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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 6, issue 1, 2007

Using Linear Mixed Models for Normalization of cDNA Microarrays pp. 1-25 Downloads
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. 1-25 Downloads
Morton Jason, Pachter Lior, Shiu Anne and Sturmfels Bernd
Experimental Design for Two-Color Microarrays Applied in a Pre-Existing Split-Plot Experiment pp. 1-23 Downloads
Milliken G. A., Garrett K. A. and Travers S. E.
Super Learner pp. 1-23 Downloads
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. 1-23 Downloads
Green Gerwyn H and Diggle Peter J.
Selection of Biologically Relevant Genes with a Wrapper Stochastic Algorithm pp. 1-23 Downloads
Lê Cao Kim-Anh, Gonçalves Olivier, Besse Philippe and Sébastien Gadat
Normalization of Dye Bias in Microarray Data Using the Mixture of Splines Model pp. 1-22 Downloads
Joo Yongsung, Casella George, Booth James, Lee Keunbaik and Enkemann Steven
Sparse Logistic Regression with Lp Penalty for Biomarker Identification pp. 1-22 Downloads
Liu Zhenqiu, Jiang Feng, Tian Guoliang, Wang Suna, Sato Fumiaki, Meltzer Stephen J. and Tan Ming
A Method for Meta-Analysis of Case-Control Genetic Association Studies Using Logistic Regression pp. 1-28 Downloads
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. 1-28 Downloads
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. 1-28 Downloads
Lewin Alex, Bochkina Natalia and Richardson Sylvia
A Bayesian Model of AFLP Marker Evolution and Phylogenetic Inference pp. 1-32 Downloads
Luo Ruiyan, Hipp Andrew L and Larget Bret
Likelihood-Based Inference for Multi-Color Optical Mapping pp. 1-32 Downloads
Tong Liping, Mets Laurens and McPeek Mary Sara
Approximating the Variance of the Conditional Probability of the State of a Hidden Markov Model pp. 1-21 Downloads
Siegmund David O and Yakir Benjamin
H-Tuple Approach to Evaluate Statistical Significance of Biological Sequence Comparison with Gaps pp. 1-21 Downloads
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. 1-21 Downloads
Tang Jing, Tao Jinglun, Urakawa Hidetoshi and Corander Jukka
Cox Survival Analysis of Microarray Gene Expression Data Using Correlation Principal Component Regression pp. 1-16 Downloads
Zhao Qiang and Sun Jianguo
A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments pp. 1-33 Downloads
Angelini Claudia, Daniela De Canditiis, Mutarelli Margherita and Pensky Marianna
Inference on the Limiting False Discovery Rate and the P-value Threshold Parameter Assuming Weak Dependence between Gene Expression Levels within Subject pp. 1-24 Downloads
Heller Glenn and Qin Jing
Estimating the Arm-Wise False Discovery Rate in Array Comparative Genomic Hybridization Experiments pp. 1-24 Downloads
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. 1-24 Downloads
Boulesteix Anne-Laure, Strobl Carolin, Weidinger Stefan, Wichmann H.-Erich and Wagenpfeil Stefan
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. 1-49 Downloads
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.
Using Duplicate Genotyped Data in Genetic Analyses: Testing Association and Estimating Error Rates pp. 1-29 Downloads
Tintle Nathan L, Gordon Derek, McMahon Francis J and Finch Stephen J
Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach pp. 1-20 Downloads
Rainer Opgen-Rhein and Strimmer Korbinian
Population Structure and Covariate Analysis Based on Pairwise Microsatellite Allele Matching Frequencies pp. 1-30 Downloads
Givens Geof H and Ozaksoy Isin
Case-Control Inference of Interaction between Genetic and Nongenetic Risk Factors under Assumptions on Their Distribution pp. 1-43 Downloads
Shin Ji-Hyung, McNeney Brad and Graham Jinko
A Comparison of Methods to Control Type I Errors in Microarray Studies pp. 1-19 Downloads
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. 1-19 Downloads
Li Xiaohong, Foulkes Andrea S, Yucel Recai M. and Rich Stephen M.
Statistical Inference for Quantitative Polymerase Chain Reaction Using a Hidden Markov Model: A Bayesian Approach pp. 1-36 Downloads
Lalam Nadia
Sequential Quantitative Trait Locus Mapping in Experimental Crosses pp. 1-36 Downloads
Satagopan Jaya M, Sen Saunak and Churchill Gary A.
Supervised Detection of Conserved Motifs in DNA Sequences with Cosmo pp. 1-51 Downloads
Bembom Oliver, Keles Sunduz and J. van der Laan Mark
Reconstructing Gene Regulatory Networks with Bayesian Networks by Combining Expression Data with Multiple Sources of Prior Knowledge pp. 1-47 Downloads
Werhli Adriano V and Husmeier Dirk
Improving Divergence Time Estimation in Phylogenetics: More Taxa vs. Longer Sequences pp. 1-26 Downloads
Svennblad Bodil and Britton Tom
Super Learning: An Application to the Prediction of HIV-1 Drug Resistance pp. 1-26 Downloads
Sinisi Sandra E., Polley Eric C, Petersen Maya L, Rhee Soo-Yon and J. van der Laan Mark
A Generalized Sidak-Holm Procedure and Control of Generalized Error Rates under Independence pp. 1-35 Downloads
Guo Wenge and Romano Joseph
Accounting for Dependence in Similarity Data from DNA Fingerprinting pp. 1-15 Downloads
Hepworth Graham, Gordon Ian R and McCullough Michael J
Estimation of Expression Levels in Spotted Microarrays with Saturated Pixels pp. 1-15 Downloads
Glasbey Chris A, Forster Thorsten and Ghazal Peter

Volume 5, issue 1, 2006

Quality Optimised Analysis of General Paired Microarray Experiments pp. 1-31 Downloads
Kristiansson Erik, Sjögren Anders, Rudemo Mats and Nerman Olle
Pseudo-likelihood for Non-reversible Nucleotide Substitution Models with Neighbour Dependent Rates pp. 1-31 Downloads
Christensen Ole F.
Using Complexity for the Estimation of Bayesian Networks pp. 1-23 Downloads
Salzman Peter and Almudevar Anthony
Examining Protein Structure and Similarities by Spectral Analysis Technique pp. 1-23 Downloads
Collins Krista, Gu Hong and Field Chris
Combining Results of Microarray Experiments: A Rank Aggregation Approach pp. 1-25 Downloads
DeConde Robert P, Hawley Sarah, Falcon Seth, Clegg Nigel, Knudsen Beatrice and Etzioni Ruth
Model Selection for Mixtures of Mutagenetic Trees pp. 1-25 Downloads
Yin Junming, Beerenwinkel Niko, Rahnenführer Jörg and Lengauer Thomas
An Improved Nonparametric Approach for Detecting Differentially Expressed Genes with Replicated Microarray Data pp. 1-25 Downloads
Zhang Shunpu
A Bayes Regression Approach to Array-CGH Data pp. 1-22 Downloads
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
Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk? pp. 1-11 Downloads
Klebanov Lev and Yakovlev Andrei
Numerical Solutions for Patterns Statistics on Markov Chains pp. 1-45 Downloads
Nuel Gregory
Validation in Genomics: CpG Island Methylation Revisited pp. 1-19 Downloads
Segal Mark R
Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs pp. 1-19 Downloads
Nye Tom M. W., Berzuini Carlo, Gilks Walter R, Babu M. Madan and Teichmann Sarah
Parameter Estimation for the Exponential-Normal Convolution Model for Background Correction of Affymetrix GeneChip Data pp. 1-27 Downloads
McGee Monnie and Chen Zhongxue
Cross-Validated Bagged Prediction of Survival pp. 1-26 Downloads
Sinisi Sandra E., Neugebauer Romain and J. van der Laan Mark
A Generalized Clustering Problem, with Application to DNA Microarrays pp. 1-26 Downloads
Belitskaya-Levy Ilana
A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity pp. 1-26 Downloads
Dalevi Daniel, Dubhashi Devdatt and Hermansson Malte
A Two-Step Multiple Comparison Procedure for a Large Number of Tests and Multiple Treatments pp. 1-35 Downloads
Jiang Hongmei and Doerge Rebecca W
Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies pp. 1-18 Downloads
Guedj Mickael, Robelin David, Hoebeke Mark, Lamarine Marc, Wojcik Jérôme and Nuel Gregory
Approximate Sample Size Calculations with Microarray Data: An Illustration pp. 1-18 Downloads
Ferreira José A. and Zwinderman Aeilko
Statistical Selection of Maintenance Genes for Normalization of Gene Expressions pp. 1-18 Downloads
Huang Yifan, Hsu Jason C, Peruggia Mario and Scott Abigail A
Reader's Reaction to "Dimension Reduction for Classification with Gene Expression Microarray Data" by Dai et al (2006) pp. 1-7 Downloads
Boulesteix Anne-Laure
A Method to Increase the Power of Multiple Testing Procedures Through Sample Splitting pp. 1-20 Downloads
Rubin Daniel, Dudoit Sandrine and Mark van der Laan
Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities pp. 1-20 Downloads
Gupta Rashi, Auvinen Petri, Thomas Andrew and Arjas Elja
Quantile-Function Based Null Distribution in Resampling Based Multiple Testing pp. 1-30 Downloads
J. van der Laan Mark and Hubbard Alan E.
Low-Order Conditional Independence Graphs for Inferring Genetic Networks pp. 1-34 Downloads
Wille Anja and Bühlmann Peter
A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion pp. 1-34 Downloads
Kedzierska Anna and Husmeier Dirk
Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage pp. 1-8 Downloads
Mukhopadhyay Indranil, Feingold Eleanor, Wang Tao, Elston Robert C. and Weeks Daniel E.
Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data pp. 1-24 Downloads
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. 1-24 Downloads
Klebanov Lev, Jordan Craig and Yakovlev Andrei
Dimension Reduction for Classification with Gene Expression Microarray Data pp. 1-21 Downloads
Dai Jian J, Lieu Linh and Rocke David
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