials 7:653-63. 2010
    ..Building on earlier work, the toxicity probability interval (TPI) method, we present a modified TPI (mTPI) design that is calibration-free for phase I trials...
  2. ncbi A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
    Yuan Ji
    Department of Biostatistics and Applied Mathematics, The University of Texas M D Anderson Cancer Center Houston, TX 77030, USA
    Bioinformatics 21:1055-61. 2005
    ..Large models often lead to intensive or even intractable computation, while small models may be inadequate for complex data...
  3. doi Bayesian models based on test statistics for multiple hypothesis testing problems
    Yuan Ji
    Department of Bioinformatics and Computational Biology, The University of Texas, M D Anderson Cancer Center, Houston, TX 77030, USA
    Bioinformatics 24:943-9. 2008
    ..To check if our model assumptions for the test statistics are valid for various bioinformatics experiments, we also propose a simple graphical model-assessment tool...
  4. ncbi Dose-finding in phase I clinical trials based on toxicity probability intervals
    Yuan Ji
    Department of Bioinformatics and Computational Biology, University of Texas, M D Anderson Cancer Center, Houston, TX, USA
    Clin Trials 4:235-44. 2007
    ..Most phase I clinical trials conducted at the M. D. Anderson Cancer Center use the algorithmic 3 + 3 design, despite the availability of more advanced model-based designs such as the continual reassessment method...
  5. pmc On Differential Gene Expression Using RNA-Seq Data
    JuHee Lee
    Department of Biostatistics, UT M D Anderson Cancer Center Houston, Texas, USA
    Cancer Inform 10:205-15. 2011
    ..Most published methods collapse the position-level read data into a single gene-specific expression measurement. Statistical inference proceeds by modeling these gene-level expression measurements...
  6. pmc The pan-deacetylase inhibitor panobinostat induces cell death and synergizes with everolimus in Hodgkin lymphoma cell lines
    Manuela Lemoine
    Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
    Blood 119:4017-25. 2012
    ....
  7. pmc BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data
    Yuan Yuan
    Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
    BMC Genomics 13:S9. 2012
    ..Allocating these multireads is challenging but critical for interpreting RNA-seq data. We recently developed a Bayesian stochastic model that allocates multireads more accurately than alternative methods (Ji et al. Biometrics 2011)...
  8. pmc Risk-group-specific dose finding based on an average toxicity score
    B Nebiyou Bekele
    Department of Biostatistics, Division of Quantitative Sciences, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
    Biometrics 66:541-8. 2010
    ..We demonstrate the performance of the proposed dose-finding design using simulations based on a clinical trial in multiple myeloma...
  9. ncbi Extracting three-way gene interactions from microarray data
    Jiexin Zhang
    Department of Bioinformatics and Computational Biology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 237, Houston, TX 77030 4009, USA
    Bioinformatics 23:2903-9. 2007
    ..The identified three-way interactions may constitute candidates for further experimentation using techniques such as RNA interference, so that novel gene network or pathways could be identified...
  10. pmc Dose--schedule finding in phase I/II clinical trials using a Bayesian isotonic transformation
    Yisheng Li
    Department of Biostatistics, Division of Quantitative Sciences, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Unit 447, Houston, TX 77030, USA
    Stat Med 27:4895-913. 2008
    ..We illustrate our methodology through its application to a clinical trial in leukemia and compare it with two alternative approaches...
  11. pmc Monitoring late-onset toxicities in phase I trials using predicted risks
    B Nebiyou Bekele
    Department of Biostatistics, MD Anderson Cancer Center, Houston, TX 77030, USA
    Biostatistics 9:442-57. 2008
    ..This advantage increases with accrual rate, but the price of this additional safety is that the trial takes longer to complete on average...
  12. ncbi Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratios
    Guosheng Yin
    Department of Biostatistics and Applied Mathematics, University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Biometrics 62:777-84. 2006
    ..The method is illustrated with a real trial design for a breast medical oncology study...
  13. ncbi RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms
    Yuan Ji
    Department of Biostatistics and Applied Mathematics, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030 4009, USA
    Appl Bioinformatics 5:89-98. 2006
    ..It is a sensible approach for matching probes across platforms. We conclude that UniGene alone is insufficient to match genes across platforms. Refined matching based on RefSeq significantly improves the quality of matches...
  14. doi Mocetinostat for relapsed classical Hodgkin's lymphoma: an open-label, single-arm, phase 2 trial
    Anas Younes
    Department of Lymphoma and Myeloma, The University of Texas, M D Anderson Cancer Center, Houston, TX 77030, USA
    Lancet Oncol 12:1222-8. 2011
    ..We tested the safety and efficacy of mocetinostat, an oral isotype-selective histone deacetylase inhibitor, in patients with relapsed classical Hodgkin's lymphoma...
  15. pmc Accuracy of RNA-Seq and its dependence on sequencing depth
    Guoshuai Cai
    Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    BMC Bioinformatics 13:S5. 2012
    ..RNA-Seq is becoming a common technique for surveying gene expression based on DNA sequencing. As it is not clear how increased sequencing capacity has affected measurement accuracy of mRNA, we sought to investigate that relationship...
  16. pmc BM-map: Bayesian mapping of multireads for next-generation sequencing data
    Yuan Ji
    Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
    Biometrics 67:1215-24. 2011
    ..We provide a C++ program for downloading that is being packaged into a user-friendly software...
  17. pmc Bayesian continual reassessment method for dose-finding trials infusing T cells with limited sample size
    Yuan Ji
    Department of Statistics, Rice University, Houston, Texas 77251 1892, USA
    J Biopharm Stat 22:1206-19. 2012
    ..Supplementary materials including an R function and a movie demo can be downloaded in the websites mentioned in the paper...
  18. ncbi Applications of beta-mixture models in bioinformatics
    Yuan Ji
    Department of Biostatistics, The University of Texas M D Anderson Cancer Center, Houston, 77030, USA
    Bioinformatics 21:2118-22. 2005
    ..To determine the number of components in the mixture model, we suggest an alternative criterion, ICL-BIC, which is shown to perform better in selecting the correct mixture model...
  19. doi Adaptive randomization for multiarm comparative clinical trials based on joint efficacy/toxicity outcomes
    Yuan Ji
    Department of Bioinformatics and Computational Biology, M D Anderson Cancer Center, Houston, TX 77030, USA
    Biometrics 65:876-84. 2009
    ..We illustrate our methodology with a leukemia trial that compares three treatments in terms of their 52-week molecular remission rates and 52-week toxicity rates...
  20. doi Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cells
    Michael Sun
    Department of Investigational Cancer Therapeutics Phase I Program, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Mol Cancer Ther 7:464-73. 2008
    ..The mechanisms underlying the antitumor activity of curcumin have not, however, been completely delineated...
  21. pmc Mechanism of Fas signaling regulation by human herpesvirus 8 K1 oncoprotein
    Zuzana Berkova
    Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, 77054, USA
    J Natl Cancer Inst 101:399-411. 2009
    ..Herpesvirus 8 (HHV-8) oncoprotein K1 is linked to lymphoproliferation and suppression of apoptosis mediated by the Fas death receptor. Expression of K1 in transgenic mice induces accumulation of lymphoid tissue cells and lymphoma...
  22. doi Incidence and risk factors of venous thromboembolic events in lymphoma
    Xiao Zhou
    Department of Sarcoma Medical Oncology, Section of Cytokines and Supportive Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Am J Med 123:935-41. 2010
    ..Cancer patients are at increased risk of venous thromboembolism; however, the incidence and risk factors for venous thromboembolism in lymphoma patients are not well defined...
  23. pmc Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain
    Rui Zhu
    Department of Cancer Genetics, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Unit 1006, Houston, Texas 77030, USA
    Mamm Genome 18:584-95. 2007
    ..Our data advance the use of CSS to identify disease susceptibility genes and demonstrate that the 129.MOLF-Chr19 strain serves as a useful model to elucidate the genetics and biology of germ cell transformation and tumor development...
  24. pmc The histone deacetylase inhibitor entinostat (SNDX-275) induces apoptosis in Hodgkin lymphoma cells and synergizes with Bcl-2 family inhibitors
    Adam Jona
    Department of Lymphoma and Myeloma, The University of Texas M D Anderson Cancer Center, Houston, USA
    Exp Hematol 39:1007-1017.e1. 2011
    ..Based on promising in vitro and in vivo activity of several histone deacetylase inhibitors in Hodgkin lymphoma (HL), we investigated SNDX-275, an oral class 1 isoform-selective histone deacetylase inhibitors in HL-derived cell lines...
  25. doi Phase II study of yttrium-90-ibritumomab tiuxetan in patients with relapsed or refractory mantle cell lymphoma
    Michael Wang
    Department of Lymphoma and Myeloma, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    J Clin Oncol 27:5213-8. 2009
    ..This phase II trial evaluated the safety and efficacy of yttrium-90 ((90)Y)-ibritumomab tiuxetan in patients with relapsed or refractory mantle cell lymphoma (MCL)...
  26. pmc Breast cancer risk reduction and membrane-bound catechol O-methyltransferase genetic polymorphisms
    Yuan Ji
    Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
    Cancer Res 68:5997-6005. 2008
    ....
  27. pmc Tools and strategies for physiological genomics: the Rat Genome Database
    Simon N Twigger
    Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
    Physiol Genomics 23:246-56. 2005
    ..We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics...
  28. ncbi Impact of donor gender on male rat recipients of small-for-size liver grafts
    YanLi Gu
    Department of General Surgery and Transplantation Surgery, University Hospital Duisburg Essen, Essen, Germany
    Liver Transpl 11:669-78. 2005
    ....
  29. doi Cytokeratin 10 and cytokeratin 19: predictive markers for poor prognosis in hepatocellular carcinoma patients after curative resection
    Xin Rong Yang
    Liver Cancer Institute, Zhong Shan Hospital and Shanghai Medical School, Fudan University, Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Shanghai Cancer Institute, Shanghai, PR China
    Clin Cancer Res 14:3850-9. 2008
    ..The aim of this study was to assess the value of CK10 alone or in combination with cytokeratin 19 (CK19) in predicting tumor recurrence after curative resection in HCC patients...
  30. ncbi Serous cystic neoplasms of the pancreas: a clinicopathologic and immunohistochemical analysis
    Yuan Ji
    Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
    Chin J Dig Dis 7:39-44. 2006
    ..To clarify whether the various subtypes of serous cystic neoplasms (SCNs) of the pancreas can be distinguished from each other by marker profiles...
  31. ncbi Solitary fibrous tumor of the liver
    Yuan Ji
    Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
    Hepatobiliary Pancreat Dis Int 5:151-3. 2006
    ..Solitary fibrous tumor of the liver is a rare neoplasm. So far, 23 cases have been described in the English literature. We reported an additional case...
  32. ncbi [Diagnosis and differential diagnosis of intraductal papillary mucinous neoplasm of pancreas]
    Yuan Ji
    Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
    Zhonghua Bing Li Xue Za Zhi 35:77-81. 2006
    ..To study the clinicopathologic features of intraductal papillary mucinous neoplasm (IPMN) and its distinction from mucinous cystic neoplasm of pancreas...
  33. ncbi Mucins in the diagnosis and differential diagnosis of pancreatic cystic neoplasms: report of 40 cases
    Yuan Ji
    Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 20032, China
    Chin Med J (Engl) 119:765-8. 2006
  34. ncbi Separation of DNA with different configurations on flat and nanopatterned surfaces
    Bingquan Li
    Department of Materials Science and Engineering, SUNY at Stony Brook, New York 11794, USA
    Anal Chem 78:4743-51. 2006
    ....
  35. pmc P53 immunohistochemical scoring: an independent prognostic marker for patients after hepatocellular carcinoma resection
    Lun Xiu Qin
    Liver Cancer Institute and Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai 200032, China
    World J Gastroenterol 8:459-63. 2002
    ..To confirm if p53 mutation could be a routine predictive marker for the prognosis of hepatocellular carcinoma (HCC) patients...