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2024, Volume 23, Issue 1
- 1-12 Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes
by Linder Henry & Zhang Yuping & Wang Yunqi & Ouyang Zhengqing - 1-23 A CNN-CBAM-BIGRU model for protein function prediction
by Sharma Lavkush & Deepak Akshay & Ranjan Ashish & Krishnasamy Gopalakrishnan - 1-30 A heavy-tailed model for analyzing miRNA-seq raw read counts
by Krutto Annika & Haugdahl Nøst Therese & Thoresen Magne
January 2024, Volume 23, Issue 1
- 1-12 Bayesian LASSO for population stratification correction in rare haplotype association studies
by Liu Zilu & Turkmen Asuman Seda & Lin Shili - 1-13 Choice of baseline hazards in joint modeling of longitudinal and time-to-event cancer survival data
by Hari Anand & Jinto Edakkalathoor George & Dennis Divya & Krishna Kumarapillai Mohanan Nair Jagathnath & George Preethi S. & Roshni Sivasevan & Mathew Aleyamma - 1-14 Assessing the feasibility of statistical inference using synthetic antibody-antigen datasets
by Minotto Thomas & Robert Philippe A. & Hobæk Haff Ingrid & Sandve Geir K. - 1-18 A global test of hybrid ancestry from genome-scale data
by Haque Md Rejuan & Kubatko Laura - 1-22 Flexible model-based non-negative matrix factorization with application to mutational signatures
by Laursen Ragnhild & Maretty Lasse & Hobolth Asger
January 2023, Volume 22, Issue 1
- 1-5 CAT PETR: a graphical user interface for differential analysis of phosphorylation and expression data
by Flanagan Keegan & Pelech Steven & Av-Gay Yossef & Dao Duc Khanh - 1-11 A fast and efficient approach for gene-based association studies of ordinal phenotypes
by Li Nanxing & Chen Lili & Zhou Yajing & Wei Qianran - 1-13 Mediation analysis method review of high throughput data
by Han Qiang & Wang Yu & Sun Na & Chu Jiadong & Hu Wei & Shen Yueping - 1-14 Randomized singular value decomposition for integrative subtype analysis of ‘omics data’ using non-negative matrix factorization
by Ni Yonghui & He Jianghua & Chalise Prabhakar - 1-15 Improving the accuracy and internal consistency of regression-based clustering of high-dimensional datasets
by Zhang Bo & He Jianghua & Hu Jinxiang & Chalise Prabhakar & Koestler Devin C. - 1-17 Patterns of differential expression by association in omic data using a new measure based on ensemble learning
by Arevalillo Jorge M. & Martin-Arevalillo Raquel - 1-18 A Bayesian model to identify multiple expression patterns with simultaneous FDR control for a multi-factor RNA-seq experiment
by Bian Yuanyuan & He Chong & Qiu Jing - 1-20 Integrated regulatory and metabolic networks of the tumor microenvironment for therapeutic target prioritization
by Shi Tiange & Yu Han & Blair Rachael Hageman - 1-22 Accurate and fast small p-value estimation for permutation tests in high-throughput genomic data analysis with the cross-entropy method
by Shi Yang & Shi Weiping & Wang Mengqiao & Lee Ji-Hyun & Kang Huining & Jiang Hui - 1-24 When is the allele-sharing dissimilarity between two populations exceeded by the allele-sharing dissimilarity of a population with itself?
by Liu Xiran & Ahsan Zarif & Martheswaran Tarun K. & Rosenberg Noah A.
2023, Volume 22, Issue 1
- 1-18 A novel hybrid CNN and BiGRU-Attention based deep learning model for protein function prediction
by Sharma Lavkush & Deepak Akshay & Ranjan Ashish & Krishnasamy Gopalakrishnan
January 2022, Volume 21, Issue 1
- 1-10 Use of SVM-based ensemble feature selection method for gene expression data analysis
by Zhang Shizhi & Zhang Mingjin - 1-11 Challenges for machine learning in RNA-protein interaction prediction
by Arora Viplove & Sanguinetti Guido - 1-14 A robust association test with multiple genetic variants and covariates
by Lee Jen-Yu & Shen Pao-Sheng & Cheng Kuang-Fu - 1-14 pwrBRIDGE: a user-friendly web application for power and sample size estimation in batch-confounded microarray studies with dependent samples
by Xia Qing & Thompson Jeffrey A. & Koestler Devin C. - 1-19 Sparse latent factor regression models for genome-wide and epigenome-wide association studies
by Jumentier Basile & Caye Kevin & Heude Barbara & Lepeule Johanna & François Olivier - 1-20 Estimation of the covariance structure from SNP allele frequencies
by van Waaij Jan & Li Zilong & Wiuf Carsten - 1-20 Distinct characteristics of correlation analysis at the single-cell and the population level
by Wu Guoyu & Li Yuchao - 1-22 GMEPS: a fast and efficient likelihood approach for genome-wide mediation analysis under extreme phenotype sequencing
by Liyanage Janaka S. S. & Estepp Jeremie H. & Srivastava Kumar & Li Yun & Mori Motomi & Kang Guolian
December 2021, Volume 20, Issue 4-6
- 101-119 Batch effect reduction of microarray data with dependent samples using an empirical Bayes approach (BRIDGE)
by Xia Qing & Thompson Jeffrey A. & Koestler Devin C. - 121-143 Inference of genetic regulatory networks with regulatory hubs using vector autoregressions and automatic relevance determination with model selections
by Chen Chi-Kan - 145-153 Optimizing weighted gene co-expression network analysis with a multi-threaded calculation of the topological overlap matrix
by Shuai Min & He Dongmei & Chen Xin
October 2021, Volume 20, Issue 3
- 73-84 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
by Meier Richard & Nissen Emily & Koestler Devin C. - 85-100 A hierarchical Bayesian approach for detecting global microbiome associations
by Hatami Farhad & Beamish Emma & Davies Albert & Rigby Rachael & Dondelinger Frank
April 2021, Volume 20, Issue 2
- 37-49 Collocation based training of neural ordinary differential equations
by Roesch Elisabeth & Rackauckas Christopher & Stumpf Michael P. H. - 51-71 AdaReg: data adaptive robust estimation in linear regression with application in GTEx gene expressions
by Wang Meng & Jiang Lihua & Snyder Michael P.
February 2021, Volume 20, Issue 1
- 1-15 An Empirical Bayes approach for the identification of long-range chromosomal interaction from Hi-C data
by Zhang Qi & Xu Zheng & Lai Yutong - 17-36 Fine tuned exploration of evolutionary relationships within the protein universe
by Gullotto Danilo
December 2020, Volume 19, Issue 4-6
- 1-12 Combining dependent p-values by gamma distributions
by Chien Li-Chu - 1-12 Measuring evolutionary cancer dynamics from genome sequencing, one patient at a time
by Caravagna Giulio - 1-13 Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times
by Montazeri Hesam & Little Susan & Mozaffarilegha Mozhgan & Beerenwinkel Niko & DeGruttola Victor - 1-19 Inferring dynamic gene regulatory networks with low-order conditional independencies – an evaluation of the method
by Ajmal Hamda B. & Madden Michael G.
June 2020, Volume 19, Issue 3
- 1-10 Accuracy and sensitivity of different Bayesian methods for genomic prediction using simulation and real data
by Foroutaifar Saheb - 1-14 A weighted empirical Bayes risk prediction model using multiple traits
by Li Gengxin & Hou Lin & Liu Xiaoyu & Wu Cen - 1-18 Spectral dynamic causal modelling of resting-state fMRI: an exploratory study relating effective brain connectivity in the default mode network to genetics
by Nie Yunlong & Opoku Eugene & Yasmin Laila & Song Yin & Wang Jie & Wu Sidi & Scarapicchia Vanessa & Gawryluk Jodie & Wang Liangliang & Cao Jiguo & Nathoo Farouk S.
April 2020, Volume 19, Issue 2
- 1-13 Bivariate traits association analysis using generalized estimating equations in family data
by de Andrade Mariza & Mazo Lopera Mauricio A. & Duarte Nubia E. - 1-13 Bivariate traits association analysis using generalized estimating equations in family data
by de Andrade Mariza & Mazo Lopera Mauricio A. & Duarte Nubia E. - 1-18 Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset
by Tsukuda Koji & Mano Shuhei & Yamamoto Toshimichi - 1-18 Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset
by Tsukuda Koji & Mano Shuhei & Yamamoto Toshimichi - 1-33 Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching
by Jackson Samuel E. & Vernon Ian & Liu Junli & Lindsey Keith - 1-33 Understanding hormonal crosstalk in Arabidopsis root development via emulation and history matching
by Jackson Samuel E. & Vernon Ian & Liu Junli & Lindsey Keith
February 2020, Volume 19, Issue 1
- 1-11 An extended model for phylogenetic maximum likelihood based on discrete morphological characters
by Spade David A. - 1-15 Joint variable selection and network modeling for detecting eQTLs
by Cao Xuan & Ding Lili & Mersha Tesfaye B. - 1-27 Identification of supervised and sparse functional genomic pathways
by Zhang Fan & Miecznikowski Jeffrey C. & Tritchler David L.
December 2019, Volume 18, Issue 6
- 1-15 A Bayesian framework for identifying consistent patterns of microbial abundance between body sites
by Meier Richard & Thompson Jeffrey A. & Chung Mei & Zhao Naisi & Kelsey Karl T. & Michaud Dominique S. & Koestler Devin C. - 1-20 Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics
by Crook Oliver M. & Gatto Laurent & Kirk Paul D. W. - 1-23 EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples
by Madsen Tobias & Świtnicki Michał & Juul Malene & Pedersen Jakob Skou - 1-28 Determining the number of components in PLS regression on incomplete data set
by Nengsih Titin Agustin & Bertrand Frédéric & Maumy-Bertrand Myriam & Meyer Nicolas
October 2019, Volume 18, Issue 5
- 1-9 A novel individualized drug repositioning approach for predicting personalized candidate drugs for type 1 diabetes mellitus
by Zheng Hong - 1-11 Bi-level feature selection in high dimensional AFT models with applications to a genomic study
by Huang Hailin & Shangguan Jizi & Ruan Peifeng & Liang Hua - 1-14 Stability selection for lasso, ridge and elastic net implemented with AFT models
by Khan Md Hasinur Rahaman & Bhadra Anamika & Howlader Tamanna - 1-14 Clustering methods for single-cell RNA-sequencing expression data: performance evaluation with varying sample sizes and cell compositions
by Suner Aslı
August 2019, Volume 18, Issue 4
- 1-14 A penalized regression approach for DNA copy number study using the sequencing data
by Lee Jaeeun & Chen Jie - 1-20 Inference of finite mixture models and the effect of binning
by Geissen Eva-Maria & Hasenauer Jan & Radde Nicole E. - 1-25 Truncated rank correlation (TRC) as a robust measure of test-retest reliability in mass spectrometry data
by Lim Johan & Yu Donghyeon & Kuo Hsun-chih & Choi Hyungwon & Walmsley Scott - 1-40 Properties and Evaluation of the MOBIT – a novel Linkage-based Test Statistic and Quantification Method for Imprinting
by Brugger Markus & Knapp Michael & Strauch Konstantin
June 2019, Volume 18, Issue 3
- 1-13 Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies
by Liang Yulan & Kelemen Adam & Kelemen Arpad - 1-14 Combining gene expression data and prior knowledge for inferring gene regulatory networks via Bayesian networks using structural restrictions
by de Campos Luis M. & Cano Andrés & Castellano Javier G. & Moral Serafín - 1-15 Data-adaptive multi-locus association testing in subjects with arbitrary genealogical relationships
by Gong Gail & Wang Wei & Hsieh Chih-Lin & Van Den Berg David J. & Haiman Christopher & Oakley-Girvan Ingrid & Whittemore Alice S. - 1-16 netprioR: a probabilistic model for integrative hit prioritisation of genetic screens
by Schmich Fabian & Kuipers Jack & Merdes Gunter & Beerenwinkel Niko
April 2019, Volume 18, Issue 2
- 1-9 LCox: a tool for selecting genes related to survival outcomes using longitudinal gene expression data
by Sun Jiehuan & Herazo-Maya Jose D. & Wang Jane-Ling & Kaminski Naftali & Zhao Hongyu - 1-9 A powerful test for ordinal trait genetic association analysis
by Xue Yuan & Wang Jinjuan & Ding Juan & Zhang Sanguo & Li Qizhai - 1-12 Discrete Wavelet Packet Transform Based Discriminant Analysis for Whole Genome Sequences
by Huang Hsin-Hsiung & Girimurugan Senthil Balaji - 1-13 A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate
by Padayachee Trishanta & Khamiakova Tatsiana & Shkedy Ziv & Salo Perttu & Perola Markus & Burzykowski Tomasz
February 2019, Volume 18, Issue 1
- 1-6 MLML2R: an R package for maximum likelihood estimation of DNA methylation and hydroxymethylation proportions
by Kiihl Samara F. & Martinez-Garrido Maria Jose & Domingo-Relloso Arce & Bermudez Jose & Tellez-Plaza Maria - 1-13 Meta-analytic framework for modeling genetic coexpression dynamics
by Kinzy Tyler G. & Starr Timothy K. & Tseng George C. & Ho Yen-Yi - 1-13 Sliced inverse regression for integrative multi-omics data analysis
by Jain Yashita & Ding Shanshan & Qiu Jing - 1-17 Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model
by Li Xiaohong & Wu Dongfeng & Cooper Nigel G.F. & Rai Shesh N.
December 2018, Volume 17, Issue 6
- 1-11 False discovery control for penalized variable selections with high-dimensional covariates
by He Kevin & Zhou Xiang & Jiang Hui & Wen Xiaoquan & Li Yi - 1-12 A practical approach to adjusting for population stratification in genome-wide association studies: principal components and propensity scores (PCAPS)
by Zhao Huaqing & Mitra Nandita & Kanetsky Peter A. & Nathanson Katherine L. & Rebbeck Timothy R. - 1-14 A novel method to accurately calculate statistical significance of local similarity analysis for high-throughput time series
by Zhang Fang & Shan Ang & Luan Yihui
October 2018, Volume 17, Issue 5
- 1-8 Assessing genome-wide significance for the detection of differentially methylated regions
by Page Christian M. & Vos Linda & Rounge Trine B. & Harbo Hanne F. & Andreassen Bettina K. - 1-11 A test for detecting differential indirect trans effects between two groups of samples
by Chaturvedi Nimisha & Menezes Renée X. de & Goeman Jelle J. & Wieringen Wessel van - 1-14 A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data
by Perrot-Dockès Marie & Lévy-Leduc Céline & Chiquet Julien & Sansonnet Laure & Brégère Margaux & Étienne Marie-Pierre & Robin Stéphane & Genta-Jouve Grégory
August 2018, Volume 17, Issue 4
- 1-1 Editorial change at Statistical Applications in Genetics and Molecular Biology
by Krüger Torsten - 1-2 Biology challenging statistics
by Stumpf Michael P.H. - 1-12 Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization
by Huang Hsin-Hsiung & Hao Shuai & Alarcon Saul & Yang Jie - 1-13 Empirical Bayesian approach to testing multiple hypotheses with separate priors for left and right alternatives
by Bansal Naveen K. & Maadooliat Mehdi & Schrodi Steven J. - 1-14 On the relation between the true and sample correlations under Bayesian modelling of gene expression datasets
by Jacobovic Royi
June 2018, Volume 17, Issue 3
- 1-10 Non-parametric estimation of population size changes from the site frequency spectrum
by Waltoft Berit Lindum & Hobolth Asger - 1-11 A statistical method for measuring activation of gene regulatory networks
by Esteves Gustavo H. & Reis Luiz F. L. - 1-14 Bayesian inference of selection in the Wright-Fisher diffusion model
by Gory Jeffrey J. & Herbei Radu & Kubatko Laura S. - 1-21 Multi-locus data distinguishes between population growth and multiple merger coalescents
by Koskela Jere
April 2018, Volume 17, Issue 2
- 1-6 On “A mutual information estimator with exponentially decaying bias” by Zhang and Zheng
by Zhang Jialin & Chen Chen - 1-11 Noise-robust assessment of SNP array based CNV calls through local noise estimation of log R ratios
by Cosemans Nele & Claes Peter & Brison Nathalie & Vermeesch Joris Robert & Peeters Hilde - 1-18 Additive varying-coefficient model for nonlinear gene-environment interactions
by Wu Cen & Zhong Ping-Shou & Cui Yuehua
February 2018, Volume 17, Issue 1
- 1-11 Distance-correlation based gene set analysis in longitudinal studies
by Sun Jiehuan & Herazo-Maya Jose D. & Huang Xiu & Kaminski Naftali & Zhao Hongyu - 1-13 Tests for comparison of multiple endpoints with application to omics data
by Marozzi Marco - 1-28 Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting
by Dazard Jean-Eudes & Ishwaran Hemant & Mehlotra Rajeev & Weinberg Aaron & Zimmerman Peter
December 2017, Volume 16, Issue 5-6
- 291-312 Approximate maximum likelihood estimation for population genetic inference
by Bertl Johanna & Ewing Gregory & Kosiol Carolin & Futschik Andreas - 313-331 A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type
by Lakhal-Chaieb Lajmi & Greenwood Celia M.T. & Ouhourane Mohamed & Zhao Kaiqiong & Abdous Belkacem & Oualkacha Karim - 333-347 Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
by Kotoka Ekua & Orr Megan - 349-365 A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory
by Nooney Colleen & Barber Stuart & Gusnanto Arief & Gilks Walter R. - 367-386 Multivariate association between single-nucleotide polymorphisms in Alzgene linkage regions and structural changes in the brain: discovery, refinement and validation
by Szefer Elena & Lu Donghuan & Nathoo Farouk & Beg Mirza Faisal & Graham Jinko - 387-405 Bayesian estimation of differential transcript usage from RNA-seq data
by Papastamoulis Panagiotis & Rattray Magnus - 407-419 A Bayesian hierarchical model for identifying significant polygenic effects while controlling for confounding and repeated measures
by McMahan Christopher & Baurley James & Bridges William & Joyner Chase & Kacamarga Muhamad Fitra & Lund Robert & Pardamean Carissa & Pardamean Bens
September 2017, Volume 16, Issue 4
- 217-242 FC1000: normalized gene expression changes of systematically perturbed human cells
by Lönnstedt Ingrid M. & Nelander Sven - 243-257 Bayesian comparison of protein structures using partial Procrustes distance
by Ejlali Nasim & Faghihi Mohammad Reza & Sadeghi Mehdi - 259-273 Confidence intervals for heritability via Haseman-Elston regression
by Sofer Tamar - 275-289 A statistical test for detecting parent-of-origin effects when parental information is missing
by Sacco Chiara & Viroli Cinzia & Falchi Mario
August 2017, Volume 16, Issue 3
- 159-171 Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study
by Zhang Haixiang & Zheng Yinan & Yoon Grace & Zhang Zhou & Gao Tao & Joyce Brian & Zhang Wei & Schwartz Joel & Vokonas Pantel & Colicino Elena & Baccarelli Andrea & Hou Lifang & Liu Lei - 173-187 Mixture model-based association analysis with case-control data in genome wide association studies
by Ali Fadhaa & Zhang Jian - 189-198 Genetic association test based on principal component analysis
by Chen Zhongxue & Han Shizhong & Wang Kai - 199-216 Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration
by Islam Shofiqul & Anand Sonia & Hamid Jemila & Thabane Lehana & Beyene Joseph
2017, Volume 16, Issue 2
- 83-93 No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data
by Lun Aaron T. L. & Smyth Gordon K. - 107-132 Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects
by Pecanka Jakub & Goeman Jelle
April 2017, Volume 16, Issue 2
- 95-106 Missing value imputation for gene expression data by tailored nearest neighbors
by Faisal Shahla & Tutz Gerhard - 133-144 A time warping approach to multiple sequence alignment
by Arribas-Gil Ana & Matias Catherine - 145-158 A Bayesian semiparametric factor analysis model for subtype identification
by Sun Jiehuan & Warren Joshua L. & Zhao Hongyu
March 2017, Volume 16, Issue 1
- 1-12 Statistical models and computational algorithms for discovering relationships in microbiome data
by Shaikh Mateen R. & Beyene Joseph - 13-30 Binary Markov Random Fields and interpretable mass spectra discrimination
by Kong Ao & Azencott Robert - 31-45 Comparison and visualisation of agreement for paired lists of rankings
by Donald Margaret R. & Wilson Susan R. - 47-58 Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset
by Su Pei-Fang & Mau Yu-Lin & Guo Yan & Li Chung-I & Liu Qi & Boice John D. & Shyr Yu - 59-74 Generalized partial linear varying multi-index coefficient model for gene-environment interactions
by Liu Xu & Gao Bin & Cui Yuehua - 75-81 Polyunphased: an extension to polytomous outcomes of the Unphased package for family-based genetic association analysis
by Bureau Alexandre & Croteau Jordie
December 2016, Volume 15, Issue 6
- 447-471 Estimating intrinsic and extrinsic noise from single-cell gene expression measurements
by Fu Audrey Qiuyan & Pachter Lior - 473-490 Tree-based quantitative trait mapping in the presence of external covariates
by Thompson Katherine L. & Linnen Catherine R. & Kubatko Laura - 491-505 Sample size calculation based on generalized linear models for differential expression analysis in RNA-seq data
by Li Chung-I & Shyr Yu - 507-520 Adaptive input data transformation for improved network reconstruction with information theoretic algorithms
by Kannan Venkateshan & Tegner Jesper
October 2016, Volume 15, Issue 5
- 363-379 Diagnostics for assessing the linear noise and moment closure approximations
by Gillespie Colin S. & Golightly Andrew - 381-400 Search of latent periodicity in amino acid sequences by means of genetic algorithm and dynamic programming
by Pugacheva Valentina & Korotkov Alexander & Korotkov Eugene - 401-414 A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments
by Kruppa Jochen & Kramer Frank & Beißbarth Tim & Jung Klaus - 415-430 Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies
by Kakourou Alexia & Vach Werner & Nicolardi Simone & van der Burgt Yuri & Mertens Bart - 431-445 Evaluation of low-template DNA profiles using peak heights
by Steele Christopher D. & Greenhalgh Matthew & Balding David J.
August 2016, Volume 15, Issue 4
- 273-290 Bayesian state space models for dynamic genetic network construction across multiple tissues
by Liang Yulan & Kelemen Arpad - 291-304 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
by Perualila-Tan Nolen & Kasim Adetayo & Talloen Willem & Verbist Bie & Göhlmann Hinrich W.H. & QSTAR Consortium & Shkedy Ziv - 305-320 The use of vector bootstrapping to improve variable selection precision in Lasso models
by Laurin Charles & Boomsma Dorret & Lubke Gitta - 321-347 Finding causative genes from high-dimensional data: an appraisal of statistical and machine learning approaches
by Wang Chamont & Gevertz Jana L. - 349-361 LandScape: a simple method to aggregate p-values and other stochastic variables without a priori grouping
by Wiuf Carsten & Schaumburg-Müller Pallesen Jonatan & Foldager Leslie & Grove Jakob
June 2016, Volume 15, Issue 3
- 193-212 Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks
by Vinciotti Veronica & Augugliaro Luigi & Abbruzzo Antonino & Wit Ernst C. - 213-235 Testing differentially expressed genes in dose-response studies and with ordinal phenotypes
by Sweeney Elizabeth & Crainiceanu Ciprian & Gertheiss Jan - 237-251 Differential methylation tests of regulatory regions
by Ryu Duchwan & Xu Hongyan & George Varghese & Su Shaoyong & Wang Xiaoling & Shi Huidong & Podolsky Robert H. - 253-272 Sparse factor model for co-expression networks with an application using prior biological knowledge
by Blum Yuna & Houée-Bigot Magalie & Causeur David
April 2016, Volume 15, Issue 2
- 87-105 What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment
by Cui Shiqi & Ji Tieming & Li Jilong & Cheng Jianlin & Qiu Jing - 107-122 A graph theoretical approach to data fusion
by Žurauskienė Justina & Kirk Paul D.W. & Stumpf Michael P.H. - 123-138 Resistant multiple sparse canonical correlation
by Coleman Jacob & Replogle Joseph & Chandler Gabriel & Hardin Johanna - 139-150 A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
by Lin Zhixiang & Li Mingfeng & Sestan Nenad & Zhao Hongyu - 151-171 AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies
by Emily Mathieu - 173-191 Comparing five statistical methods of differential methylation identification using bisulfite sequencing data
by Yu Xiaoqing & Sun Shuying
March 2016, Volume 15, Issue 1
- 1-18 Identification of consistent functional genetic modules
by Miecznikowski Jeffrey C. & Gaile Daniel P. & Chen Xiwei & Tritchler David L. - 19-38 Using persistent homology and dynamical distances to analyze protein binding
by Kovacev-Nikolic Violeta & Bubenik Peter & Nikolić Dragan & Heo Giseon - 39-53 Belief propagation in genotype-phenotype networks
by Moharil Janhavi & May Paul & Gaile Daniel P. & Blair Rachael Hageman - 55-67 HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test
by Sun Shuying & Yu Xiaoqing - 69-81 HMM-DM: identifying differentially methylated regions using a hidden Markov model
by Yu Xiaoqing & Sun Shuying - 83-86 MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing
by Mason Samuel A. & Sayyid Faiz & Kirk Paul D.W. & Starr Colin & Wild David L.
December 2015, Volume 14, Issue 6
- 507-516 Homology cluster differential expression analysis for interspecies mRNA-Seq experiments
by Gelfond Jonathan A. & Ibrahim Joseph G. & Chen Ming-Hui & Sun Wei & Lewis Kaitlyn & Kinahan Sean & Hibbs Matthew & Buffenstein Rochelle - 517-532 Using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling
by Samb Rawane & Khadraoui Khader & Belleau Pascal & Deschênes Astrid & Lakhal-Chaieb Lajmi & Droit Arnaud - 533-549 On the validity of within-nuclear-family genetic association analysis in samples of extended families
by Bureau Alexandre & Duchesne Thierry - 551-573 An Empirical Bayes risk prediction model using multiple traits for sequencing data
by Li Gengxin & Cui Yuehua & Zhao Hongyu - 575-583 Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
by Thorne Thomas
November 2015, Volume 14, Issue 5
- 413-428 A model selection criterion for model-based clustering of annotated gene expression data
by Gallopin Mélina & Celeux Gilles & Jaffrézic Florence & Rau Andrea - 429-442 Sample size reassessment for a two-stage design controlling the false discovery rate
by Zehetmayer Sonja & Graf Alexandra C. & Posch Martin - 443-464 A robust distribution-free test for genetic association studies of quantitative traits
by Kozlitina Julia & Schucany William R. - 465-479 A parametric approach to kinship hypothesis testing using identity-by-descent parameters
by García-Magariños Manuel & Egeland Thore & López-de-Ullibarri Ignacio & Hjort Nils L. & Salas Antonio - 481-495 Likelihood ratio and score burden tests for detecting disease-associated rare variants
by Lee Woojoo & Lee Donghwan & Pawitan Yudi - 497-505 On an extended interpretation of linkage disequilibrium in genetic case-control association studies
by Dickhaus Thorsten & Stange Jens & Demirhan Haydar
August 2015, Volume 14, Issue 4
- 317-332 Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions
by Muchmore Patrick & Marjoram Paul - 333-345 Outlier reset CUSUM for the exploration of copy number alteration data
by Lai Yinglei & Gastwirth Joseph L. - 347-360 Simultaneous Bayesian analysis of contingency tables in genetic association studies
by Dickhaus Thorsten - 361-374 Modeling the next generation sequencing read count data for DNA copy number variant study
by Ji Tieming & Chen Jie - 375-389 Synonymous and nonsynonymous distances help untangle convergent evolution and recombination
by Chi Peter B. & Chattopadhyay Sujay & Lemey Philippe & Sokurenko Evgeni V. & Minin Vladimir N. - 391-411 Node sampling for protein complex estimation in bait-prey graphs
by Scholtens Denise M. & Spencer Bruce D.
June 2015, Volume 14, Issue 3
- 227-241 A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance
by McNutt Patrick & Gut Ian & Hubbard Kyle & Beske Phil - 243-252 A mutual information estimator with exponentially decaying bias
by Zhang Zhiyi & Zheng Lukun - 253-264 Bayes factors based on robust TDT-type tests for family trio design
by Yuan Min & Pan Xiaoqing & Yang Yaning - 265-277 Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies
by Li Yun & O’Connor George T. & Dupuis Josée & Kolaczyk Eric - 279-293 Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis
by Charmpi Konstantina & Ycart Bernard - 295-306 Application of the fractional-stable distributions for approximation of the gene expression profiles
by Saenko Viacheslav & Saenko Yury - 307-310 CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data
by Penfold Christopher A. & Shifaz Ahmed & Brown Paul E. & Nicholson Ann & Wild David L. - 311-316 TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
by Schimek Michael G. & Budinská Eva & Kugler Karl G. & Švendová Vendula & Ding Jie & Lin Shili
April 2015, Volume 14, Issue 2
- 113-123 Study of triplet periodicity differences inside and between genomes
by Suvorova Yulia M. & Korotkov Eugene V. - 125-141 H-CLAP: hierarchical clustering within a linear array with an application in genetics
by Ghosh Samiran & Townsend Jeffrey P. - 143-167 Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles
by Grzegorczyk Marco & Aderhold Andrej & Husmeier Dirk - 169-188 Bayesian inference for Markov jump processes with informative observations
by Golightly Andrew & Wilkinson Darren J. - 189-209 Likelihood free inference for Markov processes: a comparison
by Owen Jamie & Wilkinson Darren J. & Gillespie Colin S. - 211-219 Spatio-temporal model for multiple ChIP-seq experiments
by Ranciati Saverio & Viroli Cinzia & Wit Ernst - 221-224 GenePEN: analysis of network activity alterations in complex diseases via the pairwise elastic net
by Vlassis Nikos & Glaab Enrico - 225-225 Corrigendum to: Simple estimators of false discovery rates given as few as one or two p-values without strong parametric assumptions
by Bickel David R.
February 2015, Volume 14, Issue 1
- 1-19 A region-based multiple testing method for hypotheses ordered in space or time
by Meijer Rosa J. & Krebs Thijmen J.P. & Goeman Jelle J. - 21-34 A hidden Markov-model for gene mapping based on whole-genome next generation sequencing data
by Claesen Jürgen & Burzykowski Tomasz - 35-51 Bayesian mixed-effects model for the analysis of a series of FRAP images
by Feilke Martina & Schneider Katrin & Schmid Volker J. - 53-64 A Bayesian mixture model for chromatin interaction data
by Niu Liang & Lin Shili - 65-81 Inference for one-step beneficial mutations using next generation sequencing
by Wojtowicz Andrzej J. & Miller Craig R. & Joyce Paul - 83-92 Testing genotypes-phenotype relationships using permutation tests on association rules
by Shaikh Mateen & Beyene Joseph - 93-111 Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data
by Hou Jiayi & Archer Kellie J.
December 2014, Volume 13, Issue 6
- 633-644 When is Menzerath-Altmann law mathematically trivial? A new approach
by Ferrer-i-Cancho Ramon & Hernández-Fernández Antoni & Baixeries Jaume & Dębowski Łukasz & Mačutek Ján - 645-658 Covariate adjusted differential variability analysis of DNA methylation with propensity score method
by Kuan Pei Fen - 659-673 P-value calibration for multiple testing problems in genomics
by Ferguson John P. & Palejev Dean - 675-692 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
by Langaas Mette & Bakke Øyvind - 693-716 Markovianness and conditional independence in annotated bacterial DNA
by Hart Andrew & Martínez Servet - 717-732 Exploring homogeneity of correlation structures of gene expression datasets within and between etiological disease categories
by Jong Victor L. & Novianti Putri W. & Roes Kit C.B. & Eijkemans Marinus J.C.