Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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

From De Gruyter
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Volume 11, issue 6, 2012

Time Dependent ROC Curves for the Estimation of True Prognostic Capacity of Microarray Data pp. 22

Foucher Yohann and Danger Richard

A maximum likelihood approach to functional mapping of longitudinal binary traits pp. 25

Wang Chenguang, Li Hongying, Wang Zhong, Wang Yaqun, Wang Ningtao, Wang Zuoheng and Wu Rongling

Hierarchical Shrinkage Priors and Model Fitting for High-dimensional Generalized Linear Models pp. 25

Yi Nengjun and Ma Shuangge

An Order Estimation Based Approach to Identify Response Genes for Microarray Time Course Data pp. 34

Lu Zhiheng K., O. Brian Allen and Desmond Anthony F.

Volume 11, issue 5, 2012

Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data pp. 21

Hayashi Takeshi

ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments pp. 22

Mary-Huard Tristan, Jaffrezic Florence and Robin Stéphane

Analyzing Genetic Association Studies with an Extended Propensity Score Approach pp. 24

Zhao Huaqing, Rebbeck Timothy R. and Mitra Nandita

A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection pp. 26

Schmid Matthias, Hothorn Torsten, Krause Friedemann and Rabe Christina

Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms pp. 26

Lin Chang-Yun, Lo Yungtai and Ye Kenny Q.

Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations pp. 28

Anderson Eric C.

Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks pp. 29

Geeven Geert, J. van der Laan Mark and C.M. de Gunst Mathisca

Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data pp. 32

Pounds Stanley B., Gao Cuilan L. and Zhang Hui

DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms pp. 34

David Ramsey and Futschik Andreas

Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data pp. 37

Olbricht Gayla R., Craig Bruce A. and Doerge Rebecca W.

Estimators of the local false discovery rate designed for small numbers of tests pp. 42

Padilla Marta and Bickel David R.

Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates pp. 44

Lund Steven P., Nettleton Dan, McCarthy Davis J. and Smyth Gordon K.

Volume 11, issue 4, 2012

Performance of MAX Test and Degree of Dominance Index in Predicting the Mode of Inheritance pp. 17

Zintzaras Elias and Santos Mauro

Correction for Founder Effects in Host-Viral Association Studies via Principal Components pp. 17

Reeves Karyn L., McKinnon Elizabeth J. and James Ian R.

Incorporating the Empirical Null Hypothesis into the Benjamini-Hochberg Procedure pp. 21

Ghosh Debashis

QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function pp. 26

Frommlet Florian, Ljubic Ivana, Arnardóttir Helga Björk and Bogdan Malgorzata

Estimating the Number of One-step Beneficial Mutations pp. 28

Wojtowicz Andrzej J., Miller Craig R. and Joyce Paul

An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping pp. 30

Scott-Boyer Marie Pier, Imholte Gregory C., Tayeb Arafat, Labbe Aurelie, Deschepper Christian F. and Gottardo Raphael

Testing clonality of three and more tumors using their loss of heterozygosity profiles pp. 30

Ostrovnaya Irina

Cluster-Localized Sparse Logistic Regression for SNP Data pp. 31

Binder Harald, Müller Tina, Schwender Holger, Golka Klaus, Steffens Michael, Hengstler Jan G., Ickstadt Katja and Schumacher Martin

A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in Microarray time course data pp. 31

Alessio Farcomeni and Arima Serena

A Novel and Fast Normalization Method for High-Density Arrays pp. 31

Maarten van Iterson, Duijkers Floor A.M., Meijerink Jules P.P., Admiraal Pieter, B. van Ommen Gert-Jan, Boer Judith M., M. van Noesel Max and Menezes Renee X.

How to analyze many contingency tables simultaneously in genetic association studies pp. 33

Thorsten Dickhaus, Straßburger Klaus, Daniel Schunk, Morcillo-Suarez Carlos, Illig Thomas and Navarro Arcadi

Computing Posterior Probabilities for Score-based Alignments Using ppALIGN pp. 37

Wolfsheimer Stefan, Hartmann Alexander, Rabus Ralf and Nuel Gregory

Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications pp. 46

Kenney Toby and Gu Hong

A New Explained-Variance Based Genetic Risk Score for Predictive Modeling of Disease Risk pp. 56

Che Ronglin and Motsinger-Reif Alison A.

A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology pp. 62

Grzegorczyk Marco and Husmeier Dirk

Volume 11, issue 3, 2012

GENOVA: Gene Overlap Analysis of GWAS Results pp. 15

Tang Clara S. and Ferreira Manuel A. R.

Detecting Sample Misidentifications in Genetic Association Studies pp. 19

Ekstrøm Claus T. and Feenstra Bjarke

Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model pp. 20

Ambroise Jérôme, Bearzatto Bertrand, Robert Annie, Macq Benoit and Gala Jean-Luc

A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification pp. 21

Ferguson John P., Cho Judy H. and Zhao Hongyu

Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies pp. 21

Bogojeska Jasmina and Lengauer Thomas

The practical effect of batch on genomic prediction pp. 22

Parker Hilary S. and Leek Jeffrey T.

Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes pp. 24

French Benjamin, Lumley Thomas, Cappola Thomas P. and Mitra Nandita

Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis pp. 29

Ji Tieming, Liu Peng and Nettleton Dan

Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set pp. 30

Lim Johan, Kim Jayoun, Kim Sang-cheol, Yu Donghyeon, Kim Kyunga and Kim Byung Soo

Normalization, bias correction, and peak calling for ChIP-seq pp. 31

Diaz Aaron, Park Kiyoub, Lim Daniel A. and Song Jun S.

The Beta-Binomial SGoF method for multiple dependent tests pp. 32

Jacobo de Uña-Alvarez

Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals pp. 34

Bickel David R.

Exploring Multicollinearity Using a Random Matrix Theory Approach pp. 35

Feher Kristen, Whelan James and Müller Samuel

Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry pp. 42

Nyangoma Stephen O., Collins Stuart I., Altman Douglas G., Johnson Philip and Billingham Lucinda J.

Graph Selection with GGMselect pp. 52

Giraud Christophe, Huet Sylvie and Verzelen Nicolas

Volume 11, issue 2, 2012

Special Issue on Computational Statistical Methods for Genomics and Systems Biology pp. 5

Labbe Aurélie and Dudoit Sandrine

Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families pp. 18

Glazner Chris and Thompson Elizabeth Alison

Gene Filtering in the Analysis of Illumina Microarray Experiments pp. 19

Forcheh Anyiawung Chiara, Verbeke Geert, Kasim Adetayo, Lin Dan, Shkedy Ziv, Talloen Willem, Göhlmann Hinrich Wh and Clement Lieven

Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate pp. 21

Zhang Tian-Xiao, Beaty Terri H. and Ruczinski Ingo

A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning pp. 23

Moser Carlee and Gupta Mayetri

Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads pp. 23

Shin Ji-Hyung, Infante-Rivard Claire, Graham Jinko and McNeney Brad

Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees pp. 27

Oualkacha Karim, Labbe Aurelie, Ciampi Antonio, Roy Marc-Andre and Maziade Michel

A Model-Based Analysis to Infer the Functional Content of a Gene List pp. 27

Newton Michael A., He Qiuling and Kendziorski Christina

Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors pp. 31

Lee Anthony, Caron Francois, Doucet Arnaud and Holmes Chris

A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data pp. 32

Cartwright Reed A., Hussin Julie, Keebler Jonathan E. M., Stone Eric A. and Awadalla Philip

Querying Genomic Databases: Refining the Connectivity Map pp. 37

Segal Mark R., Xiong Hao, Bengtsson Henrik, Bourgon Richard and Gentleman Robert

Volume 11, issue 1, 2012

Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning pp. 1-27

Bulla Ingo, Schultz Anne-Kathrin and Meinicke Peter

Optimality Criteria for the Design of 2-Color Microarray Studies pp. 1-9

Kerr Kathleen F.

The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses pp. 1-18

Goeman Jelle J. and Finos Livio

Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach pp. 1-24

Ambroise Jérôme, Robert Annie, Macq Benoit and Gala Jean-Luc

MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection pp. 1-25

Bhattacharyya Malay, Feuerbach Lars, Bhadra Tapas, Lengauer Thomas and Bandyopadhyay Sanghamitra

A Mixture-Model Approach for Parallel Testing for Unequal Variances pp. 1-21

Bar Haim Y., Booth James G. and Wells Martin T.

Stopping-Time Resampling and Population Genetic Inference under Coalescent Models pp. 1-20

Jenkins Paul A.

Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps pp. 1-43

Silver Matt, Giovanni Montana and Alzheimer's Disease Neuroimaging Initiative

Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length pp. 1-28

Burden Conrad J., Jing Junmei and Wilson Susan R.

A Context Dependent Pair Hidden Markov Model for Statistical Alignment pp. 1-29

Arribas-Gil Ana and Matias Catherine

Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays pp. 1-36

Clement Lieven, Kristof De Beuf, Thas Olivier, Vuylsteke Marnik, Irizarry Rafael A. and Crainiceanu Ciprian M.