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Statistical Applications in Genetics and Molecular Biology

2002 - 2020

Current editor(s): Michael P. H. Stumpf

From De Gruyter
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Volume 4, issue 1, 2005

Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies pp. 1-12 Downloads
Jaeger Jochen, Weichenhan Dieter, Ivandic Boris and Spang Rainer
Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models pp. 1-28 Downloads
Plötz Thomas and Fink Gernot A.
FADO: A Statistical Method to Detect Favored or Avoided Distances between Occurrences of Motifs using the Hawkes' Model pp. 1-28 Downloads
Gusto Gaelle and Schbath Sophie
Generalized Rank Tests for Replicated Microarray Data pp. 1-28 Downloads
Lee Mei-Ling Ting, Gray Robert J, Björkbacka Harry and Freeman Mason W
Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits pp. 1-28 Downloads
Zhao Wei, Hou Wei, Littell Ramon C. and Wu Rongling
Reproducible Research: A Bioinformatics Case Study pp. 1-25 Downloads
Gentleman Robert
Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data pp. 1-23 Downloads
Pan Wei
A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes pp. 1-23 Downloads
Baker Stuart G.
Stepwise Normalization of Two-Channel Spotted Microarrays pp. 1-31 Downloads
Xiao Yuanyuan, Segal Mark R and Yang Yee Hwa
Combined Association and Linkage Analysis for General Pedigrees and Genetic Models pp. 1-42 Downloads
Hössjer Ola
Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction pp. 1-22 Downloads
Schmidt Mike, Hauser Elizabeth R, Martin Eden R. and Schmidt Silke
Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm pp. 1-22 Downloads
Hobolth Asger and Jensen Jens Ledet
Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis pp. 1-27 Downloads
Lim Sooyeol, Beyene Joseph and Greenwood Celia M. T.
Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes pp. 1-27 Downloads
Erickson Stephen and Sabatti Chiara
Computing Asymptotic Power and Sample Size for Case-Control Genetic Association Studies in the Presence of Phenotype and/or Genotype Misclassification Errors pp. 1-27 Downloads
Ji Fei, Yang Yaning, Haynes Chad, Finch Stephen J and Gordon Derek
Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation pp. 1-36 Downloads
Xiao Yuanyuan and Segal Mark R
Test on the Structure of Biological Sequences via Chaos Game Representation pp. 1-36 Downloads
Cénac Peggy
Weighted Analysis of Paired Microarray Experiments pp. 1-47 Downloads
Kristiansson Erik, Sjögren Anders, Rudemo Mats and Nerman Olle
A General Framework for Weighted Gene Co-Expression Network Analysis pp. 1-45 Downloads
Zhang Bin and Horvath Steve
A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles pp. 1-53 Downloads
Schrodi Steven J
Estimating Motifs Under Order Restrictions pp. 1-18 Downloads
W van Zwet Erik, Kechris Katherina J, Bickel Peter J and Eisen Michael B.
Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors pp. 1-18 Downloads
Feten Guri, Almøy Trygve and Aastveit Are H.
The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix pp. 1-18 Downloads
Newberg Lee A, McCue Lee Ann and Lawrence Charles E
Bayesian Statistical Studies of the Ramachandran Distribution pp. 1-18 Downloads
Pertsemlidis Alexander, Zelinka Jan, Fondon John W., Henderson R. Keith and Otwinowski Zbyszek
Error Distribution for Gene Expression Data pp. 1-35 Downloads
Purdom Elizabeth and Holmes Susan P
Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives pp. 1-32 Downloads
J. van der Laan Mark, Birkner Merrill D. and Hubbard Alan E.
A Shrinkage Approach to Large-Scale Covariance Matrix Estimation and Implications for Functional Genomics pp. 1-32 Downloads
Schäfer Juliane and Strimmer Korbinian
Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes pp. 1-32 Downloads
Qiu Xing, Klebanov Lev and Yakovlev Andrei
On Reference Designs For Microarray Experiments pp. 1-21 Downloads
Steibel Juan P. and Rosa Guilherme J. M.
Comparing Bacterial DNA Microarray Fingerprints pp. 1-38 Downloads
Willse Alan, Chandler Darrell P, White Amanda, Protic Miroslava, Daly Don S and Wunschel Sharon
Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays pp. 1-16 Downloads
Ekstrøm Claus T, Bak Søren and Rudemo Mats
Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data pp. 1-24 Downloads
Labbe Aurelie and Thompson Mary
Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model pp. 1-24 Downloads
Gusnanto Arief, Ploner Alexander and Pawitan Yudi
Reverse Engineering Galactose Regulation in Yeast through Model Selection pp. 1-24 Downloads
Thorsson Vesteinn, Hörnquist Michael, Siegel Andrew F and Hood Leroy
Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels pp. 1-34 Downloads
Lönnstedt Ingrid, Rimini Rebecca and Nilsson Peter
Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis pp. 1-20 Downloads
Leyk Malgorzata, Nguyen Danh V, Attoor Sanju N, Dougherty Edward R, Turner Nancy D, Bancroft Laura K, Chapkin Robert S, Lupton Joanne R and Carroll Raymond J
Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data pp. 1-30 Downloads
Birkner Merrill D., Sinisi Sandra E. and J. van der Laan Mark

Volume 3, issue 1, 2004

Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives pp. 1-27 Downloads
J. van der Laan Mark, Dudoit Sandrine and Pollard Katherine S.
Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities pp. 1-18 Downloads
García de la Nava Jorge, Sacha van Hijum and Trelles Oswaldo
Maximum Likelihood for Genome Phylogeny on Gene Content pp. 1-18 Downloads
Zhang Hongmei and Gu Xun
Confidence Levels for the Comparison of Microarray Experiments pp. 1-18 Downloads
Shedden Kerby
Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate pp. 1-35 Downloads
J. van der Laan Mark, Dudoit Sandrine and Pollard Katherine S.
Increasing Power for Tests of Genetic Association in the Presence of Phenotype and/or Genotype Error by Use of Double-Sampling pp. 1-35 Downloads
Gordon Derek, Yang Yaning, Haynes Chad, Finch Stephen J, Mendell Nancy R, Brown Abraham M and Haroutunian Vahram
Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances pp. 1-35 Downloads
Vitek Olga, Vitek Jan, Craig Bruce and Bailey-Kellogg Chris
Using Alpha Wisely: Improving Power to Detect Multiple QTL pp. 1-26 Downloads
Simonsen Katy L and McIntyre Lauren M
A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks pp. 1-26 Downloads
Ruschhaupt Markus, Huber Wolfgang, Poustka Annemarie and Mansmann Ulrich
MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data pp. 1-15 Downloads
Cope Leslie, Zhong Xiaogang, Garrett Elizabeth and Parmigiani Giovanni
Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics pp. 1-40 Downloads
Sinisi Sandra E and J. van der Laan Mark
PLS Dimension Reduction for Classification with Microarray Data pp. 1-32 Downloads
Boulesteix Anne-Laure
Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data pp. 1-32 Downloads
Cheng Cheng, Pounds Stanley B., Boyett James M., Pei Deqing, Kuo Mei-Ling and Roussel Martine F.
Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection pp. 1-21 Downloads
Paik Minhui and Yang Yuhong
BayesMendel: an R Environment for Mendelian Risk Prediction pp. 1-21 Downloads
Chen Sining, Wang Wenyi, Broman Karl W, Katki Hormuzd A and Parmigiani Giovanni
Making Sense of High-Throughput Protein-Protein Interaction Data pp. 1-33 Downloads
Scholtens Denise and Gentleman Robert
A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects pp. 1-29 Downloads
Lange Christoph, Kristel van Steen, Andrew Toby, Lyon Helen, DeMeo Dawn L, Raby Benjamin, Murphy Amy, Silverman Edwin K, MacGregor Alex, Weiss Scott T and Laird Nan M
Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays pp. 1-29 Downloads
Burden Conrad J, Pittelkow Yvonne E and Wilson Susan R
Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma pp. 1-24 Downloads
Hardin Johanna, Waddell Michael, Page C. David, Zhan Fenghuang, Barlogie Bart, Shaughnessy John and Crowley John J
Statistical Analysis of Genomic Tag Data pp. 1-24 Downloads
LaFramboise Thomas L, Hayes D. Neil and Tengs Torstein
Using Importance Sampling to Improve Simulation in Linkage Analysis pp. 1-24 Downloads
Ängquist Lars and Hössjer Ola
Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment pp. 1-30 Downloads
Ahola Virpi, Aittokallio Tero, Uusipaikka Esa and Vihinen Mauno
Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests pp. 1-20 Downloads
Segal Mark R, Barbour Jason D and Grant Robert M
Validation and Discovery in Markov Models of Genetics Data pp. 1-17 Downloads
Victor De Gruttola and Foulkes Andrea S
Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments pp. 1-28 Downloads
Smyth Gordon K
Reader Reaction pp. 1-6 Downloads
Foulkes Andrea S and Victor De Gruttola
Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors pp. 1-4 Downloads
Handley Daniel, Serban Nicoleta, Peters David G and Glymour Clark
Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates pp. 1-71 Downloads
Dudoit Sandrine, J. van der Laan Mark and Pollard Katherine S.
Response to Foulkes and De Gruttola pp. 1-9 Downloads
Segal Mark R, Barbour Jason D and Grant Robert M
Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns pp. 1-25 Downloads
Liang Yulan and Kelemen Arpad G
Asymptotic Optimality of Likelihood-Based Cross-Validation pp. 1-25 Downloads
J. van der Laan Mark, Dudoit Sandrine and Keles Sunduz
Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data pp. 1-23 Downloads
Thallman R. Mark, Hanford Kathryn J, Kachman Stephen D and Dale Van Vleck L.
Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data pp. 1-31 Downloads
Rahnenführer Jörg, Domingues Francisco S, Maydt Jochen and Lengauer Thomas
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description pp. 1-14 Downloads
Newberg Lee A and Lawrence Charles E
On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices pp. 1-14 Downloads
Frommlet Florian and Futschik Andreas
Classifying Gene Expression Profiles from Pairwise mRNA Comparisons pp. 1-22 Downloads
Geman Donald, d'Avignon Christian, Naiman Daniel Q. and Winslow Raimond L.
A Mixed Model Approach to Identify Yeast Transcriptional Regulatory Motifs via Microarray Experiments pp. 1-22 Downloads
Yu Xiang, Chu Tzu-Ming, Gibson Greg and Wolfinger Russell D
A Method for Evaluating the Impact of Individual Haplotypes on Disease Incidence in Molecular Epidemiology Studies pp. 1-22 Downloads
Venkatraman E. S, Mitra Nandita and Begg Colin B
Error-Rate and Decision-Theoretic Methods of Multiple Testing: Which Genes Have High Objective Probabilities of Differential Expression? pp. 1-22 Downloads
Bickel David R.
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