Statistical Applications in Genetics and Molecular Biology

2002 - 2025

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

From De Gruyter
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Volume 24, issue 1, 2025

A fast (CNN + MCWS-transformer) based architecture for protein function prediction pp. 17

Mahala Abhipsa, Ranjan Ashish, Priyadarshini Rojalina, Vikram Raj and Dansena Prabhat

Volume 23, issue 1, 2024

Bayesian LASSO for population stratification correction in rare haplotype association studies pp. 12

Liu Zilu, Turkmen Asuman Seda and Lin Shili

Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes pp. 12

Linder Henry, Zhang Yuping, Wang Yunqi and Ouyang Zhengqing

Choice of baseline hazards in joint modeling of longitudinal and time-to-event cancer survival data pp. 13

Hari Anand, Jinto Edakkalathoor George, Dennis Divya, Krishna Kumarapillai Mohanan Nair Jagathnath, George Preethi S., Roshni Sivasevan and Mathew Aleyamma

Assessing the feasibility of statistical inference using synthetic antibody-antigen datasets pp. 14

Minotto Thomas, Robert Philippe A., Hobæk Haff Ingrid and Sandve Geir K.

Empirically adjusted fixed-effects meta-analysis methods in genomic studies pp. 14

Jayanetti Wimarsha T. and Sikdar Sinjini

A global test of hybrid ancestry from genome-scale data pp. 18

Haque Md Rejuan and Kubatko Laura

Flexible model-based non-negative matrix factorization with application to mutational signatures pp. 22

Laursen Ragnhild, Maretty Lasse and Hobolth Asger

A CNN-CBAM-BIGRU model for protein function prediction pp. 23

Sharma Lavkush, Deepak Akshay, Ranjan Ashish and Krishnasamy Gopalakrishnan

A heavy-tailed model for analyzing miRNA-seq raw read counts pp. 30

Krutto Annika, Haugdahl Nøst Therese and Thoresen Magne

Volume 22, issue 1, 2023

CAT PETR: a graphical user interface for differential analysis of phosphorylation and expression data pp. 5

Flanagan Keegan, Pelech Steven, Av-Gay Yossef and Dao Duc Khanh

A fast and efficient approach for gene-based association studies of ordinal phenotypes pp. 11

Li Nanxing, Chen Lili, Zhou Yajing and Wei Qianran

Mediation analysis method review of high throughput data pp. 13

Han Qiang, Wang Yu, Sun Na, Chu Jiadong, Hu Wei and Shen Yueping

Randomized singular value decomposition for integrative subtype analysis of ‘omics data’ using non-negative matrix factorization pp. 14

Ni Yonghui, He Jianghua and Chalise Prabhakar

Improving the accuracy and internal consistency of regression-based clustering of high-dimensional datasets pp. 15

Zhang Bo, He Jianghua, Hu Jinxiang, Chalise Prabhakar and Koestler Devin C.

Patterns of differential expression by association in omic data using a new measure based on ensemble learning pp. 17

Arevalillo Jorge M. and Martin-Arevalillo Raquel

A Bayesian model to identify multiple expression patterns with simultaneous FDR control for a multi-factor RNA-seq experiment pp. 18

Bian Yuanyuan, He Chong and Qiu Jing

A novel hybrid CNN and BiGRU-Attention based deep learning model for protein function prediction pp. 18

Sharma Lavkush, Deepak Akshay, Ranjan Ashish and Krishnasamy Gopalakrishnan

Integrated regulatory and metabolic networks of the tumor microenvironment for therapeutic target prioritization pp. 20

Shi Tiange, Yu Han and Blair Rachael Hageman

Accurate and fast small p-value estimation for permutation tests in high-throughput genomic data analysis with the cross-entropy method pp. 22

Shi Yang, Shi Weiping, Wang Mengqiao, Lee Ji-Hyun, Kang Huining and Jiang Hui

When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself? pp. 24

Liu Xiran, Ahsan Zarif, Martheswaran Tarun K. and Rosenberg Noah A.

Volume 21, issue 1, 2022

Use of SVM-based ensemble feature selection method for gene expression data analysis pp. 10

Zhang Shizhi and Zhang Mingjin

Challenges for machine learning in RNA-protein interaction prediction pp. 11

Arora Viplove and Sanguinetti Guido

A robust association test with multiple genetic variants and covariates pp. 14

Lee Jen-Yu, Shen Pao-Sheng and Cheng Kuang-Fu

pwrBRIDGE: a user-friendly web application for power and sample size estimation in batch-confounded microarray studies with dependent samples pp. 14

Xia Qing, Thompson Jeffrey A. and Koestler Devin C.

Sparse latent factor regression models for genome-wide and epigenome-wide association studies pp. 19

Jumentier Basile, Caye Kevin, Heude Barbara, Lepeule Johanna and François Olivier

Distinct characteristics of correlation analysis at the single-cell and the population level pp. 20

Wu Guoyu and Li Yuchao

Estimation of the covariance structure from SNP allele frequencies pp. 20

Jan van Waaij, Li Zilong and Wiuf Carsten

GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing pp. 22

Liyanage Janaka S. S., Estepp Jeremie H., Srivastava Kumar, Li Yun, Mori Motomi and Kang Guolian

Volume 20, issue 4-6, 2021

Batch effect reduction of microarray data with dependent samples using an empirical Bayes approach (BRIDGE) pp. 101-119

Xia Qing, Thompson Jeffrey A. and Koestler Devin C.

Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections pp. 121-143

Chen Chi-Kan

Optimizing weighted gene co-expression network analysis with a multi-threaded calculation of the topological overlap matrix pp. 145-153

Shuai Min, He Dongmei and Chen Xin

Volume 20, issue 3, 2021

Low variability in the underlying cellular landscape adversely affects the performance of interaction-based approaches for conducting cell-specific analyses of DNA methylation in bulk samples pp. 73-84

Meier Richard, Nissen Emily and Koestler Devin C.

A hierarchical Bayesian approach for detecting global microbiome associations pp. 85-100

Hatami Farhad, Beamish Emma, Davies Albert, Rigby Rachael and Dondelinger Frank

Volume 20, issue 2, 2021

Collocation based training of neural ordinary differential equations pp. 37-49

Roesch Elisabeth, Rackauckas Christopher and Stumpf Michael P. H.

AdaReg: data adaptive robust estimation in linear regression with application in GTEx gene expressions pp. 51-71

Wang Meng, Jiang Lihua and Snyder Michael P.

Volume 20, issue 1, 2021

An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data pp. 1-15

Zhang Qi, Xu Zheng and Lai Yutong

Fine tuned exploration of evolutionary relationships within the protein universe pp. 17-36

Gullotto Danilo

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, Little Susan, Mozaffarilegha Mozhgan, 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, Opoku Eugene, Yasmin Laila, Song Yin, Wang Jie, Wu Sidi, Scarapicchia Vanessa, Gawryluk Jodie, Wang Liangliang, Cao Jiguo and Nathoo Farouk S.

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.

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

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

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.