Articles
Sparse Canonical Correlation Analysis with Application to Genomic Data Integration
Elena Parkhomenko, David Tritchler, and Joseph Beyene
Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs
Benjamin A. Ogorek and Leonard A. Stefanski
Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis
Guillemette Marot and Claus-Dieter Mayer
Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study
Tuan S. Nguyen and Javier Rojo
A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins
Pushpike J. Thilakarathne, Geert Verbeke, Kristof Engelen, and Kathleen Marchal
Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates
Ling Deng and Dirk F. Moore
A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms
José A. Ferreira, Johannes Berkhof, Olga Souverein, and Koos Zwinderman
Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values
Sandra Taylor and Katherine Pollard
Normalization Method for Transcriptional Studies of Heterogeneous Samples – Simultaneous Array Normalization and Identification of Equivalent Expression
Li-Xuan Qin and Jaya M. Satagopan
A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers
Joseph Lucas, Carlos Carvalho, and Mike West
Modified FDR Controlling Procedure for Multi-Stage Analyses
Catherine Tuglus and Mark J. van der Laan
Detecting Outlier Samples in Microarray Data
Albert D. Shieh and Yeung Sam Hung
Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies
David Engler and Yi Li
Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis
Marta Łuksza, Bogusław Kluge, Jerzy Ostrowski, Jakub Karczmarski, and Anna Gambin
Score Statistics for Mapping Quantitative Trait Loci
Myron N. Chang, Rongling Wu, Samuel S. Wu, and George Casella
Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements
Xiao Ding, Scott Weiss, Benjamin Raby, Christoph Lange, and Nan M. Laird
A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations
Qin Li and Rongling Wu
Testing of Chromosomal Clumping of Gene Properties
Luciano Fernandez-Ricaud, Daniel Dalevi, Anders Blomberg, and Olle Nerman
Univariate Shrinkage in the Cox Model for High Dimensional Data
Robert J. Tibshirani
Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications
János Podani, Attila Engloner, and Agnes Major
Weighted Multiple Hypothesis Testing Procedures
Guolian Kang, Keying Ye, Nianjun Liu, David B. Allison, and Guimin Gao
Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness
Bryce Borchers, Marshall Brown, Brian McLellan, Airat Bekmetjev, and Nathan L. Tintle
Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates
Kwangmi Ahn, Derek Gordon, and Stephen J. Finch
A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families
Klaus Larsen, Janne Petersen, Inge Bernstein, and Mef Nilbert
Bayesian Unsupervised Learning with Multiple Data Types
Phaedra Agius, Yiming Ying, and Colin Campbell
Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data
Daniela M. Witten and Robert J. Tibshirani
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions
Pei Fen Kuan, Dana Huebert, Audrey Gasch, and Sunduz Keles
Adaptive Transmission Disequilibrium Test for Family Trio Design
Min Yuan, Xin Tian, Gang Zheng, and Yaning Yang
Model Selection Based on FDR-Thresholding Optimizing the Area under the ROC-Curve
Alexandra C. Graf and Peter Bauer
Estimation of Selection Intensity under Overdominance by Bayesian Methods
Erkan Ozge Buzbas, Paul Joyce, and Zaid Abdo
A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data
Jemila S. Hamid and Joseph Beyene
Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments
Guro Dørum, Lars Snipen, Margrete Solheim, and Solve Sæbø
Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping
Ola Hössjer, Linda Hartman, and Keith Humphreys
Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data
Elizabeth A. Siewert and Katerina J. Kechris
Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry
Joshua Sampson and Hongyu Zhao
A Statistical Model for Genetic Mapping of Viral Infection by Integrating Epidemiological Behavior
Yao Li, Arthur Berg, Myron N. Chang, Ping Du, Kwangmi Ahn, David Mauger, Duanping Liao, and Rongling Wu
Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis
Nathan J. Morris, Robert Elston, and Catherine M. Stein
Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas
Michelle R. Lacey and Melanie Ehrlich
M-quantile Regression Analysis of Temporal Gene Expression Data
Veronica Vinciotti and Keming Yu
MC-Normalization: A Novel Method for Dye-Normalization of Two-Channel Microarray Data
Mattias Landfors, Jessica Fahlén, and Patrik Rydén
Characterizing the D2 Statistic: Word Matches in Biological Sequences
Sylvain Forêt, Susan R. Wilson, and Conrad J. Burden
Transmission Disequilibrium Test Power and Sample Size in the Presence of Locus Heterogeneity
Chuanwen Chen, Guang Yang, Steven Buyske, Tara Matise, Stephen J. Finch, and Derek Gordon
A Regularized Regression Approach for Dissecting Genetic Conflicts that Increase Disease Risk in Pregnancy
Shaoyu Li, Qing Lu, Wenjiang Fu, Roberto Romero, and Yuehua Cui
Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study
Yasunori Sato, Nan Laird, Hideki Suganami, Chikuma Hamada, Naoto Niki, Isao Yoshimura, and Teruhiko Yoshida
A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments
Lily Wang, Xi Chen, Russell D. Wolfinger, Jeffrey L. Franklin, Robert J. Coffey, and Bing Zhang