Supplemental Research

Additional subset analyses supplemental to: 

Berry DA, Ueno NT, Johnson MM, et al., High-dose chemotherapy with autologous stem-cell support versus standard-dose chemotherapy for high-risk adjuvant breast cancer: Overview of individual patient data from 15 randomized trials. Journal of Clinical Oncology 2011; 29:3214-3223.  



Technical Reports

Additional working papers may be accessed through the COBRA Berkeley Electronic Press Repository.

Note: Reports will open in pdf format.


Beavers DP, Stamey JD, Bekele BN: Bayesian approaches to analysis and study design for repeated binary testing experiments: Supplementary materials. UTMDABTR-001-10


Cook JD: Efficacy-toxicity trade-offs based on Lp norms. UTMDABTR-003-06

Wathen JK, Cook JD: Power and bias in adaptively randomized clinical trials. UTMDABTR-002-06

Cook J: Numerical evaluation of gamma inequalities. UTMDABTR-001-06


Cook J: Continuous safety monitoring in single-arm, time-to-event trials without software. UTMDABTR-006-05

Cook J: Exact calculation of beta inequalities. UTMDABTR-005-05

Gold DL, Coombes KR, Wang J, Mallick B: Testing gene class enrichment in high-throughput genomics. UTMDABTR-004-05

Bekele BN, Kirk RE: Cell means analysis of ANCOVA designs. UTMDABTR-003-05

Ghosh P, Rosner GL: A semiparametric Bayesian approach to average bioequivalence. UTMDABTR-002-05

Gold DL, Wang J, Coombes KR: Inter-gene correlation on oligonucleotide arrays: how much does normalization matter? UTMDABTR-001-05


Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM: Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. UTMDABTR-001-04

Coombes KR, Koomen JM, Baggerly KA, Morris JS, Kobayashi R: Understanding the characteristics of mass spectrometry data through the use of simulation.

Braun TM, Thall PF, Yuan Z: Determining a maximum tolerated schedule of a cytotoxic agent. UTMDABTR-003-04

Thall PF, Wang X: Bayesian sensitivity analyses of confounded treatment effects. UTMDABTR-004-04, Figure 1 , Figure 2 , Figure 3

Broemeling LD: Studies in the history of probability and statistics: Semmelweis and childbed fever. A statistical analysis 147 years later. UTMDABTR-005-04

Morris JS, Carroll RJ: Wavelet-based functional mixed models. UTMDABTR-006-04

Coombes KR, Wang J, Baggerly KA: A statistical method for finding biomarkers from microarray data, with application to prostate cancer. UTMDABTR-007-04

Baggerly KA, Morris JS, Edmonson S, Coombes KR: Signal in noise: Can experimental bias explain some results of serum proteomics tests for ovarian cancer? UTMDABTR-008-04

Baggerly KA, Coombes KR, Morris JS: Are the NCI / FDA ovarian proteomic data biased? A reply to "Producers and Consumers." UTMDABTR-009-04

Morris JS, Coombes KR, Koomen J, Baggerly KA, Kobayashi R: Feature extraction methodology for mass spectrometry data in biomedical applications using the mean spectrum. UTMDABTR-010-04

Bekele BN, Shen Y: A Bayesian approach to jointly modeling toxicity and biomarker expression in a phase I / II dose-finding trial. UTMDABTR-011-04

Cheng Y, Shen Y: Bayesian adaptive designs for clinical trials. UTMDABTR-012-04

Broemeling LD: The predictive distribution and area under the ROC curve. UTMDABTR-013-04

Cook J: Simulation results for phase II clinical trial durations. UTMDABTR-014-04


Baggerly KA, Morris JS, Coombes KR: Cautions about reproducibility in mass spectrometry patterns: Joint analysis of several proteomic data sets. UTMDABTR-001-03

Bekele BN, Lee JJ, Cantor SB, Zhou X, Lee JS: Decision analysis of prophylactic cranial irradiation for patients with small cell lung cancer. UTMDABTR-002-03

Thall PF, Wathen JK: Covariate-adjusted adaptive randomization in a multi-stage sarcoma trial. UTMDABTR-003-03

Thall PF, Champlin RE, Andersson BS: Comparison of 100-day mortalty rates associated with IV busulfan and cyclophosphamide versus other preparative regimens in allogeneic bone marrow transplantation for chronic myelogenous leukemia: Bayesian sensitivity analyses of confounded treatment and center effects. UTMDABTR-004-03

Baggerly KA: Detecting and correcting misalignment in Affymetrix data. UTMDABTR-005-03

Thall PF, Cook JD: Dose-finding based on efficacy-toxicity trade-offs. UTMDABTR-006-03

Rosner, GL: Bayesian monitoring of clinical trials with failure-time end points. UTMDABTR-007-03

Cook J: Numerical computation of stochastic inequality probabilities. [Now available in COBRA, Berkeley Electronic Press] UTMDABTR-008-03


Cheng Y, Su F, Berry DA: Asymptotic optimal group sequential strategies in two-armed bandit problems. UTMDABTR-001-02

Thall PF, Wathen JK, Bekele BN, Champlin RE, Baker LO, Benjamin RS: Hierarchical Bayesian approaches to phase II trials in diseases with multiple subtypes. UTMDABTR-002-02

Broemeling, LD: Studies in the history of probability and statistics: The Bayesian contributions of Edmond Lhoste. UTMDABTR-003-02

Cheng Y, Rosner GL: Asymptotic optimal sample sizes for discovering a promising treatment in phase II group sequential clinical trials. UTMDABTR-004-02

Moon H, Lee JJ, Ahn H, Nikolova RG: Web-based simulator for sample size and power estimation in animal carcinogenicity studies. UTMDABTR-005-02

Moon H, Ahn H, Lee JJ, Kodell RL: A weight-adjusted Peto's test when cause of death is not assigned. UTMDABTR-006-02

De Iorio M, Muller P, Rosner GL, MacEachern SN: An ANOVA model for dependent random measures. UTMDABTR-007-02

Thall PF, Millikan RE, Muller P, Lee S-J: Dose-finding with two agents in phase I oncology trials. UTMDABTR-008-02

Estey EH, Thall PF: New designs for phase II clinical trials. UTMDABTR-009-02

Morris JS, Baggerly KA, Coombes KR: Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE. UTMDABTR-010-02

Do KA, Broom B, Wen S: GeneClust. UTMDABTR-011-02

Do K, McLachlan GJ, Bean R, Wen S: Some recent methods in clustering microarray gene expression data and applications. UTMDABTR-012-02

Huang X, Wolfe RA, Hu C: A test for independent censoring using correlated survival data. UTMDABTR-013-02

Bekele BN, Thall PF: Dose-finding based on multiple ordinal toxicities in phase I oncology trials. UTMDABTR-014-02

Baggerly KA, Deng L, Morris JS, Aldaz CM: Differential expression in SAGE: accounting for normal between-library variation. UTMDABTR-015-02

Thall PF, Lee SJ: Practical model-based dose-finding in phase I clinical trials: methods based on toxicity. UTMDABTR-016-02


Do K-A, Kuhnert P, Lee S-J, Aitken JF, Green A, Martin NG: Genetic analysis of melanoma onset by using estimating equations and Bayesian random effects modeling. UTMDABTR-001-0

Do K-A, Broom BM, Wang X: Importance bootstrap resampling for proportional hazards regression. UTMDABTR-002-01

Kuhnert PM, Do K-A: Fitting genetic models to twin data with binary and ordered categorical responses: a comparison of structural equation modeling and Bayesian hierarchical modeling. UTMDABTR-003-01

Baggerly KA, Coombes KR, Hess KR, Stivers DN, Abruzzo LV, Zhang W: Identifying differentially expressed genes in cDNA microarray experiments. UTMDABTR-004-01

Thall PF, Sung H-G, Estey EH: Selecting therapeutic strategies based on efficacy and death in multi-course clinical trials. UTMDABTR-005-01

Thall PF, Inoue L, Berry DA: Seamlessly expanding a randomized phase II trial to phase III. UTMDABTR-006-01

Thall PF, Sung H-G, Choudhury A: Dose-finding based on feasibility and toxicity in T-cell infusion trials. UTMDABTR-007-01

Stallard N, Thall PF: Decision-theoretic designs for pre-phase II screening trials in oncology. UTMDABTR-008-01

Thall PF: Bayesian clinical trial design in a cancer center. UTMDABTR-009-01

Thall PF, Sung H-G, Estey EH: Multi-course treatment strategies for clinical trials of rapidly fatal disease. UTMDABTR-010-01

Thall PF, Estey EH: Graphical methods for evaluating covariate effects in the Cox model. UTMDABTR-011-01

Cheung YK, Thall PF: Monitoring the rates of composite events with censored data in phase II clinical trials. UTMDABTR-012-01

Rosner GL, Stadler W, Ratain MJ: The randomized discontinuation design: application to cytostatic antineoplastic agents. UTMDABTR-013-01

Thall PF, Inoue LYT, Martin TG: Adaptive decision-making in a lymphocyte infusion trial. UTMDABTR-014-01

Wu D, Rosner GL, Broemeling LD: Bayesian inference of age-dependent sensitivity, sojourn time and transition rate in screening. UTMDABTR-015-01

Broemeling LD, Wu D: Power functions for Bayesian tests with application to the design of clinical trials: the fixed-sample case. UTMDABTR-016-01

Coombes KR, Highsmith WE, Krogmann TA, Baggerly KA, Stivers DN, Abruzzo LV: Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays. UTMDABTR-017-01

Thall PF: Ethical issues in oncology biostatistics. UTMDABTR-018-01

Morris JS, Wang N, Lupton JR, Chapkin RS, Turner ND, Hong MY, Carroll RJ: A Bayesian analysis of colonic crypt structure and coordinated response to carcinogen exposure incorporating missing crypts. UTMDABTR-019-01

Morris JS, Vannucci M, Brown PJ, Carroll RJ: Wavelet-based nonparametric modeling of hierarchical functions in colon carcinogenesis. UTMDABTR-020-01