Articles
Accounting for Dependence in Similarity Data from DNA Fingerprinting
Graham Hepworth, Ian R. Gordon, and Michael J. McCullough
Normalization of Dye Bias in Microarray Data Using the Mixture of Splines Model
Yongsung Joo, George Casella, James Booth, Keunbaik Lee, and Steven Enkemann
A Generalized Sidak-Holm Procedure and Control of Generalized Error Rates under Independence
Wenge Guo and Joseph Romano
Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates
Nathan L. Tintle, Derek Gordon, Francis J. McMahon, and Stephen J. Finch
Likelihood-Based Inference for Multi-Color Optical Mapping
Liping Tong, Laurens Mets, and Mary Sara McPeek
Sparse Logistic Regression with Lp Penalty for Biomarker Identification
Zhenqiu Liu, Feng Jiang, Guoliang Tian, Suna Wang, Fumiaki Sato, Stephen J. Meltzer, and Ming Tan
Super Learning: An Application to the Prediction of HIV-1 Drug Resistance
Sandra E. Sinisi, Eric C. Polley, Maya L. Petersen, Soo-Yon Rhee, and Mark J. van der Laan
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo
Oliver Bembom, Sunduz Keles, and Mark J. van der Laan
Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach
Rainer Opgen-Rhein and Korbinian Strimmer
A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference
Ruiyan Luo, Andrew L. Hipp, and Bret Larget
Sequential Quantitative Trait Locus Mapping in Experimental Crosses
Jaya M. Satagopan, Saunak Sen, and Gary A. Churchill
Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution
Ji-Hyung Shin, Brad McNeney, and Jinko Graham
Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject
Glenn Heller and Jing Qin
Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
Adriano V. Werhli and Dirk Husmeier
Cox Survival Analysis of Microarray Gene Expression Data Using Correlation Principal Component Regression
Qiang Zhao and Jianguo Sun
A Method for Meta-Analysis of Case-Control Genetic Association Studies Using Logistic Regression
Pantelis G. Bagos and Georgios K. Nikolopoulos
Approximating the Variance of the Conditional Probability of the State of a Hidden Markov Model
David O. Siegmund and Benjamin Yakir
Using Linear Mixed Models for Normalization of cDNA Microarrays
Philippe Haldermans, Ziv Shkedy, Suzy Van Sanden, Tomasz Burzykowski, and Marc Aerts
Experimental Design for Two-Color Microarrays Applied in a Pre-Existing Split-Plot Experiment
G. A. Milliken, K. A. Garrett, and S. E. Travers
The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies
Jason Morton, Lior Pachter, Anne Shiu, and Bernd Sturmfels
H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps
Afshin Fayyaz movaghar, Sabine Mercier, and Louis Ferré
Multiple Testing Issues in Discriminating Compound-Related Peaks and Chromatograms from High Frequency Noise, Spikes and Solvent-Based Noise in LC – MS Data Sets
Stephen O. Nyangoma, Antoine A. H. C. van Kampen, Theo H. Reijmers, Natalia I. Govorukhina, Ate G. J. van der Zee, Lucinda J. Billingham, Rainer Bischoff, and Ritsert C. Jansen
A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments
Claudia Angelini, Daniela De Canditiis, Margherita Mutarelli, and Marianna Pensky
Super Learner
Mark J. van der Laan, Eric C. Polley, and Alan E. Hubbard
Testing for Trends in Dose-Response Microarray Experiments: A Comparison of Several Testing Procedures, Multiplicity and Resampling-Based Inference
Dan Lin, Ziv Shkedy, Dani Yekutieli, Tomasz Burzykowski, Hinrich W.H. Göhlmann, An De Bondt, Tim Perera, Tamara Geerts, and Luc Bijnens
On the Operational Characteristics of the Benjamini and Hochberg False Discovery Rate Procedure
Gerwyn H. Green and Peter J. Diggle
A Comparison of Methods to Control Type I Errors in Microarray Studies
Jinsong Chen, Mark J. van der Laan, Martyn T. Smith, and Alan E. Hubbard
Selection of Biologically Relevant Genes with a Wrapper Stochastic Algorithm
Kim-Anh Lê Cao, Olivier Gonçalves, Philippe Besse, and Sébastien Gadat
T-BAPS: A Bayesian Statistical Tool for Comparison of Microbial Communities Using Terminal-restriction Fragment Length Polymorphism (T-RFLP) Data
Jing Tang, Jinglun Tao, Hidetoshi Urakawa, and Jukka Corander
Population Structure and Covariate Analysis Based on Pairwise Microsatellite Allele Matching Frequencies
Geof H. Givens and Isin Ozaksoy
Estimating the Arm-Wise False Discovery Rate in Array Comparative Genomic Hybridization Experiments
Daniel P. Gaile, Elizabeth D. Schifano, Jeffrey C. Miecznikowski, James J. Java, Jeffrey M. Conroy, and Norma J. Nowak
An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children
Xiaohong Li, Andrea S. Foulkes, Recai M. Yucel, and Stephen M. Rich
Estimation of Expression Levels in Spotted Microarrays with Saturated Pixels
Chris A. Glasbey, Thorsten Forster, and Peter Ghazal
Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences
Bodil Svennblad and Tom Britton
Fully Bayesian Mixture Model for Differential Gene Expression: Simulations and Model Checks
Alex Lewin, Natalia Bochkina, and Sylvia Richardson
Multiple Testing for SNP-SNP Interactions
Anne-Laure Boulesteix, Carolin Strobl, Stefan Weidinger, H.-Erich Wichmann, and Stefan Wagenpfeil