Articles
Using Alpha Wisely: Improving Power to Detect Multiple QTL
Katy L. Simonsen and Lauren M. McIntyre
Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests
Mark R. Segal, Jason D. Barbour, and Robert M. Grant
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
Gordon K. Smyth
Asymptotic Optimality of Likelihood-Based Cross-Validation
Mark J. van der Laan, Sandrine Dudoit, and Sunduz Keles
Using Importance Sampling to Improve Simulation in Linkage Analysis
Lars Ängquist and Ola Hössjer
Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances
Olga Vitek, Jan Vitek, Bruce Craig, and Chris Bailey-Kellogg
Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma
Johanna Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, and John J. Crowley
Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities
Jorge García de la Nava, Sacha van Hijum, and Oswaldo Trelles
Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection
Minhui Paik and Yuhong Yang
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates
Sandrine Dudoit, Mark J. van der Laan, and Katherine S. Pollard
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate
Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard
Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives
Mark J. van der Laan, Sandrine Dudoit, and Katherine S. Pollard
Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
Jörg Rahnenführer, Francisco S. Domingues, Jochen Maydt, and Thomas Lengauer
A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects
Christoph Lange, Kristel van Steen, Toby Andrew, Helen Lyon, Dawn L. DeMeo, Benjamin Raby, Amy Murphy, Edwin K. Silverman, Alex MacGregor , Scott T. Weiss, and Nan M. Laird
Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics
Sandra E. Sinisi and Mark J. van der Laan
Classifying Gene Expression Profiles from Pairwise mRNA Comparisons
Donald Geman, Christian d'Avignon, Daniel Q. Naiman, and Raimond L. Winslow
Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns
Yulan Liang and Arpad G. Kelemen
A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments
Xiang Yu, Tzu-Ming Chu, Greg Gibson, and Russell D. Wolfinger
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description
Lee A. Newberg and Charles E. Lawrence
On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices
Florian Frommlet and Andreas Futschik
Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling
Derek Gordon, Yaning Yang, Chad Haynes, Stephen J. Finch, Nancy R. Mendell, Abraham M. Brown, and Vahram Haroutunian
A Method for Evaluating the Impact of Individual Haplotypes on Disease Incidence in Molecular Epidemiology Studies
E. S. Venkatraman, Nandita Mitra, and Colin B. Begg
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment
Virpi Ahola, Tero Aittokallio, Esa Uusipaikka, and Mauno Vihinen
MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data
Leslie Cope, Xiaogang Zhong, Elizabeth Garrett, and Giovanni Parmigiani
Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data
R. Mark Thallman, Kathryn J. Hanford, Stephen D. Kachman, and L. Dale Van Vleck
Maximum Likelihood for Genome Phylogeny on Gene Content
Hongmei Zhang and Xun Gu
PLS Dimension Reduction for Classification with Microarray Data
Anne-Laure Boulesteix
Statistical Analysis of Genomic Tag Data
Thomas L. LaFramboise, D. Neil Hayes, and Torstein Tengs
Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays
Conrad J. Burden, Yvonne E. Pittelkow, and Susan R. Wilson
Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data
Cheng Cheng, Stanley B. Pounds, James M. Boyett, Deqing Pei, Mei-Ling Kuo, and Martine F. Roussel
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks
Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, and Ulrich Mansmann
Validation and Discovery in Markov Models of Genetics Data
Victor De Gruttola and Andrea S. Foulkes
Making Sense of High-Throughput Protein-Protein Interaction Data
Denise Scholtens and Robert Gentleman
Software Communications
BayesMendel: an R Environment for Mendelian Risk Prediction
Sining Chen, Wenyi Wang, Karl W. Broman, Hormuzd A. Katki, and Giovanni Parmigiani
Readers' Reactions
Reader Reaction
Andrea S. Foulkes and Victor De Gruttola
Response to Foulkes and De Gruttola
Mark R. Segal, Jason D. Barbour, and Robert M. Grant
Letters to the Editor
Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors
Daniel Handley, Nicoleta Serban, David G. Peters, and Clark Glymour