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Berkeley Electronic Press

Statistical Applications in Genetics and Molecular Biology

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Web page: http://www.bepress.com/sagmb/

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Editor: Nicholas P. Jewell
Editor: Gary Churchill
Editor: Elizabeth Thompson
For technical questions regarding this series, please contact (Christopher F. Baum)
Series handle: repec:bep:sagmbi

2008, Volume 7, Issue 2

1 International Competition on Mass Spectrometry Proteomic Diagnosis
by Bart Mertens [Downloadable! (restricted)]
2 Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples
by Martijn van der Werff & Bart Mertens & Mirre de Noo & Marco Bladergroen & Hans Dalebout & Rob Tollenaar & Andre Deelder [Downloadable! (restricted)]
3 Organizing a Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis
by Bart Mertens [Downloadable! (restricted)]
4 Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls
by Jennifer Barrett & David Cairns [Downloadable! (restricted)]
5 Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach
by A. Geert Heidema & Nico Nagelkerke [Downloadable! (restricted)]
6 Principal Component Discriminant Analysis
by Tom Fearn [Downloadable! (restricted)]
7 Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest
by Somnath Datta [Downloadable! (restricted)]
8 A Classification Model for the Leiden Proteomics Competition
by Huub Hoefsloot & Suzanne Smit & Age Smilde [Downloadable! (restricted)]
9 Empirical Bayes Logistic Regression
by Foteini Strimenopoulou & Philip Brown [Downloadable! (restricted)]
10 Autocorrelated Logistic Ridge Regression for Prediction Based on Proteomics Spectra
by Jelle Goeman [Downloadable! (restricted)]
11 Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples
by Thang Pham & Mark van de Wiel & Connie Jimenez [Downloadable! (restricted)]

2008, Volume 7, Issue 1

1 Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data
by Chang Sik Kim [Downloadable! (restricted)]
2 Coalescent Time Distributions in Trees of Arbitrary Size
by Sam Efromovich & Laura Salter Kubatko [Downloadable! (restricted)]
3 Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis
by Sandra Waaijenborg & Philip Verselewel de Witt Hamer & Aeilko Zwinderman [Downloadable! (restricted)]
4 Nonparametric Functional Mapping of Quantitative Trait Loci Underlying Programmed Cell Death
by Yuehua Cui & Rongling Wu & George Casella & Jun Zhu [Downloadable! (restricted)]
5 Accommodating Uncertainty in a Tree Set for Function Estimation
by Brian Healy & Victor DeGruttola & Chengcheng Hu [Downloadable! (restricted)]
6 Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences
by Nicolas Vergne [Downloadable! (restricted)]
7 Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods
by Manuela Zucknick & Sylvia Richardson & Euan Stronach [Downloadable! (restricted)]

2008, Volume 6, Issue 1

35 Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences
by Bodil Svennblad & Tom Britton [Downloadable! (restricted)]

2007, Volume 6, Issue 1

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

2007, Volume 5, Issue 1

1 Low-Order Conditional Independence Graphs for Inferring Genetic Networks
by Anja Wille & Peter Bühlmann [Downloadable! (restricted)]
2 A Generalized Clustering Problem, with Application to DNA Microarrays
by Ilana Belitskaya-Levy [Downloadable! (restricted)]
3 A Bayes Regression Approach to Array-CGH Data
by Chi-Chung Wen & Yuh-Jenn Wu & Yung-Hsiang Huang & Wei-Chen Chen & Shu-Chen Liu & Shih Sheng Jiang & Jyh-Lyh Juang & Chung-Yen Lin & Wen-Tsen Fang & Chao Hsiung & I-Shou Chang [Downloadable! (restricted)]
4 Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
by Yifan Huang & Jason Hsu & Mario Peruggia & Abigail Scott [Downloadable! (restricted)]
5 Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
by Tom Nye & Carlo Berzuini & Walter Gilks & M. Madan Babu & Sarah Teichmann [Downloadable! (restricted)]
6 Dimension Reduction for Classification with Gene Expression Microarray Data
by Jian Dai & Linh Lieu & David Rocke [Downloadable! (restricted)]
7 A New Type of Stochastic Dependence Revealed in Gene Expression Data
by Lev Klebanov & Craig Jordan & Andrei Yakovlev [Downloadable! (restricted)]
8 A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
by Daniel Dalevi & Devdatt Dubhashi & Malte Hermansson [Downloadable! (restricted)]
9 Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
by Lev Klebanov & Andrei Yakovlev [Downloadable! (restricted)]
10 Quality Optimised Analysis of General Paired Microarray Experiments
by Erik Kristiansson & Anders Sjögren & Mats Rudemo & Olle Nerman [Downloadable! (restricted)]
11 Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
by Merrill Birkner & Alan Hubbard & Mark van der Laan & Christine Skibola & Christine Hegedus & Martyn Smith [Downloadable! (restricted)]
12 Cross-Validated Bagged Prediction of Survival
by Sandra Sinisi & Romain Neugebauer & Mark van der Laan [Downloadable! (restricted)]
13 Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
by Indranil Mukhopadhyay & Eleanor Feingold & Tao Wang & Robert Elston & Daniel Weeks [Downloadable! (restricted)]
14 Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
by Mark van der Laan & Alan Hubbard [Downloadable! (restricted)]
15 Combining Results of Microarray Experiments: A Rank Aggregation Approach
by Robert DeConde & Sarah Hawley & Seth Falcon & Nigel Clegg & Beatrice Knudsen & Ruth Etzioni [Downloadable! (restricted)]
16 Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
by Anne-Laure Boulesteix [Downloadable! (restricted)]
17 Model Selection for Mixtures of Mutagenetic Trees
by Junming Yin & Niko Beerenwinkel & Jörg Rahnenführer & Thomas Lengauer [Downloadable! (restricted)]
18 Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
by Ole Christensen [Downloadable! (restricted)]
19 A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
by Daniel Rubin & Sandrine Dudoit & Mark van der Laan [Downloadable! (restricted)]
20 Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
by Rashi Gupta & Petri Auvinen & Andrew Thomas & Elja Arjas [Downloadable! (restricted)]
21 Using Complexity for the Estimation of Bayesian Networks
by Peter Salzman & Anthony Almudevar [Downloadable! (restricted)]
22 Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
by Mickael Guedj & David Robelin & Mark Hoebeke & Marc Lamarine & Jérôme Wojcik & Gregory Nuel [Downloadable! (restricted)]
23 Examining Protein Structure and Similarities by Spectral Analysis Technique
by Krista Collins & Hong Gu & Chris Field [Downloadable! (restricted)]
24 Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
by Monnie McGee & Zhongxue Chen [Downloadable! (restricted)]
25 Approximate Sample Size Calculations with Microarray Data: An Illustration
by José Ferreira & Aeilko Zwinderman [Downloadable! (restricted)]
26 Numerical Solutions for Patterns Statistics on Markov Chains
by Gregory Nuel [Downloadable! (restricted)]
27 A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
by Anna Kedzierska & Dirk Husmeier [Downloadable! (restricted)]
28 A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
by Hongmei Jiang & Rebecca Doerge [Downloadable! (restricted)]
29 Validation in Genomics: CpG Island Methylation Revisited
by Mark Segal [Downloadable! (restricted)]
30 An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
by Shunpu Zhang [Downloadable! (restricted)]

2007, Volume 4, Issue 1

1 Estimating Motifs Under Order Restrictions
by Erik van Zwet & Katherina Kechris & Peter Bickel & Michael Eisen [Downloadable! (restricted)]
2 Reproducible Research: A Bioinformatics Case Study
by Robert Gentleman [Downloadable! (restricted)]
3 Generalized Rank Tests for Replicated Microarray Data
by Mei-Ling Lee & Robert Gray & Harry BjÃÂ¶rkbacka & Mason Freeman [Downloadable! (restricted)]
4 Stepwise Normalization of Two-Channel Spotted Microarrays
by Yuanyuan Xiao & Mark Segal & Yee Hwa Yang [Downloadable! (restricted)]
5 Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
by Malgorzata Leyk & Danh Nguyen & Sanju Attoor & Edward Dougherty & Nancy Turner & Laura Bancroft & Robert Chapkin & Joanne Lupton & Raymond Carroll [Downloadable! (restricted)]
6 Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
by Claus EkstrÃÂ¸m & SÃÂ¸ren Bak & Mats Rudemo [Downloadable! (restricted)]
7 Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
by Ingrid LÃÂ¶nnstedt & Rebecca Rimini & Peter Nilsson [Downloadable! (restricted)]
8 Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data
by Merrill Birkner & Sandra Sinisi & Mark van der Laan [Downloadable! (restricted)]
9 Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
by Jochen Jaeger & Dieter Weichenhan & Boris Ivandic & Rainer Spang [Downloadable! (restricted)]
10 Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
by Guri Feten & Trygve AlmÃÂ¸y & Are Aastveit [Downloadable! (restricted)]
11 Combined Association and Linkage Analysis for General Pedigrees and Genetic Models
by Ola HÃÂ¶ssjer [Downloadable! (restricted)]
12 Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data
by Wei Pan [Downloadable! (restricted)]
13 The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
by Lee Newberg & Lee Ann McCue & Charles Lawrence [Downloadable! (restricted)]
14 A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
by Stuart Baker [Downloadable! (restricted)]
15 Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
by Mike Schmidt & Elizabeth Hauser & Eden Martin & Silke Schmidt [Downloadable! (restricted)]
16 Error Distribution for Gene Expression Data
by Elizabeth Purdom & Susan Holmes [Downloadable! (restricted)]
17 A General Framework for Weighted Gene Co-Expression Network Analysis
by Bin Zhang & Steve Horvath [Downloadable! (restricted)]
18 Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
by Asger Hobolth & Jens Jensen [Downloadable! (restricted)]
19 Comparing Bacterial DNA Microarray Fingerprints
by Alan Willse & Darrell Chandler & Amanda White & Miroslava Protic & Don Daly & Sharon Wunschel [Downloadable! (restricted)]
20 Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
by Sooyeol Lim & Joseph Beyene & Celia Greenwood [Downloadable! (restricted)]
21 Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
by Thomas PlÃÂ¶tz & Gernot Fink [Downloadable! (restricted)]
22 Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
by Stephen Erickson & Chiara Sabatti [Downloadable! (restricted)]
23 Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
by Aurelie Labbe & Mary Thompson [Downloadable! (restricted)]
24 FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
by Gaelle Gusto & Sophie Schbath [Downloadable! (restricted)]
25 Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
by Yuanyuan Xiao & Mark Segal [Downloadable! (restricted)]
26 Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
by Arief Gusnanto & Alexander Ploner & Yudi Pawitan [Downloadable! (restricted)]
27 Test on the Structure of Biological Sequences via Chaos Game Representation
by Peggy Cénac [Downloadable! (restricted)]
28 Reverse Engineering Galactose Regulation in Yeast through Model Selection
by Vesteinn Thorsson & Michael Hörnquist & Andrew Siegel & Leroy Hood [Downloadable! (restricted)]
29 Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives
by Mark van der Laan & Merrill Birkner & Alan Hubbard [Downloadable! (restricted)]
30 Weighted Analysis of Paired Microarray Experiments
by Erik Kristiansson & Anders Sjögren & Mats Rudemo & Olle Nerman [Downloadable! (restricted)]
31 A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
by Steven Schrodi [Downloadable! (restricted)]
32 A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
by Juliane Schäfer & Korbinian Strimmer [Downloadable! (restricted)]
33 Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
by Wei Zhao & Wei Hou & Ramon Littell & Rongling Wu [Downloadable! (restricted)]
34 Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
by Xing Qiu & Lev Klebanov & Andrei Yakovlev [Downloadable! (restricted)]
35 Bayesian Statistical Studies of the Ramachandran Distribution
by Alexander Pertsemlidis & Jan Zelinka & John Fondon & R. Henderson & Zbyszek Otwinowski [Downloadable! (restricted)]
36 On Reference Designs For Microarray Experiments
by Juan Steibel & Guilherme Rosa [Downloadable! (restricted)]
37 Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors
by Fei Ji & Yaning Yang & Chad Haynes & Stephen Finch & Derek Gordon [Downloadable! (restricted)]

2007, Volume 3, Issue 1

1 Using Alpha Wisely: Improving Power to Detect Multiple QTL
by Katy Simonsen & Lauren McIntyre [Downloadable! (restricted)]
2 Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests
by Mark Segal & Jason Barbour & Robert Grant [Downloadable! (restricted)]
3 Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
by Gordon Smyth [Downloadable! (restricted)]
4 Asymptotic Optimality of Likelihood-Based Cross-Validation
by Mark van der Laan & Sandrine Dudoit & Sunduz Keles [Downloadable! (restricted)]
5 Using Importance Sampling to Improve Simulation in Linkage Analysis
by Lars ÃÂngquist & Ola HÃÂ¶ssjer [Downloadable! (restricted)]
6 Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances
by Olga Vitek & Jan Vitek & Bruce Craig & Chris Bailey-Kellogg [Downloadable! (restricted)]
7 Reader Reaction
by Andrea Foulkes & Victor De Gruttola [Downloadable! (restricted)]
8 Error-Rate and Decision-Theoretic Methods of Multiple Testing: Which Genes Have High Objective Probabilities of Differential Expression?
by David Bickel [Downloadable! (restricted)]
9 Response to Foulkes and De Gruttola
by Mark Segal & Jason Barbour & Robert Grant [Downloadable! (restricted)]
10 Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma
by Johanna Hardin & Michael Waddell & C. David Page & Fenghuang Zhan & Bart Barlogie & John Shaughnessy & John Crowley [Downloadable! (restricted)]
11 Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities
by Jorge GarcÃÂa de la Nava & Sacha van Hijum & Oswaldo Trelles [Downloadable! (restricted)]
12 Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection
by Minhui Paik & Yuhong Yang [Downloadable! (restricted)]
13 Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates
by Sandrine Dudoit & Mark van der Laan & Katherine Pollard [Downloadable! (restricted)]
14 Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate
by Mark van der Laan & Sandrine Dudoit & Katherine Pollard [Downloadable! (restricted)]
15 Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives
by Mark van der Laan & Sandrine Dudoit & Katherine Pollard [Downloadable! (restricted)]
16 Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
by JÃÂ¶rg RahnenfÃÂ¼hrer & Francisco Domingues & Jochen Maydt & Thomas Lengauer [Downloadable! (restricted)]
17 A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects
by Christoph Lange & Kristel van Steen & Toby Andrew & Helen Lyon & Dawn DeMeo & Benjamin Raby & Amy Murphy & Edwin Silverman & Alex MacGregor & Scott Weiss & Nan Laird [Downloadable! (restricted)]
18 Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics
by Sandra Sinisi & Mark van der Laan [Downloadable! (restricted)]
19 Classifying Gene Expression Profiles from Pairwise mRNA Comparisons
by Donald Geman & Christian d'Avignon & Daniel Naiman & Raimond Winslow [Downloadable! (restricted)]
20 Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns
by Yulan Liang & Arpad Kelemen [Downloadable! (restricted)]
21 BayesMendel: an R Environment for Mendelian Risk Prediction
by Sining Chen & Wenyi Wang & Karl Broman & Hormuzd Katki & Giovanni Parmigiani [Downloadable! (restricted)]
22 A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments
by Xiang Yu & Tzu-Ming Chu & Greg Gibson & Russell Wolfinger [Downloadable! (restricted)]
23 Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description
by Lee Newberg & Charles Lawrence [Downloadable! (restricted)]
24 On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices
by Florian Frommlet & Andreas Futschik [Downloadable! (restricted)]
25 Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors
by Daniel Handley & Nicoleta Serban & David Peters & Clark Glymour [Downloadable! (restricted)]
26 Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling
by Derek Gordon & Yaning Yang & Chad Haynes & Stephen Finch & Nancy Mendell & Abraham Brown & Vahram Haroutunian [Downloadable! (restricted)]
27 A Method for Evaluating the Impact of Individual Haplotypes on Disease Incidence in Molecular Epidemiology Studies
by E. Venkatraman & Nandita Mitra & Colin Begg [Downloadable! (restricted)]
28 Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment
by Virpi Ahola & Tero Aittokallio & Esa Uusipaikka & Mauno Vihinen [Downloadable! (restricted)]
29 MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data
by Leslie Cope & Xiaogang Zhong & Elizabeth Garrett & Giovanni Parmigiani [Downloadable! (restricted)]
30 Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data
by R. Mark Thallman & Kathryn Hanford & Stephen Kachman & L. Dale Van Vleck [Downloadable! (restricted)]
31 Maximum Likelihood for Genome Phylogeny on Gene Content
by Hongmei Zhang & Xun Gu [Downloadable! (restricted)]
32 Confidence Levels for the Comparison of Microarray Experiments
by Kerby Shedden [Downloadable! (restricted)]
33 PLS Dimension Reduction for Classification with Microarray Data
by Anne-Laure Boulesteix [Downloadable! (restricted)]
34 Statistical Analysis of Genomic Tag Data
by Thomas LaFramboise & D. Hayes & Torstein Tengs [Downloadable! (restricted)]
35 Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays
by Conrad Burden & Yvonne Pittelkow & Susan Wilson [Downloadable! (restricted)]
36 Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data
by Cheng Cheng & Stanley Pounds & James Boyett & Deqing Pei & Mei-Ling Kuo & Martine Roussel [Downloadable! (restricted)]
37 A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks
by Markus Ruschhaupt & Wolfgang Huber & Annemarie Poustka & Ulrich Mansmann [Downloadable! (restricted)]
38 Validation and Discovery in Markov Models of Genetics Data
by Victor De Gruttola & Andrea Foulkes [Downloadable! (restricted)]
39 Making Sense of High-Throughput Protein-Protein Interaction Data
by Denise Scholtens & Robert Gentleman [Downloadable! (restricted)]

2007, Volume 2, Issue 1

1 Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants
by Rafael Irizarry & Siew Loon Ooi & Zhijin Wu & Jef Boeke [Downloadable! (restricted)]
2 Sampling Correction in Pedigree Analysis
by Emil Ginsburg & Ida Malkin & Robert Elston [Downloadable! (restricted)]
3 Parameter estimation for the calibration and variance stabilization of microarray data
by Wolfgang Huber & Anja von Heydebreck & Holger Sueltmann & Annemarie Poustka & Martin Vingron [Downloadable! (restricted)]
4 Transformations for cDNA Microarray Data
by Xiangqin Cui & M. Kerr & Gary Churchill [Downloadable! (restricted)]
5 Supervised Detection of Regulatory Motifs in DNA Sequences
by Sunduz Keles & Mark van der Laan & Sandrine Dudoit & Biao Xing & Michael Eisen [Downloadable! (restricted)]
6 Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot
by Yvonne Pittelkow & Susan Wilson [Downloadable! (restricted)]
7 On the Power of Profiles for Transcription Factor Binding Site Detection
by Sven Rahmann & Tobias MÃÂ¼ller & Martin Vingron [Downloadable! (restricted)]
8 An Empirical Bayesian Method for Differential Expression Studies Using One-Channel Microarray Data
by Yan Lin & Paul Reynolds & Eleanor Feingold [Downloadable! (restricted)]

2007, Volume 1, Issue 1

1 Pre-validation and inference in microarrays
by Robert Tibshirani & Brad Efron [Downloadable! (restricted)]
2 An additive genetic gamma frailty model for two-locus linkage analysis using sibship age of onset data
by Xiaoyun Zhong & Hongzhe Li [Downloadable! (restricted)]

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