Statistical Applications in Genetics and Molecular Biology

2002 - 2024

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

From De Gruyter
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Volume 15, issue 6, 2016

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements pp. 447-471

Fu Audrey Qiuyan and Pachter Lior

Tree-based quantitative trait mapping in the presence of external covariates pp. 473-490

Thompson Katherine L., Linnen Catherine R. and Kubatko Laura

Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data pp. 491-505

Li Chung-I and Shyr Yu

Adaptive input data transformation for improved network reconstruction with information theoretic algorithms pp. 507-520

Kannan Venkateshan and Tegner Jesper

Volume 15, issue 5, 2016

Diagnostics for assessing the linear noise and moment closure approximations pp. 363-379

Gillespie Colin S. and Golightly Andrew

Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming pp. 381-400

Pugacheva Valentina, Korotkov Alexander and Korotkov Eugene

A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments pp. 401-414

Kruppa Jochen, Kramer Frank, Beißbarth Tim and Jung Klaus

Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies pp. 415-430

Kakourou Alexia, Vach Werner, Nicolardi Simone, Yuri van der Burgt and Mertens Bart

Evaluation of low-template DNA profiles using peak heights pp. 431-445

Steele Christopher D., Greenhalgh Matthew and Balding David J.

Volume 15, issue 4, 2016

Bayesian state space models for dynamic genetic network construction across multiple tissues pp. 273-290

Liang Yulan and Kelemen Arpad

A joint modeling approach for uncovering associations between gene expression, bioactivity and chemical structure in early drug discovery to guide lead selection and genomic biomarker development pp. 291-304

Perualila-Tan Nolen, Kasim Adetayo, Talloen Willem, Verbist Bie, Göhlmann Hinrich W.H., Consortium Qstar and Shkedy Ziv

The use of vector bootstrapping to improve variable selection precision in Lasso models pp. 305-320

Laurin Charles, Boomsma Dorret and Lubke Gitta

Finding causative genes from high-dimensional data: an appraisal of statistical and machine learning approaches pp. 321-347

Wang Chamont and Gevertz Jana L.

LandScape: a simple method to aggregate p-values and other stochastic variables without a priori grouping pp. 349-361

Wiuf Carsten, Schaumburg-Müller Pallesen Jonatan, Foldager Leslie and Grove Jakob

Volume 15, issue 3, 2016

Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks pp. 193-212

Vinciotti Veronica, Augugliaro Luigi, Abbruzzo Antonino and Wit Ernst C.

Testing differentially expressed genes in dose-response studies and with ordinal phenotypes pp. 213-235

Sweeney Elizabeth, Crainiceanu Ciprian and Gertheiss Jan

Differential methylation tests of regulatory regions pp. 237-251

Ryu Duchwan, Xu Hongyan, George Varghese, Su Shaoyong, Wang Xiaoling, Shi Huidong and Podolsky Robert H.

Sparse factor model for co-expression networks with an application using prior biological knowledge pp. 253-272

Blum Yuna, Houée-Bigot Magalie and Causeur David

Volume 15, issue 2, 2016

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment pp. 87-105

Cui Shiqi, Ji Tieming, Li Jilong, Cheng Jianlin and Qiu Jing

A graph theoretical approach to data fusion pp. 107-122

Žurauskienė Justina, Kirk Paul D.W. and Stumpf Michael P.H.

Resistant multiple sparse canonical correlation pp. 123-138

Coleman Jacob, Replogle Joseph, Chandler Gabriel and Hardin Johanna

A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data pp. 139-150

Lin Zhixiang, Li Mingfeng, Sestan Nenad and Zhao Hongyu

AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies pp. 151-171

Emily Mathieu

Comparing five statistical methods of differential methylation identification using bisulfite sequencing data pp. 173-191

Yu Xiaoqing and Sun Shuying

Volume 15, issue 1, 2016

Identification of consistent functional genetic modules pp. 1-18

Miecznikowski Jeffrey C., Gaile Daniel P., Chen Xiwei and Tritchler David L.

Using persistent homology and dynamical distances to analyze protein binding pp. 19-38

Kovacev-Nikolic Violeta, Bubenik Peter, Nikolić Dragan and Heo Giseon

Belief propagation in genotype-phenotype networks pp. 39-53

Moharil Janhavi, May Paul, Gaile Daniel P. and Blair Rachael Hageman

HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test pp. 55-67

Sun Shuying and Yu Xiaoqing

HMM-DM: identifying differentially methylated regions using a hidden Markov model pp. 69-81

Yu Xiaoqing and Sun Shuying

MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing pp. 83-86

Mason Samuel A., Sayyid Faiz, Kirk Paul D.W., Starr Colin and Wild David L.

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.