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September 2006, Volume 5, Issue 1
- 1-18 Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies
by Guedj Mickael & Robelin David & Hoebeke Mark & Lamarine Marc & Wojcik Jérôme & Nuel Gregory - 1-23 Examining Protein Structure and Similarities by Spectral Analysis Technique
by Collins Krista & Gu Hong & Field Chris - 1-27 Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data
by McGee Monnie & Chen Zhongxue
March 2006, Volume 5, Issue 1
- 1-11 Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
by Klebanov Lev & Yakovlev Andrei - 1-24 A New Type of Stochastic Dependence Revealed in Gene Expression Data
by Klebanov Lev & Jordan Craig & Yakovlev Andrei - 1-26 A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
by Dalevi Daniel & Dubhashi Devdatt & Hermansson Malte
February 2006, Volume 5, Issue 1
- 1-18 Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
by Huang Yifan & Hsu Jason C & Peruggia Mario & Scott Abigail A - 1-19 Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
by Nye Tom M. W. & Berzuini Carlo & Gilks Walter R & Babu M. Madan & Teichmann Sarah - 1-21 Dimension Reduction for Classification with Gene Expression Microarray Data
by Dai Jian J & Lieu Linh & Rocke David - 1-22 A Bayes Regression Approach to Array-CGH Data
by Wen Chi-Chung & Wu Yuh-Jenn & Huang Yung-Hsiang & Chen Wei-Chen & Liu Shu-Chen & Jiang Shih Sheng & Juang Jyh-Lyh & Lin Chung-Yen & Fang Wen-Tsen & Hsiung Chao Agnes & Chang I-Shou
October 2006, Volume 5, Issue 1
- 1-18 Approximate Sample Size Calculations with Microarray Data: An Illustration
by Ferreira José A. & Zwinderman Aeilko - 1-34 A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
by Kedzierska Anna & Husmeier Dirk - 1-45 Numerical Solutions for Patterns Statistics on Markov Chains
by Nuel Gregory
January 2006, Volume 4, Issue 1
- 1-27 Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors
by Ji Fei & Yang Yaning & Haynes Chad & Finch Stephen J & Gordon Derek
July 2005, Volume 4, Issue 1
- 1-35 Error Distribution for Gene Expression Data
by Purdom Elizabeth & Holmes Susan P
April 2005, Volume 4, Issue 1
- 1-12 Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies
by Jaeger Jochen & Weichenhan Dieter & Ivandic Boris & Spang Rainer - 1-16 Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays
by Ekstrøm Claus T & Bak Søren & Rudemo Mats - 1-30 Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data
by Birkner Merrill D. & Sinisi Sandra E. & van der Laan Mark J. - 1-34 Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels
by Lönnstedt Ingrid & Rimini Rebecca & Nilsson Peter
June 2005, Volume 4, Issue 1
- 1-18 The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix
by Newberg Lee A & McCue Lee Ann & Lawrence Charles E - 1-22 Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction
by Schmidt Mike & Hauser Elizabeth R & Martin Eden R. & Schmidt Silke - 1-23 A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes
by Baker Stuart G.
February 2005, Volume 4, Issue 1
- 1-31 Stepwise Normalization of Two-Channel Spotted Microarrays
by Xiao Yuanyuan & Segal Mark R & Yang Yee Hwa
May 2005, Volume 4, Issue 1
- 1-18 Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors
by Feten Guri & Almøy Trygve & Aastveit Are H. - 1-23 Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data
by Pan Wei - 1-42 Combined Association and Linkage Analysis for General Pedigrees and Genetic Models
by Hössjer Ola
October 2005, Volume 4, Issue 1
- 1-32 Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives
by van der Laan Mark J. & Birkner Merrill D. & Hubbard Alan E. - 1-47 Weighted Analysis of Paired Microarray Experiments
by Kristiansson Erik & Sjögren Anders & Rudemo Mats & Nerman Olle
November 2005, Volume 4, Issue 1
- 1-18 Bayesian Statistical Studies of the Ramachandran Distribution
by Pertsemlidis Alexander & Zelinka Jan & Fondon John W. & Henderson R. Keith & Otwinowski Zbyszek - 1-28 Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits
by Zhao Wei & Hou Wei & Littell Ramon C. & Wu Rongling - 1-32 Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes
by Qiu Xing & Klebanov Lev & Yakovlev Andrei - 1-32 A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics
by Schäfer Juliane & Strimmer Korbinian - 1-53 A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles
by Schrodi Steven J
January 2005, Volume 4, Issue 1
- 1-18 Estimating Motifs Under Order Restrictions
by van Zwet Erik W & Kechris Katherina J & Bickel Peter J & Eisen Michael B. - 1-25 Reproducible Research: A Bioinformatics Case Study
by Gentleman Robert - 1-28 Generalized Rank Tests for Replicated Microarray Data
by Lee Mei-Ling Ting & Gray Robert J & Björkbacka Harry & Freeman Mason W
March 2005, Volume 4, Issue 1
- 1-20 Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis
by Leyk Malgorzata & Nguyen Danh V & Attoor Sanju N & Dougherty Edward R & Turner Nancy D & Bancroft Laura K & Chapkin Robert S & Lupton Joanne R & Carroll Raymond J
September 2005, Volume 4, Issue 1
- 1-24 Reverse Engineering Galactose Regulation in Yeast through Model Selection
by Thorsson Vesteinn & Hörnquist Michael & Siegel Andrew F & Hood Leroy - 1-24 Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model
by Gusnanto Arief & Ploner Alexander & Pawitan Yudi - 1-24 Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data
by Labbe Aurelie & Thompson Mary - 1-27 Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes
by Erickson Stephen & Sabatti Chiara - 1-28 FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model
by Gusto Gaelle & Schbath Sophie - 1-28 Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models
by Plötz Thomas & Fink Gernot A. - 1-36 Test on the Structure of Biological Sequences via Chaos Game Representation
by Cénac Peggy - 1-36 Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation
by Xiao Yuanyuan & Segal Mark R
December 2005, Volume 4, Issue 1
- 1-21 On Reference Designs For Microarray Experiments
by Steibel Juan P. & Rosa Guilherme J. M.
August 2005, Volume 4, Issue 1
- 1-22 Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
by Hobolth Asger & Jensen Jens Ledet - 1-27 Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis
by Lim Sooyeol & Beyene Joseph & Greenwood Celia M. T. - 1-38 Comparing Bacterial DNA Microarray Fingerprints
by Willse Alan & Chandler Darrell P & White Amanda & Protic Miroslava & Daly Don S & Wunschel Sharon - 1-45 A General Framework for Weighted Gene Co-Expression Network Analysis
by Zhang Bin & Horvath Steve
January 2005, Volume 3, Issue 1
- 1-33 Making Sense of High-Throughput Protein-Protein Interaction Data
by Scholtens Denise & Gentleman Robert
May 2004, Volume 3, Issue 1
- 1-6 Reader Reaction
by Foulkes Andrea S & De Gruttola Victor - 1-9 Response to Foulkes and De Gruttola
by Segal Mark R & Barbour Jason D & Grant Robert M - 1-22 Error-Rate and Decision-Theoretic Methods of Multiple Testing: Which Genes Have High Objective Probabilities of Differential Expression?
by Bickel David R. - 1-24 Using Importance Sampling to Improve Simulation in Linkage Analysis
by Ängquist Lars & Hössjer Ola - 1-35 Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances
by Vitek Olga & Vitek Jan & Craig Bruce & Bailey-Kellogg Chris
August 2004, Volume 3, Issue 1
- 1-22 Classifying Gene Expression Profiles from Pairwise mRNA Comparisons
by Geman Donald & d'Avignon Christian & Naiman Daniel Q. & Winslow Raimond L. - 1-29 A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects
by Lange Christoph & van Steen Kristel & Andrew Toby & Lyon Helen & DeMeo Dawn L & Raby Benjamin & Murphy Amy & Silverman Edwin K & MacGregor Alex & Weiss Scott T & Laird Nan M - 1-40 Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics
by Sinisi Sandra E & van der Laan Mark J.
September 2004, Volume 3, Issue 1
- 1-14 Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description
by Newberg Lee A & Lawrence Charles E - 1-21 BayesMendel: an R Environment for Mendelian Risk Prediction
by Chen Sining & Wang Wenyi & Broman Karl W & Katki Hormuzd A & Parmigiani Giovanni - 1-22 A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments
by Yu Xiang & Chu Tzu-Ming & Gibson Greg & Wolfinger Russell D - 1-25 Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns
by Liang Yulan & Kelemen Arpad G
June 2004, Volume 3, Issue 1
- 1-18 Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities
by García de la Nava Jorge & van Hijum Sacha & Trelles Oswaldo - 1-21 Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection
by Paik Minhui & Yang Yuhong - 1-24 Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma
by Hardin Johanna & Waddell Michael & Page C. David & Zhan Fenghuang & Barlogie Bart & Shaughnessy John & Crowley John J - 1-27 Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives
by van der Laan Mark J. & Dudoit Sandrine & Pollard Katherine S. - 1-31 Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
by Rahnenführer Jörg & Domingues Francisco S & Maydt Jochen & Lengauer Thomas - 1-35 Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate
by van der Laan Mark J. & Dudoit Sandrine & Pollard Katherine S. - 1-71 Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates
by Dudoit Sandrine & van der Laan Mark J. & Pollard Katherine S.
November 2004, Volume 3, Issue 1
- 1-18 Maximum Likelihood for Genome Phylogeny on Gene Content
by Zhang Hongmei & Gu Xun - 1-18 Confidence Levels for the Comparison of Microarray Experiments
by Shedden Kerby - 1-23 Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data
by Thallman R. Mark & Hanford Kathryn J & Kachman Stephen D & Van Vleck L. Dale - 1-32 PLS Dimension Reduction for Classification with Microarray Data
by Boulesteix Anne-Laure
March 2004, Volume 3, Issue 1
- 1-25 Asymptotic Optimality of Likelihood-Based Cross-Validation
by van der Laan Mark J. & Dudoit Sandrine & Keles Sunduz
February 2004, Volume 3, Issue 1
- 1-20 Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests
by Segal Mark R & Barbour Jason D & Grant Robert M - 1-26 Using Alpha Wisely: Improving Power to Detect Multiple QTL
by Simonsen Katy L & McIntyre Lauren M - 1-28 Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments
by Smyth Gordon K
December 2004, Volume 3, Issue 1
- 1-17 Validation and Discovery in Markov Models of Genetics Data
by De Gruttola Victor & Foulkes Andrea S - 1-24 Statistical Analysis of Genomic Tag Data
by LaFramboise Thomas L & Hayes D. Neil & Tengs Torstein - 1-26 A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks
by Ruschhaupt Markus & Huber Wolfgang & Poustka Annemarie & Mansmann Ulrich - 1-29 Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays
by Burden Conrad J & Pittelkow Yvonne E & Wilson Susan R - 1-32 Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data
by Cheng Cheng & Pounds Stanley B. & Boyett James M. & Pei Deqing & Kuo Mei-Ling & Roussel Martine F.
October 2004, Volume 3, Issue 1
- 1-4 Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors
by Handley Daniel & Serban Nicoleta & Peters David G & Glymour Clark - 1-14 On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices
by Frommlet Florian & Futschik Andreas - 1-15 MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data
by Cope Leslie & Zhong Xiaogang & Garrett Elizabeth & Parmigiani Giovanni - 1-22 A Method for Evaluating the Impact of Individual Haplotypes on Disease Incidence in Molecular Epidemiology Studies
by Venkatraman E. S & Mitra Nandita & Begg Colin B - 1-30 Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment
by Ahola Virpi & Aittokallio Tero & Uusipaikka Esa & Vihinen Mauno - 1-35 Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling
by Gordon Derek & Yang Yaning & Haynes Chad & Finch Stephen J & Mendell Nancy R & Brown Abraham M & Haroutunian Vahram
April 2003, Volume 2, Issue 1
- 1-24 Parameter estimation for the calibration and variance stabilization of microarray data
by Huber Wolfgang & von Heydebreck Anja & Sueltmann Holger & Poustka Annemarie & Vingron Martin
November 2003, Volume 2, Issue 1
- 1-18 An Empirical Bayesian Method for Differential Expression Studies Using One-Channel Microarray Data
by Lin Yan & Reynolds Paul & Feingold Eleanor - 1-27 On the Power of Profiles for Transcription Factor Binding Site Detection
by Rahmann Sven & Müller Tobias & Vingron Martin
March 2003, Volume 2, Issue 1
- 1-19 Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants
by Irizarry Rafael A & Ooi Siew Loon & Wu Zhijin & Boeke Jef D - 1-24 Sampling Correction in Pedigree Analysis
by Ginsburg Emil & Malkin Ida & Elston Robert C
June 2003, Volume 2, Issue 1
- 1-22 Transformations for cDNA Microarray Data
by Cui Xiangqin & Kerr M. Kathleen & Churchill Gary A.
August 2003, Volume 2, Issue 1
- 1-40 Supervised Detection of Regulatory Motifs in DNA Sequences
by Keles Sunduz & van der Laan Mark J. & Dudoit Sandrine & Xing Biao & Eisen Michael B.
September 2003, Volume 2, Issue 1
- 1-19 Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot
by Pittelkow Yvonne E & Wilson Susan R
August 2002, Volume 1, Issue 1
- 1-20 Pre-validation and inference in microarrays
by Tibshirani Robert J. & Efron Brad
November 2002, Volume 1, Issue 1
- 1-26 An additive genetic gamma frailty model for two-locus linkage analysis using sibship age of onset data
by Zhong Xiaoyun & Li Hongzhe