Statistical Applications in Genetics and Molecular Biology

2002 - 2020

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

From De Gruyter
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Volume 19, issue 4-6, 2020

Combining dependent p-values by gamma distributions pp. 12

Chien Li-Chu

Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time pp. 12

Caravagna Giulio

Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times pp. 13

Montazeri Hesam, Mozaffarilegha Mozhgan, Little Susan, Beerenwinkel Niko and DeGruttola Victor

Inferring dynamic gene regulatory networks with low-order conditional independencies – an evaluation of the method pp. 19

Ajmal Hamda B. and Madden Michael G.

Volume 19, issue 3, 2020

Accuracy and sensitivity of different Bayesian methods for genomic prediction using simulation and real data pp. 10

Foroutaifar Saheb

A weighted empirical Bayes risk prediction model using multiple traits pp. 14

Li Gengxin, Hou Lin, Liu Xiaoyu and Wu Cen

Spectral dynamic causal modelling of resting-state fMRI: an exploratory study relating effective brain connectivity in the default mode network to genetics pp. 18

Nie Yunlong, Wang Jie, Wu Sidi, Wang Liangliang, Cao Jiguo, Opoku Eugene, Yasmin Laila, Song Yin, Nathoo Farouk S., Scarapicchia Vanessa and Gawryluk Jodie

Volume 19, issue 2, 2020

Bivariate traits association analysis using generalized estimating equations in family data pp. 13

Mariza de Andrade, Mazo Lopera Mauricio A. and Duarte Nubia E.

Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset pp. 18

Tsukuda Koji, Mano Shuhei and Yamamoto Toshimichi

Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching pp. 33

Jackson Samuel E., Vernon Ian, Liu Junli and Lindsey Keith

Volume 19, issue 1, 2020

An extended model for phylogenetic maximum likelihood based on discrete morphological characters pp. 11

Spade David A.

Joint variable selection and network modeling for detecting eQTLs pp. 15

Cao Xuan, Ding Lili and Mersha Tesfaye B.

Identification of supervised and sparse functional genomic pathways pp. 27

Zhang Fan, Miecznikowski Jeffrey C. and Tritchler David L.

Volume 18, issue 6, 2019

A Bayesian framework for identifying consistent patterns of microbial abundance between body sites pp. 15

Meier Richard, Thompson Jeffrey A., Koestler Devin C., Chung Mei, Zhao Naisi, Michaud Dominique S. and Kelsey Karl T.

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics pp. 20

Crook Oliver M., Gatto Laurent and Kirk Paul D. W.

EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples pp. 23

Madsen Tobias, Świtnicki Michał, Juul Malene and Pedersen Jakob Skou

Determining the number of components in PLS regression on incomplete data set pp. 28

Nengsih Titin Agustin, Bertrand Frédéric, Maumy-Bertrand Myriam and Meyer Nicolas

Volume 18, issue 5, 2019

A novel individualized drug repositioning approach for predicting personalized candidate drugs for type 1 diabetes mellitus pp. 9

Zheng Hong

Bi-level feature selection in high dimensional AFT models with applications to a genomic study pp. 11

Huang Hailin, Shangguan Jizi, Ruan Peifeng and Liang Hua

Stability selection for lasso, ridge and elastic net implemented with AFT models pp. 14

Khan Md Hasinur Rahaman, Bhadra Anamika and Howlader Tamanna

Clustering methods for single-cell RNA-sequencing expression data: performance evaluation with varying sample sizes and cell compositions pp. 14

Suner Aslı

Volume 18, issue 4, 2019

A penalized regression approach for DNA copy number study using the sequencing data pp. 14

Lee Jaeeun and Chen Jie

Inference of finite mixture models and the effect of binning pp. 20

Geissen Eva-Maria, Hasenauer Jan and Radde Nicole E.

Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data pp. 25

Lim Johan, Yu Donghyeon, Kuo Hsun-chih, Choi Hyungwon and Walmsley Scott

Properties and Evaluation of the MOBIT – a novel Linkage-based Test Statistic and Quantification Method for Imprinting pp. 40

Brugger Markus, Strauch Konstantin and Knapp Michael

Volume 18, issue 3, 2019

Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies pp. 13

Liang Yulan, Kelemen Adam and Kelemen Arpad

Combining gene expression data and prior knowledge for inferring gene regulatory networks via Bayesian networks using structural restrictions pp. 14

M. de Campos Luis, Cano Andrés, Castellano Javier G. and Moral Serafín

Data-adaptive multi-locus association testing in subjects with arbitrary genealogical relationships pp. 15

Gong Gail, Wang Wei, Whittemore Alice S., Hsieh Chih-Lin, J. Van Den Berg David, Haiman Christopher and Oakley-Girvan Ingrid

netprioR: a probabilistic model for integrative hit prioritisation of genetic screens pp. 16

Schmich Fabian, Kuipers Jack, Merdes Gunter and Beerenwinkel Niko

Volume 18, issue 2, 2019

LCox: a tool for selecting genes related to survival outcomes using longitudinal gene expression data pp. 9

Sun Jiehuan, Herazo-Maya Jose D., Kaminski Naftali, Wang Jane-Ling and Zhao Hongyu

A powerful test for ordinal trait genetic association analysis pp. 9

Xue Yuan, Zhang Sanguo, Wang Jinjuan, Ding Juan and Li Qizhai

Discrete Wavelet Packet Transform Based Discriminant Analysis for Whole Genome Sequences pp. 12

Huang Hsin-Hsiung and Girimurugan Senthil Balaji

A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate pp. 13

Padayachee Trishanta, Khamiakova Tatsiana, Shkedy Ziv, Burzykowski Tomasz, Salo Perttu and Perola Markus

Volume 18, issue 1, 2019

MLML2R: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions pp. 6

Kiihl Samara F., Martinez-Garrido Maria Jose, Domingo-Relloso Arce, Bermudez Jose and Tellez-Plaza Maria

Meta-analytic framework for modeling genetic coexpression dynamics pp. 13

Kinzy Tyler G., Starr Timothy K., Tseng George C. and Ho Yen-Yi

Sliced inverse regression for integrative multi-omics data analysis pp. 13

Jain Yashita, Ding Shanshan and Qiu Jing

Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model pp. 17

Li Xiaohong, Wu Dongfeng, Rai Shesh N. and Cooper Nigel G.F.

Volume 17, issue 6, 2018

False discovery control for penalized variable selections with high-dimensional covariates pp. 11

He Kevin, Zhou Xiang, Jiang Hui, Wen Xiaoquan and Li Yi

A practical approach to adjusting for population stratification in genome-wide association studies: principal components and propensity scores (PCAPS) pp. 12

Zhao Huaqing, Mitra Nandita, Kanetsky Peter A., Nathanson Katherine L. and Rebbeck Timothy R.

A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series pp. 14

Zhang Fang, Shan Ang and Luan Yihui

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