Articles
Estimating Motifs Under Order Restrictions
Erik W. van Zwet, Katherina J. Kechris, Peter J. Bickel, and Michael B. Eisen
Reproducible Research: A Bioinformatics Case Study
Robert Gentleman
Generalized Rank Tests for Replicated Microarray Data
Mei-Ling Ting Lee, Robert J. Gray, Harry Björkbacka, and Mason W. Freeman
Stepwise Normalization of Two-Channel Spotted Microarrays
Yuanyuan Xiao, Mark R. Segal, and Yee Hwa Yang
Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
Malgorzata Leyk, Danh V. Nguyen, Sanju N. Attoor, Edward R. Dougherty, Nancy D. Turner, Laura K. Bancroft, Robert S. Chapkin, Joanne R. Lupton, and Raymond J. Carroll
Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
Claus T. Ekstrøm, Søren Bak, and Mats Rudemo
Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
Ingrid Lönnstedt, Rebecca Rimini, and Peter Nilsson
Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data.
Merrill D. Birkner, Sandra E. Sinisi, and Mark J. van der Laan
Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
Jochen Jaeger, Dieter Weichenhan, Boris Ivandic, and Rainer Spang
Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
Guri Feten, Trygve Almøy, and Are H. Aastveit
The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
Lee A. Newberg, Lee Ann McCue, and Charles E. Lawrence
A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
Stuart G. Baker
Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
Mike Schmidt, Elizabeth R. Hauser, Eden R. Martin, and Silke Schmidt
Error Distribution for Gene Expression Data
Elizabeth Purdom and Susan P. Holmes
A General Framework for Weighted Gene Co-Expression Network Analysis
Bin Zhang and Steve Horvath
Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
Asger Hobolth and Jens Ledet Jensen
Comparing Bacterial DNA Microarray Fingerprints
Alan Willse, Darrell P. Chandler, Amanda White, Miroslava Protic, Don S. Daly, and Sharon Wunschel
Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
Sooyeol Lim, Joseph Beyene, and Celia M. T. Greenwood
Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
Thomas Plötz and Gernot A. Fink
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
Stephen Erickson and Chiara Sabatti
Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
Aurelie Labbe and Mary Thompson
FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
Gaelle Gusto and Sophie Schbath
Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
Yuanyuan Xiao and Mark R. Segal
Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
Arief Gusnanto, Alexander Ploner, and Yudi Pawitan
Reverse Engineering Galactose Regulation in Yeast through Model Selection
Vesteinn Thorsson, Michael Hörnquist, Andrew F. Siegel, and Leroy Hood
Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives.
Mark J. van der Laan, Merrill D. Birkner, and Alan E. Hubbard
Weighted Analysis of Paired Microarray Experiments
Erik Kristiansson, Anders Sjögren, Mats Rudemo, and Olle Nerman
A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
Steven J. Schrodi
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
Juliane Schäfer and Korbinian Strimmer
Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
Wei Zhao, Wei Hou, Ramon C. Littell, and Rongling Wu
Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
Xing Qiu, Lev Klebanov, and Andrei Yakovlev
Bayesian Statistical Studies of the Ramachandran Distribution
Alexander Pertsemlidis, Jan Zelinka, John W. Fondon III, R. Keith Henderson, and Zbyszek Otwinowski
On Reference Designs For Microarray Experiments
Juan P. Steibel and Guilherme J. M. Rosa
Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors
Fei Ji, Yaning Yang, Chad Haynes, Stephen J. Finch, and Derek Gordon