Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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. 12

Jaeger Jochen, Weichenhan Dieter, Ivandic Boris and Spang Rainer

Pixel-level Signal Modelling with Spatial Correlation for Two-Colour Microarrays pp. 16

Ekstrøm Claus T, Bak Søren and Rudemo Mats

Estimating Motifs Under Order Restrictions pp. 18

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. 18

Feten Guri, Almøy Trygve and Aastveit Are H.

The Relative Inefficiency of Sequence Weights Approaches in Determining a Nucleotide Position Weight Matrix pp. 18

Newberg Lee A, McCue Lee Ann and Lawrence Charles E

Bayesian Statistical Studies of the Ramachandran Distribution pp. 18

Pertsemlidis Alexander, Zelinka Jan, Fondon John W., Henderson R. Keith and Otwinowski Zbyszek

Comparing Automatic and Manual Image Processing in FLARE Assay Analysis for Colon Carcinogenesis pp. 20

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

On Reference Designs For Microarray Experiments pp. 21

Steibel Juan P. and Rosa Guilherme J. M.

Extension of the SIMLA Package for Generating Pedigrees with Complex Inheritance Patterns: Environmental Covariates, Gene-Gene and Gene-Environment Interaction pp. 22

Schmidt Mike, Hauser Elizabeth R, Martin Eden R. and Schmidt Silke

Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm pp. 22

Hobolth Asger and Jensen Jens Ledet

Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data pp. 23

Pan Wei

A Simple Loglinear Model for Haplotype Effects in a Case-Control Study Involving Two Unphased Genotypes pp. 23

Baker Stuart G.

Hierarchical Inverse Gaussian Models and Multiple Testing: Application to Gene Expression Data pp. 24

Labbe Aurelie and Thompson Mary

Fold-Change Estimation of Differentially Expressed Genes using Mixture Mixed-Model pp. 24

Gusnanto Arief, Ploner Alexander and Pawitan Yudi

Reverse Engineering Galactose Regulation in Yeast through Model Selection pp. 24

Thorsson Vesteinn, Hörnquist Michael, Siegel Andrew F and Hood Leroy

Reproducible Research: A Bioinformatics Case Study pp. 25

Gentleman Robert

Continuous Covariates in Genetic Association Studies of Case-Parent Triads: Gene and Gene-Environment Interaction Effects, Population Stratification, and Power Analysis pp. 27

Lim Sooyeol, Beyene Joseph and Greenwood Celia M. T.

Empirical Bayes Estimation of a Sparse Vector of Gene Expression Changes pp. 27

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. 27

Ji Fei, Yang Yaning, Haynes Chad, Finch Stephen J and Gordon Derek

Robust Remote Homology Detection by Feature Based Profile Hidden Markov Models pp. 28

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. 28

Gusto Gaelle and Schbath Sophie

Generalized Rank Tests for Replicated Microarray Data pp. 28

Lee Mei-Ling Ting, Gray Robert J, Björkbacka Harry and Freeman Mason W

Structured Antedependence Models for Functional Mapping of Multiple Longitudinal Traits pp. 28

Zhao Wei, Hou Wei, Littell Ramon C. and Wu Rongling

Multiple Testing and Data Adaptive Regression: An Application to HIV-1 Sequence Data pp. 30

Birkner Merrill D., Sinisi Sandra E. and J. van der Laan Mark

Stepwise Normalization of Two-Channel Spotted Microarrays pp. 31

Xiao Yuanyuan, Segal Mark R and Yang Yee Hwa

Empirical Bayes and Resampling Based Multiple Testing Procedure Controlling Tail Probability of the Proportion of False Positives pp. 32

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. 32

Schäfer Juliane and Strimmer Korbinian

Correlation Between Gene Expression Levels and Limitations of the Empirical Bayes Methodology for Finding Differentially Expressed Genes pp. 32

Qiu Xing, Klebanov Lev and Yakovlev Andrei

Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels pp. 34

Lönnstedt Ingrid, Rimini Rebecca and Nilsson Peter

Error Distribution for Gene Expression Data pp. 35

Purdom Elizabeth and Holmes Susan P

Prediction of Genomewide Conserved Epitope Profiles of HIV-1: Classifier Choice and Peptide Representation pp. 36

Xiao Yuanyuan and Segal Mark R

Test on the Structure of Biological Sequences via Chaos Game Representation pp. 36

Cénac Peggy

Comparing Bacterial DNA Microarray Fingerprints pp. 38

Willse Alan, Chandler Darrell P, White Amanda, Protic Miroslava, Daly Don S and Wunschel Sharon

Combined Association and Linkage Analysis for General Pedigrees and Genetic Models pp. 42

Hössjer Ola

A General Framework for Weighted Gene Co-Expression Network Analysis pp. 45

Zhang Bin and Horvath Steve

Weighted Analysis of Paired Microarray Experiments pp. 47

Kristiansson Erik, Sjögren Anders, Rudemo Mats and Nerman Olle

A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles pp. 53

Schrodi Steven J

Volume 3, issue 1, 2004

Concerns About Unreliable Data from Spotted cDNA Microarrays Due to Cross-Hybridization and Sequence Errors pp. 4

Handley Daniel, Serban Nicoleta, Peters David G and Glymour Clark

Reader Reaction pp. 6

Foulkes Andrea S and Victor De Gruttola

Response to Foulkes and De Gruttola pp. 9

Segal Mark R, Barbour Jason D and Grant Robert M

Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description pp. 14

Newberg Lee A and Lawrence Charles E

On the Dependence Structure of Sequence Alignment Scores Calculated with Multiple Scoring Matrices pp. 14

Frommlet Florian and Futschik Andreas

MergeMaid: R Tools for Merging and Cross-Study Validation of Gene Expression Data pp. 15

Cope Leslie, Zhong Xiaogang, Garrett Elizabeth and Parmigiani Giovanni

Validation and Discovery in Markov Models of Genetics Data pp. 17

Victor De Gruttola and Foulkes Andrea S

Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities pp. 18

García de la Nava Jorge, Sacha van Hijum and Trelles Oswaldo

Maximum Likelihood for Genome Phylogeny on Gene Content pp. 18

Zhang Hongmei and Gu Xun

Confidence Levels for the Comparison of Microarray Experiments pp. 18

Shedden Kerby

Relating HIV-1 Sequence Variation to Replication Capacity via Trees and Forests pp. 20

Segal Mark R, Barbour Jason D and Grant Robert M

Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection pp. 21

Paik Minhui and Yang Yuhong

BayesMendel: an R Environment for Mendelian Risk Prediction pp. 21

Chen Sining, Wang Wenyi, Broman Karl W, Katki Hormuzd A and Parmigiani Giovanni

Classifying Gene Expression Profiles from Pairwise mRNA Comparisons pp. 22

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. 22

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. 22

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. 22

Bickel David R.

Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data pp. 23

Thallman R. Mark, Hanford Kathryn J, Kachman Stephen D and Dale Van Vleck L.

Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma pp. 24

Hardin Johanna, Waddell Michael, Page C. David, Zhan Fenghuang, Barlogie Bart, Shaughnessy John and Crowley John J

Statistical Analysis of Genomic Tag Data pp. 24

LaFramboise Thomas L, Hayes D. Neil and Tengs Torstein

Using Importance Sampling to Improve Simulation in Linkage Analysis pp. 24

Ängquist Lars and Hössjer Ola

Hierarchical Bayesian Neural Network for Gene Expression Temporal Patterns pp. 25

Liang Yulan and Kelemen Arpad G

Asymptotic Optimality of Likelihood-Based Cross-Validation pp. 25

J. van der Laan Mark, Dudoit Sandrine and Keles Sunduz

Using Alpha Wisely: Improving Power to Detect Multiple QTL pp. 26

Simonsen Katy L and McIntyre Lauren M

A Compendium to Ensure Computational Reproducibility in High-Dimensional Classification Tasks pp. 26

Ruschhaupt Markus, Huber Wolfgang, Poustka Annemarie and Mansmann Ulrich

Augmentation Procedures for Control of the Generalized Family-Wise Error Rate and Tail Probabilities for the Proportion of False Positives pp. 27

J. van der Laan Mark, Dudoit Sandrine and Pollard Katherine S.

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments pp. 28

Smyth Gordon K

A Family-Based Association Test for Repeatedly Measured Quantitative Traits Adjusting for Unknown Environmental and/or Polygenic Effects pp. 29

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. 29

Burden Conrad J, Pittelkow Yvonne E and Wilson Susan R

Statistical Methods for Identifying Conserved Residues in Multiple Sequence Alignment pp. 30

Ahola Virpi, Aittokallio Tero, Uusipaikka Esa and Vihinen Mauno

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data pp. 31

Rahnenführer Jörg, Domingues Francisco S, Maydt Jochen and Lengauer Thomas

PLS Dimension Reduction for Classification with Microarray Data pp. 32

Boulesteix Anne-Laure

Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data pp. 32

Cheng Cheng, Pounds Stanley B., Boyett James M., Pei Deqing, Kuo Mei-Ling and Roussel Martine F.

Making Sense of High-Throughput Protein-Protein Interaction Data pp. 33

Scholtens Denise and Gentleman Robert

Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate pp. 35

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. 35

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. 35

Vitek Olga, Vitek Jan, Craig Bruce and Bailey-Kellogg Chris

Deletion/Substitution/Addition Algorithm in Learning with Applications in Genomics pp. 40

Sinisi Sandra E and J. van der Laan Mark

Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates pp. 71

Dudoit Sandrine, J. van der Laan Mark and Pollard Katherine S.