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De Gruyter

Statistical Applications in Genetics and Molecular Biology

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Series handle: RePEc:bpj:sagmbi

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Content

January 2010, Volume 9, Issue 1

1-12 An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes
by Lim Johan & Kim Jayeon & Kim Byung Soo
1-17 Detecting Genotyping Error Using Measures of Degree of Hardy-Weinberg Disequilibrium
by Attia John & Thakkinstian Ammarin & McElduff Patrick & Milne Elizabeth & Dawson Somer & Scott Rodney J & Klerk Nicholas de & Armstrong Bruce & Thompson John
1-21 A Bayesian Hierarchical Model for Quantitative Real-Time PCR Data
by Follestad Turid & Jørstad Tommy S & Erlandsen Sten E & Sandvik Arne K & Bones Atle M & Langaas Mette
1-22 Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis
by Wang Chaolong & Szpiech Zachary A & Degnan James H & Jakobsson Mattias & Pemberton Trevor J & Hardy John A & Singleton Andrew B & Rosenberg Noah A
1-22 Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies
by Lebrec Jeremie J & Stijnen Theo & van Houwelingen Hans C
1-23 An Internal Calibration Method for Protein-Array Studies
by Daly Don Simone & Anderson Kevin K & Seurynck-Servoss Shannon L & Gonzalez Rachel M & White Amanda M & Zangar Richard C
1-24 Epistatic Interactions
by VanderWeele Tyler J
1-25 Asymptotic Distribution of the "Orthogonal" Quantitative Transmission Disequilibrium Test in a Structured Population: Exact Formula
by Boitard Simon & Mangin Brigitte & Azaïs Jean-Marc
1-27 Optimisation of HMM Topologies Enhances DNA and Protein Sequence Modelling
by Friedrich Torben & Koetschan Christian & Müller Tobias
1-28 An Empirical Bayesian Method for Estimating Biological Networks from Temporal Microarray Data
by Rau Andrea & Jaffrézic Florence & Foulley Jean-Louis & Doerge Rebecca W
1-29 Testing for Gene-Gene Interaction with AMMI Models
by Barhdadi Amina & Dubé Marie-Pierre
1-31 Informative or Noninformative Calls for Gene Expression: A Latent Variable Approach
by Kasim Adetayo & Lin Dan & Van Sanden Suzy & Clevert Djork-Arné & Bijnens Luc & Göhlmann Hinrich & Amaratunga Dhammika & Hochreiter Sepp & Shkedy Ziv & Talloen Willem
1-34 The Apportionment of Total Genetic Variation by Categorical Analysis of Variance
by Khang Tsung Fei & Yap Von Bing
1-37 Parameter Estimation in Multiple-Hidden I.I.D. Models from Biological Multiple Alignment
by Arribas-Gil Ana

August 2010, Volume 9, Issue 1

1-17 On the Optimal Design of Genetic Variant Discovery Studies
by Ionita-Laza Iuliana & Laird Nan M
1-21 Mapping Quantitative Trait Loci in a Non-Equilibrium Population
by Wu Song & Yang Jie & Wu Rongling
1-24 Granger Causality Analysis of Human Cell-Cycle Gene Expression Profiles
by Nagarajan Radhakrishnan & Upreti Meenakshi
1-30 Lasso Logistic Regression, GSoft and the Cyclic Coordinate Descent Algorithm: Application to Gene Expression Data
by Garcia-Magariños Manuel & Antoniadis Anestis & Cao Ricardo & González-Manteiga Wenceslao
1-31 Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics
by Kechris Katerina J & Biehs Brian & Kornberg Thomas B

July 2010, Volume 9, Issue 1

1-14 Classification of Genomic Sequences via Wavelet Variance and a Self-Organizing Map with an Application to Mitochondrial DNA
by Jach Agnieszka E & Marín Juan M
1-23 Confidently Estimating the Number of DNA Replication Origins
by Bhaskar Anand & Keich Uri

February 2010, Volume 9, Issue 1

1-24 Trilocus Disequilibrium Analysis of Multiallelic Markers in Outcrossing Populations
by Berg Arthur & He Qiuling & Shen Ye & Chen Ying & Huang Minren & Wu Rongling
1-29 Weighted-LASSO for Structured Network Inference from Time Course Data
by Charbonnier Camille & Chiquet Julien & Ambroise Christophe

March 2010, Volume 9, Issue 1

1-27 Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases
by Shervais Stephen & Kramer Patricia L & Westaway Shawn K. & Cox Nancy J & Zwick Martin
1-32 Sparse Partial Least Squares Classification for High Dimensional Data
by Chung Dongjun & Keles Sunduz

November 2010, Volume 9, Issue 1

1-23 Predicting Patient Survival from Longitudinal Gene Expression
by Zhang Yuping & Tibshirani Robert J. & Davis Ronald W.
1-25 Spatial Clustering of Array CGH Features in Combination with Hierarchical Multiple Testing
by Kim Kyung In & Roquain Etienne & van de Wiel Mark A

April 2010, Volume 9, Issue 1

1-25 Space Oriented Rank-Based Data Integration
by Lin Shili
1-43 Sub-Modular Resolution Analysis by Network Mixture Models
by Marras Elisabetta & Travaglione Antonella & Capobianco Enrico

June 2009, Volume 8, Issue 1

1-13 A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families
by Larsen Klaus & Petersen Janne & Bernstein Inge & Nilbert Mef
1-22 Adaptive Transmission Disequilibrium Test for Family Trio Design
by Yuan Min & Tian Xin & Zheng Gang & Yang Yaning
1-22 Model Selection Based on FDR-Thresholding Optimizing the Area under the ROC-Curve
by Graf Alexandra C. & Bauer Peter
1-24 Estimation of Selection Intensity under Overdominance by Bayesian Methods
by Buzbas Erkan Ozge & Joyce Paul & Abdo Zaid
1-29 Bayesian Unsupervised Learning with Multiple Data Types
by Agius Phaedra & Ying Yiming & Campbell Colin
1-29 Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data
by Witten Daniela M & Tibshirani Robert J.
1-47 A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions
by Kuan Pei Fen & Huebert Dana & Gasch Audrey & Keles Sunduz

July 2009, Volume 8, Issue 1

1-26 Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments
by Dørum Guro & Snipen Lars & Solheim Margrete & Sæbø Solve
1-28 A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data
by Hamid Jemila S & Beyene Joseph

September 2009, Volume 8, Issue 1

1-22 M-quantile Regression Analysis of Temporal Gene Expression Data
by Vinciotti Veronica & Yu Keming
1-24 A Statistical Model for Genetic Mapping of Viral Infection by Integrating Epidemiological Behavior
by Li Yao & Berg Arthur & Chang Myron N & Du Ping & Ahn Kwangmi & Mauger David & Liao Duanping & Wu Rongling
1-29 Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry
by Sampson Joshua & Zhao Hongyu
1-29 Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas
by Lacey Michelle R & Ehrlich Melanie
1-34 Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis
by Morris Nathan J & Elston Robert & Stein Catherine M
1-36 Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data
by Siewert Elizabeth A & Kechris Katerina J
1-46 Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping
by Hössjer Ola & Hartman Linda & Humphreys Keith

May 2009, Volume 8, Issue 1

1-11 Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates
by Ahn Kwangmi & Gordon Derek & Finch Stephen J
1-22 Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness
by Borchers Bryce & Brown Marshall & McLellan Brian & Bekmetjev Airat & Tintle Nathan L

October 2009, Volume 8, Issue 1

1-18 Transmission Disequilibrium Test Power and Sample Size in the Presence of Locus Heterogeneity
by Chen Chuanwen & Yang Guang & Buyske Steven & Matise Tara & Finch Stephen J & Gordon Derek
1-23 Characterizing the D2 Statistic: Word Matches in Biological Sequences
by Forêt Sylvain & Wilson Susan R & Burden Conrad J
1-30 MC-Normalization: A Novel Method for Dye-Normalization of Two-Channel Microarray Data
by Landfors Mattias & Fahlén Jessica & Rydén Patrik
1-30 A Regularized Regression Approach for Dissecting Genetic Conflicts that Increase Disease Risk in Pregnancy
by Li Shaoyu & Lu Qing & Fu Wenjiang & Romero Roberto & Cui Yuehua

February 2009, Volume 8, Issue 1

1-17 Modified FDR Controlling Procedure for Multi-Stage Analyses
by Tuglus Catherine & van der Laan Mark J.
1-19 Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements
by Ding Xiao & Weiss Scott & Raby Benjamin & Lange Christoph & Laird Nan M
1-24 Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies
by Engler David & Li Yi
1-25 Normalization Method for Transcriptional Studies of Heterogeneous Samples - Simultaneous Array Normalization and Identification of Equivalent Expression
by Qin Li-Xuan & Satagopan Jaya M
1-26 Detecting Outlier Samples in Microarray Data
by Shieh Albert D & Hung Yeung Sam
1-27 A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations
by Li Qin & Wu Rongling
1-28 A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers
by Lucas Joseph & Carvalho Carlos & West Mike
1-29 Testing of Chromosomal Clumping of Gene Properties
by Fernandez-Ricaud Luciano & Dalevi Daniel & Blomberg Anders & Nerman Olle
1-36 Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis
by ?uksza Marta & Kluge Bogus?aw & Ostrowski Jerzy & Karczmarski Jakub & Gambin Anna
1-37 Score Statistics for Mapping Quantitative Trait Loci
by Chang Myron N & Wu Rongling & Wu Samuel S & Casella George
1-40 Inferring Dynamic Genetic Networks with Low Order Independencies
by Lèbre Sophie
1-45 Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values
by Taylor Sandra & Pollard Katherine

January 2009, Volume 8, Issue 1

1-22 Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates
by Deng Ling & Moore Dirk F.
1-27 A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins
by Thilakarathne Pushpike J & Verbeke Geert & Engelen Kristof & Marchal Kathleen
1-35 Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis
by Marot Guillemette & Mayer Claus-Dieter
1-36 Sparse Canonical Correlation Analysis with Application to Genomic Data Integration
by Parkhomenko Elena & Tritchler David & Beyene Joseph
1-40 Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study
by Nguyen Tuan S & Rojo Javier
1-49 Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs
by Ogorek Benjamin A & Stefanski Leonard A
1-58 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
by Ferreira José A. & Berkhof Johannes & Souverein Olga & Zwinderman Koos

April 2009, Volume 8, Issue 1

1-16 Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications
by Podani János & Engloner Attila & Major Agnes
1-20 Univariate Shrinkage in the Cox Model for High Dimensional Data
by Tibshirani Robert J.
1-21 Balanced Gradient Boosting from Imbalanced Data for Clinical Outcome Prediction
by Teramoto Reiji
1-24 Weighted Multiple Hypothesis Testing Procedures
by Kang Guolian & Ye Keying & Liu Nianjun & Allison David B. & Gao Guimin

November 2009, Volume 8, Issue 1

1-20 A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments
by Wang Lily & Chen Xi & Wolfinger Russell D & Franklin Jeffrey L & Coffey Robert J & Zhang Bing
1-23 Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study
by Sato Yasunori & Laird Nan & Suganami Hideki & Hamada Chikuma & Niki Naoto & Yoshimura Isao & Yoshida Teruhiko

December 2008, Volume 7, Issue 2

1-23 Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation
by Hand David J

September 2008, Volume 7, Issue 2

1-37 Assessing the Validity Domains of Graphical Gaussian Models in Order to Infer Relationships among Components of Complex Biological Systems
by Villers Fanny & Schaeffer Brigitte & Bertin Caroline & Huet Sylvie

February 2008, Volume 7, Issue 2

1-6 Principal Component Discriminant Analysis
by Fearn Tom
1-11 Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach
by Heidema A. Geert & Nagelkerke Nico
1-11 A Classification Model for the Leiden Proteomics Competition
by Hoefsloot Huub C. J. & Smit Suzanne & Smilde Age K.
1-11 Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples
by Pham Thang V & van de Wiel Mark A & Jimenez Connie R
1-12 Autocorrelated Logistic Ridge Regression for Prediction Based on Proteomics Spectra
by Goeman Jelle J
1-14 Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest
by Datta Somnath
1-16 Empirical Bayes Logistic Regression
by Strimenopoulou Foteini & Brown Philip J
1-20 Organizing a Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis
by Mertens Bart
1-22 Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls
by Barrett Jennifer H & Cairns David A

January 2008, Volume 7, Issue 2

1-4 International Competition on Mass Spectrometry Proteomic Diagnosis
by Mertens Bart
1-14 Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples
by van der Werff Martijn P. J. & Mertens Bart & de Noo Mirre E & Bladergroen Marco R & Dalebout Hans C & Tollenaar Rob A. E. M. & Deelder Andre M

July 2008, Volume 7, Issue 2

1-12 Clinical Mass Spectrometry Proteomic Diagnosis by Conformal Predictors
by Gammerman Alex & Nouretdinov Ilia & Burford Brian & Chervonenkis Alexey & Vovk Vladimir & Luo Zhiyuan

March 2008, Volume 7, Issue 2

1-22 A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry
by Valkenborg Dirk & Van Sanden Suzy & Lin Dan & Kasim Adetayo & Zhu Qi & Haldermans Philippe & Jansen Ivy & Shkedy Ziv & Burzykowski Tomasz

August 2008, Volume 7, Issue 1

1-18 Approximately Sufficient Statistics and Bayesian Computation
by Joyce Paul & Marjoram Paul
1-24 Data Distribution of Short Oligonucleotide Expression Arrays and Its Application to the Construction of a Generalized Intellectual Framework
by Konishi Tomokazu
1-25 Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data
by Fallah Shafagh & Tritchler David & Beyene Joseph
1-33 A Composite-Conditional-Likelihood Approach for Gene Mapping Based on Linkage Disequilibrium in Windows of Marker Loci
by Larribe Fabrice & Lessard Sabin

July 2008, Volume 7, Issue 1

1-17 Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power
by Matthews Abigail G & Haynes Chad & Liu Chang & Ott Jurg
1-20 A Comparison of Normalization Techniques for MicroRNA Microarray Data
by Rao Youlan & Lee Yoonkyung & Jarjoura David & Ruppert Amy S & Liu Chang-gong & Hsu Jason C & Hagan John P
1-21 Predicting Protein Concentrations with ELISA Microarray Assays, Monotonic Splines and Monte Carlo Simulation
by Daly Don Simone & Anderson Kevin K & White Amanda M & Gonzalez Rachel M & Varnum Susan M & Zangar Richard C

March 2008, Volume 7, Issue 1

1-11 TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background
by Parmigiani Giovanni & Chen Sining & Velculescu Victor E.
1-21 Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing
by Guo Wenge & Peddada Shyamal
1-22 Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling
by Jiang Wenyu & Varma Sudhir & Simon Richard
1-27 Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study
by Bickel David R.
1-28 Structure Learning in Nested Effects Models
by Tresch Achim & Markowetz Florian
1-28 Adapting Prediction Error Estimates for Biased Complexity Selection in High-Dimensional Bootstrap Samples
by Binder Harald & Schumacher Martin

May 2008, Volume 7, Issue 1

1-19 A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent
by Leibon Gregory & Rockmore Daniel N & Pollak Martin R

February 2008, Volume 7, Issue 1

1-19 Accommodating Uncertainty in a Tree Set for Function Estimation
by Healy Brian C & DeGruttola Victor G & Hu Chengcheng
1-32 Nonparametric Functional Mapping of Quantitative Trait Loci Underlying Programmed Cell Death
by Cui Yuehua & Wu Rongling & Casella George & Zhu Jun
1-34 Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods
by Zucknick Manuela & Richardson Sylvia & Stronach Euan A
1-45 Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences
by Vergne Nicolas

June 2008, Volume 7, Issue 1

1-16 Detecting Two-Locus Gene-Gene Effects Using Monotonisation of the Penetrance Matrix
by Henningsson Susanne & Nilsson Staffan I
1-20 Phenotyping Genetic Diseases Using an Extension of µ-Scores for Multivariate Data
by Morales José F. & Song Tingting & Auerbach Arleen D. & Wittkowski Knut M.
1-23 Modeling DNA Methylation in a Population of Cancer Cells
by Siegmund Kimberly D. & Marjoram Paul & Shibata Darryl
1-25 The Estimator of the Optimal Measure of Allelic Association: Mean, Variance and Probability Distribution When the Sample Size Tends to Infinity
by Mangin Brigitte & Garnier-Géré Pauline & Cierco-Ayrolles Christine

October 2008, Volume 7, Issue 1

1-19 Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information
by Arteaga-Salas Jose Manuel & Harrison Andrew P & Upton Graham J. G.
1-22 Pattern Classification of Phylogeny Signals
by Shi Xiaofei & Gu Hong & Field Chris
1-23 Statistical Methods in Integrative Analysis for Gene Regulatory Modules
by Zeng Lingmin & Wu Jing & Xie Jun
1-26 Importance Sampling for the Infinite Sites Model
by Hobolth Asger & Uyenoyama Marcy K & Wiuf Carsten
1-35 A Unification of Multivariate Methods for Meta-Analysis of Genetic Association Studies
by Bagos Pantelis G

January 2008, Volume 7, Issue 1

1-29 Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis
by Waaijenborg Sandra & Verselewel de Witt Hamer Philip C. & Zwinderman Aeilko H
1-30 Coalescent Time Distributions in Trees of Arbitrary Size
by Efromovich Sam & Salter Kubatko Laura
1-34 Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data
by Kim Chang Sik

November 2008, Volume 7, Issue 1

1-30 Supervised Distance Matrices
by Pollard Katherine S. & van der Laan Mark J.
1-32 A Sparse PLS for Variable Selection when Integrating Omics Data
by Lê Cao Kim-Anh & Rossouw Debra & Robert-Granié Christèle & Besse Philippe
1-41 Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments
by Husmeier Dirk & Mantzaris Alexander V.

April 2008, Volume 7, Issue 1

1-24 Re-Cracking the Nucleosome Positioning Code
by Segal Mark R
1-29 Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation
by Rossell David & Guerra Rudy & Scott Clayton

March 2007, Volume 6, Issue 1

1-36 Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach
by Lalam Nadia

June 2007, Volume 6, Issue 1

1-28 A Method for Meta-Analysis of Case-Control Genetic Association Studies Using Logistic Regression
by Bagos Pantelis G & Nikolopoulos Georgios K

October 2007, Volume 6, Issue 1

1-19 A Comparison of Methods to Control Type I Errors in Microarray Studies
by Chen Jinsong & van der Laan Mark J. & Smith Martyn T. & Hubbard Alan E.
1-23 On the Operational Characteristics of the Benjamini and Hochberg False Discovery Rate Procedure
by Green Gerwyn H & Diggle Peter J.
1-28 Testing for Trends in Dose-Response Microarray Experiments: A Comparison of Several Testing Procedures, Multiplicity and Resampling-Based Inference
by Lin Dan & Shkedy Ziv & Yekutieli Dani & Burzykowski Tomasz & Göhlmann Hinrich W.H. & De Bondt An & Perera Tim & Geerts Tamara & Bijnens Luc

July 2007, Volume 6, Issue 1

1-21 Approximating the Variance of the Conditional Probability of the State of a Hidden Markov Model
by Siegmund David O & Yakir Benjamin
1-23 Experimental Design for Two-Color Microarrays Applied in a Pre-Existing Split-Plot Experiment
by Milliken G. A. & Garrett K. A. & Travers S. E.
1-25 Using Linear Mixed Models for Normalization of cDNA Microarrays
by Haldermans Philippe & Shkedy Ziv & Van Sanden Suzy & Burzykowski Tomasz & Aerts Marc

January 2007, Volume 6, Issue 1

1-15 Accounting for Dependence in Similarity Data from DNA Fingerprinting
by Hepworth Graham & Gordon Ian R & McCullough Michael J
1-22 Normalization of Dye Bias in Microarray Data Using the Mixture of Splines Model
by Joo Yongsung & Casella George & Booth James & Lee Keunbaik & Enkemann Steven
1-35 A Generalized Sidak-Holm Procedure and Control of Generalized Error Rates under Independence
by Guo Wenge & Romano Joseph

August 2007, Volume 6, Issue 1

1-21 H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps
by Fayyaz movaghar Afshin & Mercier Sabine & Ferré Louis
1-25 The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies
by Morton Jason & Pachter Lior & Shiu Anne & Sturmfels Bernd

February 2007, Volume 6, Issue 1

1-20 Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach
by Opgen-Rhein Rainer & Strimmer Korbinian
1-22 Sparse Logistic Regression with Lp Penalty for Biomarker Identification
by Liu Zhenqiu & Jiang Feng & Tian Guoliang & Wang Suna & Sato Fumiaki & Meltzer Stephen J. & Tan Ming
1-26 Super Learning: An Application to the Prediction of HIV-1 Drug Resistance
by Sinisi Sandra E. & Polley Eric C & Petersen Maya L & Rhee Soo-Yon & van der Laan Mark J.
1-29 Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates
by Tintle Nathan L & Gordon Derek & McMahon Francis J & Finch Stephen J
1-32 Likelihood-Based Inference for Multi-Color Optical Mapping
by Tong Liping & Mets Laurens & McPeek Mary Sara
1-51 Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo
by Bembom Oliver & Keles Sunduz & van der Laan Mark J.

September 2007, Volume 6, Issue 1

1-23 Super Learner
by van der Laan Mark J. & Polley Eric C & Hubbard Alan E.
1-33 A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments
by Angelini Claudia & De Canditiis Daniela & Mutarelli Margherita & Pensky Marianna
1-49 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 Nyangoma Stephen O & van Kampen Antoine A. H. C. & Reijmers Theo H & Govorukhina Natalia I & van der Zee Ate G. J. & Billingham Lucinda J & Bischoff Rainer & Jansen Ritsert C.

November 2007, Volume 6, Issue 1

1-19 An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children
by Li Xiaohong & Foulkes Andrea S & Yucel Recai M. & Rich Stephen M.
1-21 T-BAPS: A Bayesian Statistical Tool for Comparison of Microbial Communities Using Terminal-restriction Fragment Length Polymorphism (T-RFLP) Data
by Tang Jing & Tao Jinglun & Urakawa Hidetoshi & Corander Jukka
1-23 Selection of Biologically Relevant Genes with a Wrapper Stochastic Algorithm
by Lê Cao Kim-Anh & Gonçalves Olivier & Besse Philippe & Gadat Sébastien
1-24 Estimating the Arm-Wise False Discovery Rate in Array Comparative Genomic Hybridization Experiments
by Gaile Daniel P & Schifano Elizabeth D & Miecznikowski Jeffrey C & Java James J & Conroy Jeffrey M & Nowak Norma J
1-30 Population Structure and Covariate Analysis Based on Pairwise Microsatellite Allele Matching Frequencies
by Givens Geof H & Ozaksoy Isin

December 2007, Volume 6, Issue 1

1-15 Estimation of Expression Levels in Spotted Microarrays with Saturated Pixels
by Glasbey Chris A & Forster Thorsten & Ghazal Peter
1-24 Multiple Testing for SNP-SNP Interactions
by Boulesteix Anne-Laure & Strobl Carolin & Weidinger Stefan & Wichmann H.-Erich & Wagenpfeil Stefan
1-26 Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences
by Svennblad Bodil & Britton Tom
1-28 Fully Bayesian Mixture Model for Differential Gene Expression: Simulations and Model Checks
by Lewin Alex & Bochkina Natalia & Richardson Sylvia

May 2007, Volume 6, Issue 1

1-16 Cox Survival Analysis of Microarray Gene Expression Data Using Correlation Principal Component Regression
by Zhao Qiang & Sun Jianguo
1-24 Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject
by Heller Glenn & Qin Jing
1-47 Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge
by Werhli Adriano V & Husmeier Dirk

April 2007, Volume 6, Issue 1

1-32 A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference
by Luo Ruiyan & Hipp Andrew L & Larget Bret
1-36 Sequential Quantitative Trait Locus Mapping in Experimental Crosses
by Satagopan Jaya M & Sen Saunak & Churchill Gary A.
1-43 Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution
by Shin Ji-Hyung & McNeney Brad & Graham Jinko

January 2007, Volume 5, Issue 1

1-25 An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data
by Zhang Shunpu

April 2006, Volume 5, Issue 1

1-24 Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
by Birkner Merrill D. & Hubbard Alan E. & van der Laan Mark J. & Skibola Christine F. & Hegedus Christine M. & Smith Martyn T.
1-31 Quality Optimised Analysis of General Paired Microarray Experiments
by Kristiansson Erik & Sjögren Anders & Rudemo Mats & Nerman Olle

June 2006, Volume 5, Issue 1

1-7 Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006)
by Boulesteix Anne-Laure
1-25 Model Selection for Mixtures of Mutagenetic Trees
by Yin Junming & Beerenwinkel Niko & Rahnenführer Jörg & Lengauer Thomas
1-25 Combining Results of Microarray Experiments: A Rank Aggregation Approach
by DeConde Robert P & Hawley Sarah & Falcon Seth & Clegg Nigel & Knudsen Beatrice & Etzioni Ruth

January 2006, Volume 5, Issue 1

1-26 A Generalized Clustering Problem, with Application to DNA Microarrays
by Belitskaya-Levy Ilana
1-34 Low-Order Conditional Independence Graphs for Inferring Genetic Networks
by Wille Anja & Bühlmann Peter

December 2006, Volume 5, Issue 1

1-19 Validation in Genomics: CpG Island Methylation Revisited
by Segal Mark R
1-35 A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments
by Jiang Hongmei & Doerge Rebecca W

July 2006, Volume 5, Issue 1

1-31 Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates
by Christensen Ole F.

May 2006, Volume 5, Issue 1

1-8 Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
by Mukhopadhyay Indranil & Feingold Eleanor & Wang Tao & Elston Robert C. & Weeks Daniel E.
1-26 Cross-Validated Bagged Prediction of Survival
by Sinisi Sandra E. & Neugebauer Romain & van der Laan Mark J.
1-30 Quantile-Function Based Null Distribution in Resampling Based Multiple Testing
by van der Laan Mark J. & Hubbard Alan E.

August 2006, Volume 5, Issue 1

1-20 A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting
by Rubin Daniel & Dudoit Sandrine & van der Laan Mark
1-20 Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities
by Gupta Rashi & Auvinen Petri & Thomas Andrew & Arjas Elja
1-23 Using Complexity for the Estimation of Bayesian Networks
by Salzman Peter & Almudevar Anthony

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