Genomes and Genes
Affiliation: The University of Texas
- A modified toxicity probability interval method for dose-finding trialsYuan 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...
- A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samplesYuan 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...
- Bayesian models based on test statistics for multiple hypothesis testing problemsYuan 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...
- Dose-finding in phase I clinical trials based on toxicity probability intervalsYuan 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...
- On Differential Gene Expression Using RNA-Seq DataJuHee 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...
- The pan-deacetylase inhibitor panobinostat induces cell death and synergizes with everolimus in Hodgkin lymphoma cell linesManuela 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....
- BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing dataYuan 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)...
- Risk-group-specific dose finding based on an average toxicity scoreB 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...
- Extracting three-way gene interactions from microarray dataJiexin 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...
- Dose--schedule finding in phase I/II clinical trials using a Bayesian isotonic transformationYisheng 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...
- Monitoring late-onset toxicities in phase I trials using predicted risksB 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...
- Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratiosGuosheng 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...
- RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platformsYuan 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...
- Mocetinostat for relapsed classical Hodgkin's lymphoma: an open-label, single-arm, phase 2 trialAnas 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...
- Accuracy of RNA-Seq and its dependence on sequencing depthGuoshuai 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...
- BM-map: Bayesian mapping of multireads for next-generation sequencing dataYuan 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...
- Bayesian continual reassessment method for dose-finding trials infusing T cells with limited sample sizeYuan 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...
- Applications of beta-mixture models in bioinformaticsYuan 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...
- Adaptive randomization for multiarm comparative clinical trials based on joint efficacy/toxicity outcomesYuan 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...
- Curcumin (diferuloylmethane) alters the expression profiles of microRNAs in human pancreatic cancer cellsMichael 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...
- Mechanism of Fas signaling regulation by human herpesvirus 8 K1 oncoproteinZuzana 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...
- Incidence and risk factors of venous thromboembolic events in lymphomaXiao 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...
- Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strainRui 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...
- The histone deacetylase inhibitor entinostat (SNDX-275) induces apoptosis in Hodgkin lymphoma cells and synergizes with Bcl-2 family inhibitorsAdam 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...
- Phase II study of yttrium-90-ibritumomab tiuxetan in patients with relapsed or refractory mantle cell lymphomaMichael 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)...
- Breast cancer risk reduction and membrane-bound catechol O-methyltransferase genetic polymorphismsYuan 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....
- Tools and strategies for physiological genomics: the Rat Genome DatabaseSimon 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...
- Impact of donor gender on male rat recipients of small-for-size liver graftsYanLi Gu
Department of General Surgery and Transplantation Surgery, University Hospital Duisburg Essen, Essen, Germany
Liver Transpl 11:669-78. 2005....
- Cytokeratin 10 and cytokeratin 19: predictive markers for poor prognosis in hepatocellular carcinoma patients after curative resectionXin 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...
- Serous cystic neoplasms of the pancreas: a clinicopathologic and immunohistochemical analysisYuan 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...
- Solitary fibrous tumor of the liverYuan 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...
- [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...
- Mucins in the diagnosis and differential diagnosis of pancreatic cystic neoplasms: report of 40 casesYuan Ji
Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 20032, China
Chin Med J (Engl) 119:765-8. 2006
- Separation of DNA with different configurations on flat and nanopatterned surfacesBingquan Li
Department of Materials Science and Engineering, SUNY at Stony Brook, New York 11794, USA
Anal Chem 78:4743-51. 2006....
- P53 immunohistochemical scoring: an independent prognostic marker for patients after hepatocellular carcinoma resectionLun 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...