Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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

From De Gruyter
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Volume 13, issue 6, 2014

When is Menzerath-Altmann law mathematically trivial? A new approach pp. 633-644

Ferrer-i-Cancho Ramon, Hernández-Fernández Antoni, Baixeries Jaume, Dębowski Łukasz and Mačutek Ján

Covariate adjusted differential variability analysis of DNA methylation with propensity score method pp. 645-658

Kuan Pei Fen

P-value calibration for multiple testing problems in genomics pp. 659-673

Ferguson John P. and Palejev Dean

Robust methods to detect disease-genotype association in genetic association studies: calculate p-values using exact conditional enumeration instead of simulated permutations or asymptotic approximations pp. 675-692

Langaas Mette and Bakke Øyvind

Markovianness and conditional independence in annotated bacterial DNA pp. 693-716

Hart Andrew and Martínez Servet

Exploring homogeneity of correlation structures of gene expression datasets within and between etiological disease categories pp. 717-732

Jong Victor L., Novianti Putri W., Roes Kit C.B. and Eijkemans Marinus J.C.

Biological pathway selection through Bayesian integrative modeling pp. 733-733

Zheng Lingling, Yan Xiao, Suchindran Sunil, Dressman Holly, Chute John P. and Lucas Joseph

Volume 13, issue 5, 2014

Imputing genotypes using regularized generalized linear regression models pp. 519-529

Wong William W.L., Griesman Josh and Feng Zeny Z.

Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data pp. 531-551

Jow Howsun, Boys Richard J. and Wilkinson Darren J.

Gene set analysis for GWAS: assessing the use of modified Kolmogorov-Smirnov statistics pp. 553-566

Debrabant Birgit and Soerensen Mette

Robustness of the linear mixed effects model to error distribution assumptions and the consequences for genome-wide association studies pp. 567-587

Warrington Nicole M., Tilling Kate, Howe Laura D., Paternoster Lavinia, Pennell Craig E., Wu Yan Yan and Briollais Laurent

Bayesian modelling of compositional heterogeneity in molecular phylogenetics pp. 589-609

Heaps Sarah E., Nye Tom M.W., Boys Richard J., Williams Tom A. and Embley T. Martin

Quantifying the multi-scale performance of network inference algorithms pp. 611-631

Oates Chris J., Amos Richard and Spencer Simon E.F.

Volume 13, issue 4, 2014

Comparison of algorithms to infer genetic population structure from unlinked molecular markers pp. 391-402

Peña-Malavera Andrea, Bruno Cecilia, Fernandez Elmer and Balzarini Monica

Comparison of statistical methods for finding network motifs pp. 403-422

Albieri Vanna and Didelez Vanessa

A sequential naïve Bayes classifier for DNA barcodes pp. 423-434

Anderson Michael P. and Dubnicka Suzanne R.

Biological pathway selection through Bayesian integrative modeling pp. 435-457

Zheng Lingling, Yan Xiao, Suchindran Sunil, Dressman Holly, Chute John P. and Lucas Joseph

Investigating the performance of AIC in selecting phylogenetic models pp. 459-475

Dwueng-Chwuan Jhwueng, Huzurbazar Snehalata, O’Meara Brian C. and Liu Liang

Multiclass cancer classification based on gene expression comparison pp. 477-496

Yang Sitan and Naiman Daniel Q.

Protein domain hierarchy Gibbs sampling strategies pp. 497-517

Neuwald Andrew F.

Volume 13, issue 3, 2014

Statistical inference of regulatory networks for circadian regulation pp. 227-273

Aderhold Andrej, Husmeier Dirk and Grzegorczyk Marco

A Bayesian clustering approach for detecting gene-gene interactions in high-dimensional genotype data pp. 275-297

Chen Sui-Pi and Huang Guan-Hua

A novel characterization of the generalized family wise error rate using empirical null distributions pp. 299-322

Miecznikowski Jeffrey C. and Gaile Daniel P.

Applying shrinkage variance estimators to the TOST test in high dimensional settings pp. 323-341

Qiu Jing, Qi Yue and Cui Xiangqin

A boosting approach for adapting the sparsity of risk prediction signatures based on different molecular levels pp. 343-357

Sariyar Murat, Schumacher Martin and Binder Harald

Using the theory of added-variable plot for linear mixed models to decompose genetic effects in family data pp. 359-378

Duarte Nubia E., Giolo Suely R., Pereira Alexandre C., Mariza de Andrade and Soler Júlia P.

Efficient parametric inference for stochastic biological systems with measured variability pp. 379-390

Johnston Iain G.

Volume 13, issue 2, 2014

Combining dependent F-tests for robust association of quantitative traits under genetic model uncertainty pp. 123-139

Qu Long

Penalized differential pathway analysis of integrative oncogenomics studies pp. 141-158

N. van Wieringen Wessel and A. van de Wiel Mark

A data-smoothing approach to explore and test gene-environment interaction in case-parent trios pp. 159-171

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

Scan statistics analysis for detection of introns in time-course tiling array data pp. 173-190

Reiner-Benaim Anat, Davis Ronald W. and Juneau Kara

Variance and covariance heterogeneity analysis for detection of metabolites associated with cadmium exposure pp. 191-201

Salamanca Beatriz Valcarcel, Ebbels Timothy M.D. and Iorio Maria De

Improved variational Bayes inference for transcript expression estimation pp. 203-216

Papastamoulis Panagiotis, Hensman James, Glaus Peter and Rattray Magnus

Efficient identification of context dependent subgroups of risk from genome-wide association studies pp. 217-226

Dyson Greg and Sing Charles F.

Volume 13, issue 1, 2014

Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums pp. 1-18

Fernández-Durán Juan José and Gregorio-Domínguez MarÍa Mercedes

Second order optimization for the inference of gene regulatory pathways pp. 19-33

Das Mouli, Murthy Chivukula A. and K. De Rajat

Multiple comparisons in genetic association studies: a hierarchical modeling approach pp. 35-48

Yi Nengjun, Xu Shizhong, Lou Xiang-Yang and Mallick Himel

A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments pp. 49-65

Gómez-Villegas Miguel A., Salazar Isabel and Sanz Luis

Semi-automatic selection of summary statistics for ABC model choice pp. 67-82

Prangle Dennis, Fearnhead Paul, Cox Murray P., Biggs Patrick J. and French Nigel P.

Detection of epistatic effects with logic regression and a classical linear regression model pp. 83-104

Malina Magdalena, Ickstadt Katja, Schwender Holger, Martin Posch and Bogdan Małgorzata

Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model pp. 105-121

Jääskinen Väinö, Parkkinen Ville, Cheng Lu and Corander Jukka

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