Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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

From De Gruyter
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Volume 6, issue 1, 2007

Accounting for Dependence in Similarity Data from DNA Fingerprinting pp. 15

Hepworth Graham, Gordon Ian R and McCullough Michael J

Estimation of Expression Levels in Spotted Microarrays with Saturated Pixels pp. 15

Glasbey Chris A, Forster Thorsten and Ghazal Peter

Cox Survival Analysis of Microarray Gene Expression Data Using Correlation Principal Component Regression pp. 16

Zhao Qiang and Sun Jianguo

A Comparison of Methods to Control Type I Errors in Microarray Studies pp. 19

Chen Jinsong, J. van der Laan Mark, Smith Martyn T. and Hubbard Alan E.

An Expectation Maximization Approach to Estimate Malaria Haplotype Frequencies in Multiply Infected Children pp. 19

Li Xiaohong, Foulkes Andrea S, Yucel Recai M. and Rich Stephen M.

Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach pp. 20

Rainer Opgen-Rhein and Strimmer Korbinian

Approximating the Variance of the Conditional Probability of the State of a Hidden Markov Model pp. 21

Siegmund David O and Yakir Benjamin

H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps pp. 21

Fayyaz movaghar Afshin, Mercier Sabine and Ferré Louis

T-BAPS: A Bayesian Statistical Tool for Comparison of Microbial Communities Using Terminal-restriction Fragment Length Polymorphism (T-RFLP) Data pp. 21

Tang Jing, Tao Jinglun, Urakawa Hidetoshi and Corander Jukka

Normalization of Dye Bias in Microarray Data Using the Mixture of Splines Model pp. 22

Joo Yongsung, Casella George, Booth James, Lee Keunbaik and Enkemann Steven

Sparse Logistic Regression with Lp Penalty for Biomarker Identification pp. 22

Liu Zhenqiu, Jiang Feng, Tian Guoliang, Wang Suna, Sato Fumiaki, Meltzer Stephen J. and Tan Ming

Experimental Design for Two-Color Microarrays Applied in a Pre-Existing Split-Plot Experiment pp. 23

Milliken G. A., Garrett K. A. and Travers S. E.

Super Learner pp. 23

J. van der Laan Mark, Polley Eric C and Hubbard Alan E.

On the Operational Characteristics of the Benjamini and Hochberg False Discovery Rate Procedure pp. 23

Green Gerwyn H and Diggle Peter J.

Selection of Biologically Relevant Genes with a Wrapper Stochastic Algorithm pp. 23

Lê Cao Kim-Anh, Gonçalves Olivier, Besse Philippe and Sébastien Gadat

Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject pp. 24

Heller Glenn and Qin Jing

Estimating the Arm-Wise False Discovery Rate in Array Comparative Genomic Hybridization Experiments pp. 24

Gaile Daniel P, Schifano Elizabeth D, Miecznikowski Jeffrey C, Java James J, Conroy Jeffrey M and Nowak Norma J

Multiple Testing for SNP-SNP Interactions pp. 24

Boulesteix Anne-Laure, Strobl Carolin, Weidinger Stefan, Wichmann H.-Erich and Wagenpfeil Stefan

Using Linear Mixed Models for Normalization of cDNA Microarrays pp. 25

Haldermans Philippe, Shkedy Ziv, Suzy Van Sanden, Burzykowski Tomasz and Aerts Marc

The Cyclohedron Test for Finding Periodic Genes in Time Course Expression Studies pp. 25

Morton Jason, Pachter Lior, Shiu Anne and Sturmfels Bernd

Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences pp. 26

Svennblad Bodil and Britton Tom

Super Learning: An Application to the Prediction of HIV-1 Drug Resistance pp. 26

Sinisi Sandra E., Polley Eric C, Petersen Maya L, Rhee Soo-Yon and J. van der Laan Mark

A Method for Meta-Analysis of Case-Control Genetic Association Studies Using Logistic Regression pp. 28

Pantelis Bagos and Konstantinos Nikolopoulos

Testing for Trends in Dose-Response Microarray Experiments: A Comparison of Several Testing Procedures, Multiplicity and Resampling-Based Inference pp. 28

Lin Dan, Shkedy Ziv, Yekutieli Dani, Burzykowski Tomasz, Göhlmann Hinrich W.H., An De Bondt, Perera Tim, Geerts Tamara and Bijnens Luc

Fully Bayesian Mixture Model for Differential Gene Expression: Simulations and Model Checks pp. 28

Lewin Alex, Bochkina Natalia and Richardson Sylvia

Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates pp. 29

Tintle Nathan L, Gordon Derek, McMahon Francis J and Finch Stephen J

Population Structure and Covariate Analysis Based on Pairwise Microsatellite Allele Matching Frequencies pp. 30

Givens Geof H and Ozaksoy Isin

A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference pp. 32

Luo Ruiyan, Hipp Andrew L and Larget Bret

Likelihood-Based Inference for Multi-Color Optical Mapping pp. 32

Tong Liping, Mets Laurens and McPeek Mary Sara

A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments pp. 33

Angelini Claudia, Daniela De Canditiis, Mutarelli Margherita and Pensky Marianna

A Generalized Sidak-Holm Procedure and Control of Generalized Error Rates under Independence pp. 35

Guo Wenge and Romano Joseph

Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach pp. 36

Lalam Nadia

Sequential Quantitative Trait Locus Mapping in Experimental Crosses pp. 36

Satagopan Jaya M, Sen Saunak and Churchill Gary A.

Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution pp. 43

Shin Ji-Hyung, McNeney Brad and Graham Jinko

Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge pp. 47

Werhli Adriano V and Husmeier Dirk

Multiple Testing Issues in Discriminating Compound-Related Peaks and Chromatograms from High Frequency Noise, Spikes and Solvent-Based Noise in LC - MS Data Sets pp. 49

Nyangoma Stephen O, C. van Kampen Antoine A. H., Reijmers Theo H, Govorukhina Natalia I, J. van der Zee Ate G., Billingham Lucinda J, Bischoff Rainer and Jansen Ritsert C.

Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo pp. 51

Bembom Oliver, Keles Sunduz and J. van der Laan Mark

Volume 5, issue 1, 2006

Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006) pp. 7

Boulesteix Anne-Laure

Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage pp. 8

Mukhopadhyay Indranil, Feingold Eleanor, Wang Tao, Elston Robert C. and Weeks Daniel E.

Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk? pp. 11

Klebanov Lev and Yakovlev Andrei

Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies pp. 18

Guedj Mickael, Robelin David, Hoebeke Mark, Lamarine Marc, Wojcik Jérôme and Nuel Gregory

Approximate Sample Size Calculations with Microarray Data: An Illustration pp. 18

Ferreira José A. and Zwinderman Aeilko

Statistical Selection of Maintenance Genes for Normalization of Gene Expressions pp. 18

Huang Yifan, Hsu Jason C, Peruggia Mario and Scott Abigail A

Validation in Genomics: CpG Island Methylation Revisited pp. 19

Segal Mark R

Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs pp. 19

Nye Tom M. W., Berzuini Carlo, Gilks Walter R, Babu M. Madan and Teichmann Sarah

A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting pp. 20

Rubin Daniel, Dudoit Sandrine and Mark van der Laan

Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities pp. 20

Gupta Rashi, Auvinen Petri, Thomas Andrew and Arjas Elja

Dimension Reduction for Classification with Gene Expression Microarray Data pp. 21

Dai Jian J, Lieu Linh and Rocke David

A Bayes Regression Approach to Array-CGH Data pp. 22

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 and Chang I-Shou

Using Complexity for the Estimation of Bayesian Networks pp. 23

Salzman Peter and Almudevar Anthony

Examining Protein Structure and Similarities by Spectral Analysis Technique pp. 23

Collins Krista, Gu Hong and Field Chris

Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data pp. 24

Birkner Merrill D., Hubbard Alan E., J. van der Laan Mark, Skibola Christine F., Hegedus Christine M. and Smith Martyn T.

A New Type of Stochastic Dependence Revealed in Gene Expression Data pp. 24

Klebanov Lev, Jordan Craig and Yakovlev Andrei

Combining Results of Microarray Experiments: A Rank Aggregation Approach pp. 25

DeConde Robert P, Hawley Sarah, Falcon Seth, Clegg Nigel, Knudsen Beatrice and Etzioni Ruth

Model Selection for Mixtures of Mutagenetic Trees pp. 25

Yin Junming, Beerenwinkel Niko, Rahnenführer Jörg and Lengauer Thomas

An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data pp. 25

Zhang Shunpu

Cross-Validated Bagged Prediction of Survival pp. 26

Sinisi Sandra E., Neugebauer Romain and J. van der Laan Mark

A Generalized Clustering Problem, with Application to DNA Microarrays pp. 26

Belitskaya-Levy Ilana

A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity pp. 26

Dalevi Daniel, Dubhashi Devdatt and Hermansson Malte

Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data pp. 27

McGee Monnie and Chen Zhongxue

Quantile-Function Based Null Distribution in Resampling Based Multiple Testing pp. 30

J. van der Laan Mark and Hubbard Alan E.

Quality Optimised Analysis of General Paired Microarray Experiments pp. 31

Kristiansson Erik, Sjögren Anders, Rudemo Mats and Nerman Olle

Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates pp. 31

Christensen Ole F.

Low-Order Conditional Independence Graphs for Inferring Genetic Networks pp. 34

Wille Anja and Bühlmann Peter

A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion pp. 34

Kedzierska Anna and Husmeier Dirk

A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments pp. 35

Jiang Hongmei and Doerge Rebecca W

Numerical Solutions for Patterns Statistics on Markov Chains pp. 45

Nuel Gregory