Statistical Applications in Genetics and Molecular Biology

2002 - 2018

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

From De Gruyter
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Volume 17, issue 5, 2018

Assessing genome-wide significance for the detection of differentially methylated regions pp. 8

Page Christian M., Harbo Hanne F., Vos Linda, Rounge Trine B. and Andreassen Bettina K.

A test for detecting differential indirect trans effects between two groups of samples pp. 11

Chaturvedi Nimisha, Menezes Renée X. de, Wieringen Wessel van and Goeman Jelle J.

A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data pp. 14

Perrot-Dockès Marie, Lévy-Leduc Céline, Chiquet Julien, Sansonnet Laure, Brégère Margaux, Étienne Marie-Pierre, Robin Stéphane and Genta-Jouve Grégory

Volume 17, issue 4, 2018

Editorial change at Statistical Applications in Genetics and Molecular Biology pp. 1

Krüger Torsten

Biology challenging statistics pp. 2

Stumpf Michael P.H.

Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization pp. 12

Huang Hsin-Hsiung, Hao Shuai, Alarcon Saul and Yang Jie

Empirical Bayesian approach to testing multiple hypotheses with separate priors for left and right alternatives pp. 13

Bansal Naveen K., Maadooliat Mehdi and Schrodi Steven J.

On the relation between the true and sample correlations under Bayesian modelling of gene expression datasets pp. 14

Jacobovic Royi

Volume 17, issue 3, 2018

Non-parametric estimation of population size changes from the site frequency spectrum pp. 10

Waltoft Berit Lindum and Hobolth Asger

A statistical method for measuring activation of gene regulatory networks pp. 11

Esteves Gustavo H. and Reis Luiz F. L.

Bayesian inference of selection in the Wright-Fisher diffusion model pp. 14

Gory Jeffrey J., Herbei Radu and Kubatko Laura S.

Multi-locus data distinguishes between population growth and multiple merger coalescents pp. 21

Koskela Jere

Volume 17, issue 2, 2018

On “A mutual information estimator with exponentially decaying bias” by Zhang and Zheng pp. 6

Zhang Jialin and Chen Chen

Noise-robust assessment of SNP array based CNV calls through local noise estimation of log R ratios pp. 11

Cosemans Nele, Brison Nathalie, Vermeesch Joris Robert, Claes Peter and Peeters Hilde

Additive varying-coefficient model for nonlinear gene-environment interactions pp. 18

Wu Cen, Zhong Ping-Shou and Cui Yuehua

Volume 17, issue 1, 2018

Distance-correlation based gene set analysis in longitudinal studies pp. 11

Sun Jiehuan, Zhao Hongyu, Herazo-Maya Jose D., Kaminski Naftali and Huang Xiu

Tests for comparison of multiple endpoints with application to omics data pp. 13

Marozzi Marco

Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting pp. 28

Dazard Jean-Eudes, Ishwaran Hemant, Mehlotra Rajeev, Zimmerman Peter and Weinberg Aaron

Volume 16, issue 5-6, 2017

Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes pp. 291-312

Kotoka Ekua and Orr Megan

A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory pp. 313-331

Nooney Colleen, Barber Stuart, Gusnanto Arief and Gilks Walter R.

A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type pp. 333-347

Lakhal-Chaieb Lajmi, Greenwood Celia M.T., Ouhourane Mohamed, Zhao Kaiqiong, Abdous Belkacem and Oualkacha Karim

Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation pp. 349-365

Szefer Elena, Graham Jinko, Lu Donghuan, Beg Mirza Faisal and Nathoo Farouk

Bayesian estimation of differential transcript usage from RNA-seq data pp. 367-386

Papastamoulis Panagiotis and Rattray Magnus

Approximate maximum likelihood estimation for population genetic inference pp. 387-405

Bertl Johanna, Ewing Gregory, Kosiol Carolin and Futschik Andreas

A Bayesian hierarchical model for identifying significant polygenic effects while controlling for confounding and repeated measures pp. 407-419

McMahan Christopher, Bridges William, Joyner Chase, Lund Robert, Baurley James, Kacamarga Muhamad Fitra, Pardamean Carissa and Pardamean Bens

Volume 16, issue 4, 2017

FC1000: normalized gene expression changes of systematically perturbed human cells pp. 217-242

Lönnstedt Ingrid M. and Nelander Sven

Bayesian comparison of protein structures using partial Procrustes distance pp. 243-257

Ejlali Nasim, Faghihi Mohammad Reza and Sadeghi Mehdi

Confidence intervals for heritability via Haseman-Elston regression pp. 259-273

Sofer Tamar

A statistical test for detecting parent-of-origin effects when parental information is missing pp. 275-289

Sacco Chiara, Viroli Cinzia and Falchi Mario

Volume 16, issue 3, 2017

Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study pp. 159-171

Zhang Haixiang, Zheng Yinan, Zhang Zhou, Gao Tao, Joyce Brian, Zhang Wei, Hou Lifang, Liu Lei, Yoon Grace, Schwartz Joel, Vokonas Pantel, Colicino Elena and Baccarelli Andrea

Mixture model-based association analysis with case-control data in genome wide association studies pp. 173-187

Ali Fadhaa and Zhang Jian

Genetic association test based on principal component analysis pp. 189-198

Chen Zhongxue, Han Shizhong and Wang Kai

Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration pp. 199-216

Islam Shofiqul, Anand Sonia, Thabane Lehana, Hamid Jemila and Beyene Joseph

Volume 16, issue 2, 2017

Missing value imputation for gene expression data by tailored nearest neighbors pp. 95-106

Faisal Shahla and Tutz Gerhard

A time warping approach to multiple sequence alignment pp. 133-144

Arribas-Gil Ana and Matias Catherine

A Bayesian semiparametric factor analysis model for subtype identification pp. 145-158

Sun Jiehuan, Warren Joshua L. and Zhao Hongyu

Volume 16, issue 1, 2017

Statistical models and computational algorithms for discovering relationships in microbiome data pp. 1-12

Shaikh Mateen R. and Beyene Joseph

Binary Markov Random Fields and interpretable mass spectra discrimination pp. 13-30

Kong Ao and Azencott Robert

Comparison and visualisation of agreement for paired lists of rankings pp. 31-45

Donald Margaret R. and Wilson Susan R.

Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset pp. 47-58

Su Pei-Fang, Mau Yu-Lin, Li Chung-I, Guo Yan, Liu Qi, Shyr Yu and Boice John D.

Generalized partial linear varying multi-index coefficient model for gene-environment interactions pp. 59-74

Liu Xu, Gao Bin and Cui Yuehua

Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis pp. 75-81

Bureau Alexandre and Croteau Jordie

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, Jung Klaus, Kramer Frank and Beißbarth Tim

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

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

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

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