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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 12, issue 6, 2013

A new variance stabilizing transformation for gene expression data analysis pp. 653-666 Downloads
Kelmansky Diana M., Martínez Elena J. and Leiva Víctor
Kernel approximate Bayesian computation in population genetic inferences pp. 667-678 Downloads
Nakagome Shigeki, Fukumizu Kenji and Mano Shuhei
Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology pp. 679-701 Downloads
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 Downloads
Taylor Sandra L., Kim Kyoungmi and Leiserowitz Gary S.
Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments pp. 723-742 Downloads
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 Downloads
Hossain Ahmed and Beyene Joseph
Random forests on distance matrices for imaging genetics studies pp. 757-786 Downloads
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 Downloads
Asif H.M. Shahzad and Sanguinetti Guido
Markov chain Monte Carlo sampling of gene genealogies conditional on unphased SNP genotype data pp. 559-581 Downloads
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 Downloads
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 Downloads
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 Downloads
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 Downloads
Nilsen Gro, LiestØl Knut, Borgan Ørnulf and Lingjærde Ole Christian

Volume 12, issue 4, 2013

Genome-wide association studies with high-dimensional phenotypes pp. 413-431 Downloads
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 Downloads
Graffelman Jan and Moreno Victor
General power and sample size calculations for high-dimensional genomic data pp. 449-467 Downloads
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 Downloads
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 Downloads
Zhang Runchu and Mukerjee Rahul
Bayseian genomic models for the incorporation of pathway topology knowledge into association studies pp. 505-516 Downloads
Brisbin Abra and Fridley Brooke L.
Improving the efficiency of genomic selection pp. 517-527 Downloads
Scutari Marco, Balding David and Mackay Ian
Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions pp. 529-543 Downloads
Bickel David R.

Volume 12, issue 2, 2013

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

Volume 12, issue 1, 2013

Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data pp. 1-15 Downloads
Zheng Wei and Zhao Hongyu
Approximate Bayesian computation with functional statistics pp. 17-37 Downloads
Soubeyrand Samuel, Guiton François, Klein Etienne K. and Carpentier Florence
Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics pp. 39-48 Downloads
Herbei Radu and Kubatko Laura
Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data pp. 49-70 Downloads
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 Downloads
Rudolf Henrik, Pricop-Jeckstadt Mihaela and Reinsch Norbert
On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo pp. 87-107 Downloads
Filippi Sarah, Barnes Chris P., Stumpf Michael P.H. and Cornebise Julien
Inferring latent gene regulatory network kinetics pp. 109-127 Downloads
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. 1-22 Downloads
Foucher Yohann and Danger Richard
An Order Estimation Based Approach to Identify Response Genes for Microarray Time Course Data pp. 1-34 Downloads
Lu Zhiheng K., O. Brian Allen and Desmond Anthony F.
A maximum likelihood approach to functional mapping of longitudinal binary traits pp. 1-25 Downloads
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. 1-25 Downloads
Yi Nengjun and Ma Shuangge

Volume 11, issue 5, 2012

Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data pp. 1-32 Downloads
Pounds Stanley B., Gao Cuilan L. and Zhang Hui
Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates pp. 1-44 Downloads
Lund Steven P., Nettleton Dan, McCarthy Davis J. and Smyth Gordon K.
ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments pp. 1-22 Downloads
Mary-Huard Tristan, Jaffrezic Florence and Robin Stéphane
Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data pp. 1-37 Downloads
Olbricht Gayla R., Craig Bruce A. and Doerge Rebecca W.
Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data pp. 1-21 Downloads
Hayashi Takeshi
Estimators of the local false discovery rate designed for small numbers of tests pp. 1-42 Downloads
Padilla Marta and Bickel David R.
Analyzing Genetic Association Studies with an Extended Propensity Score Approach pp. 1-24 Downloads
Zhao Huaqing, Rebbeck Timothy R. and Mitra Nandita
Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks pp. 1-29 Downloads
Geeven Geert, J. van der Laan Mark and C.M. de Gunst Mathisca
DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms pp. 1-34 Downloads
David Ramsey and Futschik Andreas
Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations pp. 1-28 Downloads
Anderson Eric C.
A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection pp. 1-26 Downloads
Schmid Matthias, Hothorn Torsten, Krause Friedemann and Rabe Christina
Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms pp. 1-26 Downloads
Lin Chang-Yun, Lo Yungtai and Ye Kenny Q.

Volume 11, issue 4, 2012

Cluster-Localized Sparse Logistic Regression for SNP Data pp. 1-31 Downloads
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. 1-31 Downloads
Alessio Farcomeni and Arima Serena
A Novel and Fast Normalization Method for High-Density Arrays pp. 1-31 Downloads
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.
Computing Posterior Probabilities for Score-based Alignments Using ppALIGN pp. 1-37 Downloads
Wolfsheimer Stefan, Hartmann Alexander, Rabus Ralf and Nuel Gregory
Incorporating the Empirical Null Hypothesis into the Benjamini-Hochberg Procedure pp. 1-21 Downloads
Ghosh Debashis
How to analyze many contingency tables simultaneously in genetic association studies pp. 1-33 Downloads
Thorsten Dickhaus, Straßburger Klaus, Daniel Schunk, Morcillo-Suarez Carlos, Illig Thomas and Navarro Arcadi
A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology pp. 1-62 Downloads
Grzegorczyk Marco and Husmeier Dirk
Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications pp. 1-46 Downloads
Kenney Toby and Gu Hong
An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping pp. 1-30 Downloads
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. 1-30 Downloads
Ostrovnaya Irina
Performance of MAX Test and Degree of Dominance Index in Predicting the Mode of Inheritance pp. 1-17 Downloads
Zintzaras Elias and Santos Mauro
Correction for Founder Effects in Host-Viral Association Studies via Principal Components pp. 1-17 Downloads
Reeves Karyn L., McKinnon Elizabeth J. and James Ian R.
Estimating the Number of One-step Beneficial Mutations pp. 1-28 Downloads
Wojtowicz Andrzej J., Miller Craig R. and Joyce Paul
A New Explained-Variance Based Genetic Risk Score for Predictive Modeling of Disease Risk pp. 1-56 Downloads
Che Ronglin and Motsinger-Reif Alison A.
QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function pp. 1-26 Downloads
Frommlet Florian, Ljubic Ivana, Arnardóttir Helga Björk and Bogdan Malgorzata

Volume 11, issue 3, 2012

GENOVA: Gene Overlap Analysis of GWAS Results pp. 1-15 Downloads
Tang Clara S. and Ferreira Manuel A. R.
Exploring Multicollinearity Using a Random Matrix Theory Approach pp. 1-35 Downloads
Feher Kristen, Whelan James and Müller Samuel
Graph Selection with GGMselect pp. 1-52 Downloads
Giraud Christophe, Huet Sylvie and Verzelen Nicolas
Detecting Sample Misidentifications in Genetic Association Studies pp. 1-19 Downloads
Ekstrøm Claus T. and Feenstra Bjarke
Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model pp. 1-20 Downloads
Ambroise Jérôme, Bearzatto Bertrand, Robert Annie, Macq Benoit and Gala Jean-Luc
Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set pp. 1-30 Downloads
Lim Johan, Kim Jayoun, Kim Sang-cheol, Yu Donghyeon, Kim Kyunga and Kim Byung Soo
Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes pp. 1-24 Downloads
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. 1-29 Downloads
Ji Tieming, Liu Peng and Nettleton Dan
Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals pp. 1-34 Downloads
Bickel David R.
Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry pp. 1-42 Downloads
Nyangoma Stephen O., Collins Stuart I., Altman Douglas G., Johnson Philip and Billingham Lucinda J.
The practical effect of batch on genomic prediction pp. 1-22 Downloads
Parker Hilary S. and Leek Jeffrey T.
A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification pp. 1-21 Downloads
Ferguson John P., Cho Judy H. and Zhao Hongyu
Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies pp. 1-21 Downloads
Bogojeska Jasmina and Lengauer Thomas
Normalization, bias correction, and peak calling for ChIP-seq pp. 1-31 Downloads
Diaz Aaron, Park Kiyoub, Lim Daniel A. and Song Jun S.
The Beta-Binomial SGoF method for multiple dependent tests pp. 1-32 Downloads
Jacobo de Uña-Alvarez

Volume 11, issue 2, 2012

Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate pp. 1-21 Downloads
Zhang Tian-Xiao, Beaty Terri H. and Ruczinski Ingo
Querying Genomic Databases: Refining the Connectivity Map pp. 1-37 Downloads
Segal Mark R., Xiong Hao, Bengtsson Henrik, Bourgon Richard and Gentleman Robert
A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data pp. 1-32 Downloads
Cartwright Reed A., Hussin Julie, Keebler Jonathan E. M., Stone Eric A. and Awadalla Philip
A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning pp. 1-23 Downloads
Moser Carlee and Gupta Mayetri
Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads pp. 1-23 Downloads
Shin Ji-Hyung, Infante-Rivard Claire, Graham Jinko and McNeney Brad
Special Issue on Computational Statistical Methods for Genomics and Systems Biology pp. 1-5 Downloads
Labbe Aurélie and Dudoit Sandrine
Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors pp. 1-31 Downloads
Lee Anthony, Caron Francois, Doucet Arnaud and Holmes Chris
Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families pp. 1-18 Downloads
Glazner Chris and Thompson Elizabeth Alison
Gene Filtering in the Analysis of Illumina Microarray Experiments pp. 1-19 Downloads
Forcheh Anyiawung Chiara, Verbeke Geert, Kasim Adetayo, Lin Dan, Shkedy Ziv, Talloen Willem, Göhlmann Hinrich Wh and Clement Lieven
Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees pp. 1-27 Downloads
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. 1-27 Downloads
Newton Michael A., He Qiuling and Kendziorski Christina

Volume 11, issue 1, 2012

Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays pp. 1-36 Downloads
Clement Lieven, Kristof De Beuf, Thas Olivier, Vuylsteke Marnik, Irizarry Rafael A. and Crainiceanu Ciprian M.
Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps pp. 1-43 Downloads
Silver Matt, Giovanni Montana and Alzheimer's Disease Neuroimaging Initiative
Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning pp. 1-27 Downloads
Bulla Ingo, Schultz Anne-Kathrin and Meinicke Peter
Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length pp. 1-28 Downloads
Burden Conrad J., Jing Junmei and Wilson Susan R.
The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses pp. 1-18 Downloads
Goeman Jelle J. and Finos Livio
MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection pp. 1-25 Downloads
Bhattacharyya Malay, Feuerbach Lars, Bhadra Tapas, Lengauer Thomas and Bandyopadhyay Sanghamitra
Optimality Criteria for the Design of 2-Color Microarray Studies pp. 1-9 Downloads
Kerr Kathleen F.
A Mixture-Model Approach for Parallel Testing for Unequal Variances pp. 1-21 Downloads
Bar Haim Y., Booth James G. and Wells Martin T.
Stopping-Time Resampling and Population Genetic Inference under Coalescent Models pp. 1-20 Downloads
Jenkins Paul A.
A Context Dependent Pair Hidden Markov Model for Statistical Alignment pp. 1-29 Downloads
Arribas-Gil Ana and Matias Catherine
Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach pp. 1-24 Downloads
Ambroise Jérôme, Robert Annie, Macq Benoit and Gala Jean-Luc
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