Statistical Applications in Genetics and Molecular Biology

2002 - 2026

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

From De Gruyter
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Volume 12, issue 6, 2013

A new variance stabilizing transformation for gene expression data analysis pp. 653-666

Kelmansky Diana M., Martínez Elena J. and Leiva Víctor

Kernel approximate Bayesian computation in population genetic inferences pp. 667-678

Nakagome Shigeki, Fukumizu Kenji and Mano Shuhei

Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology pp. 679-701

Mramba Lazarus K., Barber Stuart, Hommola Kerstin, Dyer Lee A., Wilson Joseph S., Forister Matthew L. and Gilks Walter R.

Accounting for undetected compounds in statistical analyses of mass spectrometry ‘omic studies pp. 703-722

Taylor Sandra L., Leiserowitz Gary S. and Kim Kyoungmi

Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments pp. 723-742

Lacey Michelle R., Baribault Carl and Ehrlich Melanie

Estimation of weighted log partial area under the ROC curve and its application to MicroRNA expression data pp. 743-755

Hossain Ahmed and Beyene Joseph

Random forests on distance matrices for imaging genetics studies pp. 757-786

Sim Aaron, Tsagkrasoulis Dimosthenis and Giovanni Montana

Volume 12, issue 5, 2013

Simultaneous inference and clustering of transcriptional dynamics in gene regulatory networks pp. 545-557

Asif H.M. Shahzad and Sanguinetti Guido

Markov chain Monte Carlo sampling of gene genealogies conditional on unphased SNP genotype data pp. 559-581

Burkett Kelly M., McNeney Brad and Graham Jinko

Performance and estimation of the true error rate of classification rules built with additional information. An application to a cancer trial pp. 583-602

Conde David, Salvador Bonifacio, Rueda Cristina and Fernández Miguel A.

Optimizing threshold-schedules for sequential approximate Bayesian computation: applications to molecular systems pp. 603-618

Silk Daniel, Filippi Sarah and Stumpf Michael P. H.

Model selection for prognostic time-to-event gene signature discovery with applications in early breast cancer data pp. 619-635

Ahdesmäki Miika, Lancashire Lee, Proutski Vitali, Wilson Claire, Davison Timothy S., Harkin D. Paul and Kennedy Richard D.

Identifying clusters in genomics data by recursive partitioning pp. 637-652

Nilsen Gro, Borgan Ørnulf, LiestØl Knut and Lingjærde Ole Christian

Volume 12, issue 4, 2013

Genome-wide association studies with high-dimensional phenotypes pp. 413-431

Marttinen Pekka, Gillberg Jussi, Havulinna Aki, Corander Jukka and Kaski Samuel

The mid p-value in exact tests for Hardy-Weinberg equilibrium pp. 433-448

Graffelman Jan and Moreno Victor

General power and sample size calculations for high-dimensional genomic data pp. 449-467

Maarten van Iterson, A. van de Wiel Mark, Boer Judith M. and X. de Menezes Renée

A graphical model method for integrating multiple sources of genome-scale data pp. 469-487

Dvorkin Daniel, Biehs Brian and Kechris Katerina

Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure pp. 489-503

Zhang Runchu and Mukerjee Rahul

Bayesian genomic models for the incorporation of pathway topology knowledge into association studies pp. 505-516

Brisbin Abra and Fridley Brooke L.

Improving the efficiency of genomic selection pp. 517-527

Scutari Marco, Mackay Ian and Balding David

Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions pp. 529-543

Bickel David R.

Volume 12, issue 3, 2013

Genetic model selection in genome-wide association studies: robust methods and the use of meta-analysis pp. 285-308

Bagos Pantelis G.

Hierarchical Bayesian mixture modelling for antigen-specific T-cell subtyping in combinatorially encoded flow cytometry studies pp. 309-331

Lin Lin, Chan Cliburn, Hadrup Sine R., Froesig Thomas M., Wang Quanli and West Mike

An extension of the Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data pp. 333-346

Jan De Neve, Thas Olivier, Ottoy Jean-Pierre and Clement Lieven

Block-diagonal discriminant analysis and its bias-corrected rules pp. 347-359

Pang Herbert, Tong Tiejun and Ng Michael

Statistical issues associated with modeling of synonymous mutation data pp. 361-374

Huzurbazar Snehalata, Singh Sarabdeep and Schlueter Jessica A.

Sensitivity to prior specification in Bayesian genome-based prediction models pp. 375-391

Lehermeier Christina, Wimmer Valentin, Albrecht Theresa, Auinger Hans-Jürgen, Gianola Daniel, Schmid Volker J. and Schön Chris-Carolin

Bayesian hierarchical graph-structured model for pathway analysis using gene expression data pp. 393-412

Zhou Hui and Zheng Tian

Volume 12, issue 2, 2013

Approximate Bayesian computation (ABC) gives exact results under the assumption of model error pp. 129-141

Wilkinson Richard David

Modeling the DNA copy number aberration patterns in observational high-throughput cancer data pp. 143-174

N. van Wieringen Wessel, Roś Beata P. and Wilting Saskia M.

Exploring the sampling universe of RNA-seq pp. 175-188

Tauber Stefanie and Arndt von Haeseler

Detection of epigenetic changes using ANOVA with spatially varying coefficients pp. 189-205

Guanghua Xiao, Xinlei Wang, Quincey LaPlant, Nestler Eric J. and Xie Yang

Robustness of chemometrics-based feature selection methods in early cancer detection and biomarker discovery pp. 207-223

Lee Hae Woo, Lawton Carl, Na Young Jeong and Yoon Seongkyu

Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures pp. 225-240

Koestler Devin C., Christensen Brock C., Marsit Carmen J., Kelsey Karl T. and Houseman E. Andres

A novel method for analyzing genetic association with longitudinal phenotypes pp. 241-261

Londono Douglas, Chen Kuo-mei, Musolf Anthony, Wang Ruixue, Shen Tong, Brandon January, Herring John A., Wise Carol A., Zou Hong, Jin Meilei, Yu Lei, Finch Stephen J., Matise Tara C. and Gordon Derek

Two optimization strategies of multi-stage design in clinical proteomic studies pp. 263-283

Zeng Irene S.L., Lumley Thomas, Ruggiero Kathy, Middleditch Martin, Woon See-Tarn and Stewart Ralph A.H.

Volume 12, issue 1, 2013

Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data pp. 1-15

Zheng Wei and Zhao Hongyu

Approximate Bayesian computation with functional statistics pp. 17-37

Soubeyrand Samuel, Carpentier Florence, Guiton François and Klein Etienne K.

Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics pp. 39-48

Herbei Radu and Kubatko Laura

Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data pp. 49-70

Di Yanming, Emerson Sarah C., Schafer Daniel W., Kimbrel Jeffrey A. and Chang Jeff H.

Flexible pooling in gene expression profiles: design and statistical modeling of experiments for unbiased contrasts pp. 71-86

Rudolf Henrik, Pricop-Jeckstadt Mihaela and Reinsch Norbert

On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo pp. 87-107

Filippi Sarah, Barnes Chris P., Cornebise Julien and Stumpf Michael P.H.

Inferring latent gene regulatory network kinetics pp. 109-127

González Javier, Vujačić Ivan and Wit Ernst

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

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

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.

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.

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

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

Goeman Jelle J. and Finos Livio

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

Jenkins Paul A.

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

Arribas-Gil Ana and Matias Catherine

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

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

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

Kerr Kathleen F.