Statistical Applications in Genetics and Molecular Biology

2002 - 2026

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

From De Gruyter
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Volume 14, issue 6, 2015

Homology cluster differential expression analysis for interspecies mRNA-Seq experiments pp. 507-516

Gelfond Jonathan A., Ibrahim Joseph G., Chen Ming-Hui, Sun Wei, Lewis Kaitlyn, Kinahan Sean, Hibbs Matthew and Buffenstein Rochelle

Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling pp. 517-532

Samb Rawane, Khadraoui Khader, Belleau Pascal, Deschênes Astrid, Lakhal-Chaieb Lajmi and Droit Arnaud

On the validity of within-nuclear-family genetic association analysis in samples of extended families pp. 533-549

Bureau Alexandre and Duchesne Thierry

An Empirical Bayes risk prediction model using multiple traits for sequencing data pp. 551-573

Li Gengxin, Cui Yuehua and Zhao Hongyu

Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data pp. 575-583

Thorne Thomas

Volume 14, issue 5, 2015

A model selection criterion for model-based clustering of annotated gene expression data pp. 413-428

Gallopin Mélina, Celeux Gilles, Jaffrézic Florence and Rau Andrea

Sample size reassessment for a two-stage design controlling the false discovery rate pp. 429-442

Zehetmayer Sonja, Graf Alexandra C. and Martin Posch

A robust distribution-free test for genetic association studies of quantitative traits pp. 443-464

Kozlitina Julia and Schucany William R.

A parametric approach to kinship hypothesis testing using identity-by-descent parameters pp. 465-479

García-Magariños Manuel, Egeland Thore, López- de-Ullibarri Ignacio, Hjort Nils L. and Salas Antonio

Likelihood ratio and score burden tests for detecting disease-associated rare variants pp. 481-495

Lee Woojoo, Lee Donghwan and Pawitan Yudi

On an extended interpretation of linkage disequilibrium in genetic case-control association studies pp. 497-505

Thorsten Dickhaus, Stange Jens and Demirhan Haydar

Volume 14, issue 4, 2015

Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions pp. 317-332

Muchmore Patrick and Marjoram Paul

Outlier reset CUSUM for the exploration of copy number alteration data pp. 333-345

Lai Yinglei and Gastwirth Joseph L.

Simultaneous Bayesian analysis of contingency tables in genetic association studies pp. 347-360

Thorsten Dickhaus

Modeling the next generation sequencing read count data for DNA copy number variant study pp. 361-374

Ji Tieming and Chen Jie

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination pp. 375-389

Chi Peter B., Chattopadhyay Sujay, Lemey Philippe, Sokurenko Evgeni V. and Minin Vladimir N.

Node sampling for protein complex estimation in bait-prey graphs pp. 391-411

Scholtens Denise M. and Spencer Bruce D.

Volume 14, issue 3, 2015

A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance pp. 227-241

McNutt Patrick, Gut Ian, Hubbard Kyle and Beske Phil

A mutual information estimator with exponentially decaying bias pp. 243-252

Zhang Zhiyi and Zheng Lukun

Bayes factors based on robust TDT-type tests for family trio design pp. 253-264

Yuan Min, Pan Xiaoqing and Yang Yaning

Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies pp. 265-277

Li Yun, O’Connor George T., Dupuis Josée and Kolaczyk Eric

Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis pp. 279-293

Charmpi Konstantina and Ycart Bernard

Application of the fractional-stable distributions for approximation of the gene expression profiles pp. 295-306

Saenko Viacheslav and Saenko Yury

CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data pp. 307-310

Penfold Christopher A., Shifaz Ahmed, Brown Paul E., Nicholson Ann and Wild David L.

TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists pp. 311-316

Schimek Michael G., Budinská Eva, Kugler Karl G., Švendová Vendula, Ding Jie and Lin Shili

Volume 14, issue 2, 2015

Study of triplet periodicity differences inside and between genomes pp. 113-123

Suvorova Yulia M. and Korotkov Eugene V.

H-CLAP: hierarchical clustering within a linear array with an application in genetics pp. 125-141

Ghosh Samiran and Townsend Jeffrey P.

Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles pp. 143-167

Grzegorczyk Marco, Aderhold Andrej and Husmeier Dirk

Bayesian inference for Markov jump processes with informative observations pp. 169-188

Golightly Andrew and Wilkinson Darren J.

Likelihood free inference for Markov processes: a comparison pp. 189-209

Owen Jamie, Wilkinson Darren J. and Gillespie Colin S.

Spatio-temporal model for multiple ChIP-seq experiments pp. 211-219

Saverio Ranciati, Viroli Cinzia and Wit Ernst

GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net pp. 221-224

Vlassis Nikos and Glaab Enrico

Corrigendum to: Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions pp. 225-225

Bickel David R.

Volume 14, issue 1, 2015

A region-based multiple testing method for hypotheses ordered in space or time pp. 1-19

Meijer Rosa J., Krebs Thijmen J.P. and Goeman Jelle J.

A hidden Markov-model for gene mapping based on whole-genome next generation sequencing data pp. 21-34

Claesen Jürgen and Burzykowski Tomasz

Bayesian mixed-effects model for the analysis of a series of FRAP images pp. 35-51

Feilke Martina, Schneider Katrin and Schmid Volker J.

A Bayesian mixture model for chromatin interaction data pp. 53-64

Niu Liang and Lin Shili

Inference for one-step beneficial mutations using next generation sequencing pp. 65-81

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

Testing genotypes-phenotype relationships using permutation tests on association rules pp. 83-92

Shaikh Mateen and Beyene Joseph

Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data pp. 93-111

Hou Jiayi and Archer Kellie J.

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