Reprints and Preprints

[2005]

  1.    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 21(7):1055-61, 4/2005. e-Pub 10/2004.

  2.    Ji Y, Wu C, Liu P, Wang J, Coombes KR. Applications of beta-mixture models in bioinformatics. Bioinformatics 21(9):2118-22, 5/2005. R Script


[2006]

  3.    Kolonin MG, Sun J, Do KA, Vidal CI, Ji Y, Baggerly KA, Pasqualini R, Arap W. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J 20(7):979-81, 5/2006. e-Pub 3/2006.

  4.    Yin G, Li Y, Ji Y. Bayesian dose-finding in phase I/II clinical trials using toxicity and efficacy odds ratios. Biometrics 62(3):777-84, 9/2006.

  5.    Ji Y, Tsui K-W, Kim KM. A two-stage empirical Bayes method for identifying differentially expressed genes. Computational Statistics and Data Analysis. 50:3592-604, 2006.

  6.    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 5(2):89-98, 2006.


[2007]

  7.    Zhu R, Ji Y, Xiao L, Matin A. Testicular germ cell tumor susceptibility genes from the consomic 129.MOLF-Chr19 mouse strain. Mamm Genome 18(8):584-595, 8/2007. e-Pub 8/2007. PMCID: PMC2647748.

  8.    Zhang J, Ji Y, Zhang L. Extracting three-way gene interactions from microarray data. Bioinformatics 23(21):2903-2909, 11/2007. e-Pub 10/2007.

  9.    Ji Y, Li Y, Yin G. Bayesian dose-finding designs for phase I clinical trials. Statistica Sinica 17:531-47, 2007.

 10.   Ji Y, Yin G, Tsui K-W, Kolonin M, Sun J, Arap W, Pasqualini R, Do K-A. Bayesian mixture models for complex high-dimension count data. Applied Statistics 56:139-152, 2007.

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

 12.   Bekele BN, Ji Y, Shen Y, Thall PF. Monitoring late-onset toxicities in phase I trials using predicted risks. Biostatistics 9(3):442-57, 7/2008. e-Pub 12/2007.


[2008]

 13.   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 7(3):464-473, 3/2008.

 14.   Ji Y, Lu Y, Mills GB. Bayesian models based on test statistics for multiple hypothesis testing problems. Bioinformatics 24(7):943-949, 4/2008. e-Pub 2/2008.

 15.   Miyazaki K, Yamaguchi M, Suguro M, Choi W, Ji Y, Xiao L, Zhang W, Ogawa S, Katayama N, Shiku H, Kobayashi T. Gene Expression Profiling of Diffuse Large B-cell Lymphoma Supervised by CD21 Expression. Br J Haematol 142(4):562-570, 8/2008. e-Pub 6/2008.

 16.   Li Y, Bekele BN, Ji Y, Cook JD. Dose-schedule finding in phase I/II clinical trials using a Bayesian isotonic transformation. Stat Med 27(24):4895-4913, 10/2008.

 17.   Hu B, Ji Y*, Tsui KW. Bayesian estimation of inverse dose-response. Biometrics 64(4):1223-30, 12/2008. e-Pub 3/2008.

 18.   Fanale M, Fayad L, Pro B, Samaniego F, Zachariah G, Nunez C, Ji Y, Younes A. A phase I evaluation of bortezomib in combination with ice (BICE) as treatment for relapsed/refractory classical Hodgkin lymphoma. Annals of Oncology 19:236-236, 2008.


[2009]

 19.   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 101(6):399-411, 3/2009. e-Pub 3/2009. PMCID: PMC2720696.

 20.   Ji Y, Bekele BN. Adaptive randomization for multi-arm comparative clinical trials based on joint efficacy/toxicity outcomes. Biometrics 65(3):876-84, 9/2009. e-Pub 1/2009.

 21.   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 27(31):5213-8, 11/2009. e-Pub 9/2009.

 22.   Bekele BN, Li Y, Ji Y. Risk-group-specific dose finding based on an average toxicity score. Biometrics 66(2):541-8, 6/2010. e-Pub 7/2009.


[2010]

 23.   Hu B, Bekele BN, Ji Y*. Adaptive Dose Insertion in Early Phase Clinical Trials. Clin Trials. e-Pub 9/2010.

 24.   Ji Y, Liu P, Li Y, Bekele BN. A modified toxicity probability interval method for dose-finding trials. Clin Trials. e-Pub 10/2010. Manuscript Software in Excel   Software in R

 25.   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 123(10):935-41, 10/2010.

 26.   Baladandayuthapani V, Ji Y, Morris J, Talluri R, Nieto-Barajas L. Bayesian Random Segmentation Models to Identify Shared Copy Number Aberrations for Array CGH Data. Journal of American Statistical Association 105(492):1358-1375, 12/2010.


[2011]

 27.   Ji Y*, Xu, Y, Zhang, Q, Tsui, K-W, Yuan, Y, Liang, S, Liang, H*. BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data. Biometrics. In Press. Manuscript   Software in C with examples

 28.   Fanale M, Fayad L, Pro B, Samaniego F, Liboon MJ, Nunez C, Horowitz S, Anderlini P, Popat U, Ji Y, Kwak LW, Younes A. Phase I Study of Bortezomib Plus ICE (BICE) for the Treatment of Relapsed/Refractory Hodgkin Lymphoma. British Journal of Hematology. In Press.

 29.   Ji Y, Feng L, Shpall EJ, Kebriaei P, Champlin R, Berry D, Cooper LJN. Bayesian Continual Reassessment Method for Dose-Finding Trials Infusing T Cells with Limited Sample Size. Journal of Biopharmaceutical Statistics. In Press.

 30.   Lee JH, Mueller P*, Liang S, Cai G, Ji Y*. On Differential Gene Expression Using RNA-Seq Data. Cancer Informatics, in press. Manuscript   Software in R with examples (with a Manual )

 31.   Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S,. BABC -- Bayesian base calling for Solexa sequence data. BMC Bioinformatics, in press. Manuscript

 32.    Cai G, Li H, Lu Y, Lee JH, Mueller P, Ji Y, Liang S,. Accuracy of RNA-Seq and its dependence on sequencing depth. BMC Bioinformatics, in press. Manuscript

 33.    Younes A, Oki Y, Bociek GR, 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, and Martell, RE. Phase II Study of Mocetinostat (MGCD0103) In Patients with Relapsed and Refractory Classical Hodgkin Lymphoma. Lancet Oncology, in Press.

  34.    Nieto-Barajas L, Mueller P, Ji Y, Lu Y, Mills, G. A Time-Series DDP for Functional Proteomics Profiles. Biometrics, in press.

  35.    Derenzini E, Lemoine M, Buglio D, Katayama H, Ji Y, Davis E, Sen S, Younes A. The JAK inhibitor AZD1480 regulates proliferation and immunity in Hodgkin lymphoma. Blood Cancer, in press.

  36.    Jona A, Khaskhely N, Buglio D, Shafer JA, Derenzini E, Bollard C, Medeiros LJ, Illes 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, 39(10): 1007-1017.


[2012]

  37.     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, in press.



Preprints

    Mitra R, Mueller, P*, Liang, S, Yue, L, Ji Y*. A Bayesian Graphical Model for ChIP-Seq Data on Histone Modifications. Submitted.

    Talluri R, Baladandayuthapani V, Mallick BK, Ji Y, Coombes KR, Hennessey BT, Davies M. Bayesian Sparse Graphical Models for Classification with Application to Protein Expression Data. Submitted.

    Telesca D*, Mueller P, Kornblau S, Ji Y*. Modeling Protein Expression and Protein Signaling Pathways. Submitted.

    Chu F, Foglietta M, Nattamai D, Lee ST, Yamazaki T, Orozco NM, Dong C, Vence LM, Radvanyi L, Younes A, Ji Y, Neelapu SS. PD-1 expression on T cells in follicular lymphoma. Submitted.

     Liang H *, Yuan Y, Norris C, Xu Y, Tsui KW, Ji Y*. BM-Map: an efficient software package for accurately allocating multireads of RNA-seq data. Submitted.

     Xie F, Ji Y, Tremmel LT. A Bayesian adaptive design for multi-dose, randomized, placebo-controlled phase I/II trials. Submitted. Manuscript   R software for running trial simulation

     Lee, JH, Ji Y, Liang, S, Cai, G, Mueller, P. Bayesian Hierarchical Model for Differential Gene Expression Using RNA-Seq Data. Submitted. Manuscript   Software in R with examples

     Cai, C., Yuan, Y., Ji, Y.. A Bayesian Phase I/II Design for Oncology Clinical Trials of Combinational Biological Agents. Submitted.

     Lee, J., Mueller, P., Ji, Y.. A Nonparametric Bayesian Model for Local Clustering. Submitted. Manuscript

     Mitra, R., Mueller, P.*, Ji, Y.*. Propreity conditions for the Bayesian autologistic model -- Inference for Histone Modifications. Submitted. Manuscript

     Hu, B., Ji, Y.*, Xu, Y., Ting, AH*. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data. Submitted. Manuscript