Statistical Applications in Genetics and Molecular Biology Short Title: Stat. Appl. Genet. Mol. Biol. Publisher: De Gruyter, Berlin ISSN: 2194-6302; 1544-6115/e Online: http://www.degruyter.com/view/j/sagmb Comments: Journal; Published electronic only from 1 (2002) - 11 (2012). Documents Indexed: 571 Publications (since 2002) References Indexed: 218 Publications with 7,839 References. all top 5 Latest Issues 22, No. 1 (2023) 21, No. 1 (2022) 20, No. 4-6 (2021) 20, No. 3 (2021) 20, No. 2 (2021) 20, No. 1 (2021) 19, No. 4-6 (2020) 19, No. 3 (2020) 19, No. 2 (2020) 19, No. 1 (2020) 18, No. 6 (2019) 18, No. 5 (2019) 18, No. 4 (2019) 18, No. 3 (2019) 18, No. 2 (2019) 18, No. 1 (2019) 17, No. 6 (2018) 17, No. 5 (2018) 17, No. 4 (2018) 17, No. 3 (2018) 17, No. 2 (2018) 17, No. 1 (2018) 16, No. 5-6 (2017) 16, No. 4 (2017) 16, No. 3 (2017) 16, No. 2 (2017) 16, No. 1 (2017) 15, No. 6 (2016) 15, No. 5 (2016) 15, No. 4 (2016) 15, No. 3 (2016) 15, No. 2 (2016) 15, No. 1 (2016) 14, No. 6 (2015) 14, No. 5 (2015) 14, No. 4 (2015) 14, No. 3 (2015) 14, No. 2 (2015) 14, No. 1 (2015) 13, No. 6 (2014) 13, No. 5 (2014) 13, No. 4 (2014) 13, No. 3 (2014) 13, No. 2 (2014) 13, No. 1 (2014) 12, No. 4 (2013) 11, No. 6 (2012) 11, No. 5 (2012) 11, No. 4 (2012) 11, No. 3 (2012) 11, No. 2 (2012) 11, No. 1 (2012) 10, No. 1 (2011) 9, No. 1 (2010) 8, No. 1 (2009) 7, No. 2 (2008) 7, No. 1 (2008) 6, No. 1 (2007) 5, No. 1 (2006) 4, No. 1 (2005) 3, No. 1 (2004) 2, No. 1 (2003) 1, No. 1 (2002) all top 5 Authors 19 Van der Laan, Mark Johannes 7 Bickel, David R. 7 Wu, Rongling 6 Beyene, Joseph 6 Burzykowski, Tomasz 6 Dudoit, Sandrine 6 Husmeier, Dirk 6 Segal, Mark Robert 6 Zhao, Hongyu 5 Cui, Yuehua 5 Hubbard, Alan E. 5 Keles, Sunduz 5 Koestler, Devin C. 5 Pollard, Katherine S. 5 Shkedy, Ziv 5 Tritchler, David L. 4 Beerenwinkel, Niko 4 Doerge, Rebecca W. 4 Elston, Robert Claude 4 Finch, Stephen J. 4 Gilks, Walter R. 4 Goeman, Jelle J. 4 Gordon, Derek 4 Joyce, Paul 4 Marjoram, Paul 4 Miecznikowski, Jeffrey C. 4 Sinisi, Sandra E. 4 Smyth, Gordon K. 4 Tibshirani, Robert John 4 Wilson, Susan R. 3 Arribas-Gil, Ana 3 Bagos, Pantelis G. 3 Birkner, Merrill D. 3 Burden, Conrad John 3 Casella, George 3 Corander, Jukka 3 Degruttola, Victor G. 3 Dickhaus, Thorsten 3 Futschik, Andreas 3 Gaile, Daniel P. 3 Gentleman, Robert 3 Graham, Jinko 3 Grzegorczyk, Marco A. 3 Gu, Hong 3 Hobolth, Asger 3 Jaffrézic, Florence 3 Ji, Tieming 3 Kechris, Katherina J. 3 Kelemen, Arpad G. 3 Kirk, Paul D. W. 3 Kubatko, Laura Salter 3 Labbe, Aurelie 3 Laird, Nan McKenzie 3 Lengauer, Thomas 3 Liang, Yulan 3 Lim, Johan 3 Lin, Dan 3 Lin, Shili 3 Lucas, Joseph Edward 3 McNeney, Brad 3 Nerman, Olle 3 Nuel, Gregory 3 Nye, Tom M. W. 3 Pachter, Lior 3 Parmigiani, Giovanni 3 Pawitan, Yudi 3 Polley, Eric C. 3 Rattray, Magnus 3 Robin, Stéphane 3 Rudemo, Mats 3 Shin, Ji-Hyung 3 Sun, Jiehuan 3 Sun, Shuying 3 Thompson, Jeffrey A. 3 van Sanden, Suzy 3 van Wieringen, Wessel N. 3 Vingron, Martin 3 Wilkinson, Darren James 3 Yang, Yaning 3 Yu, Xiaoqing 2 Aderhold, Andrej 2 Ahn, Kwangmi 2 Almudevar, Anthony 2 Balding, David Joseph 2 Berg, Arthur 2 Berkhof, Johannes 2 Besse, Philippe C. 2 Bijnens, Luc 2 Billingham, Lucinda J. 2 Binder, Harald 2 Bogdan, Małgorzata 2 Booth, James G. 2 Boulesteix, Anne-Laure Isabeau 2 Boys, Richard J. 2 Bureau, Alexandre 2 Cao, Kim-Anh Lê 2 Chalise, Prabhakar 2 Chang, Myron N. 2 Chen, Jie 2 Chen, Sining ...and 1,302 more Authors all top 5 Fields 523 Biology and other natural sciences (92-XX) 370 Statistics (62-XX) 32 Probability theory and stochastic processes (60-XX) 18 Numerical analysis (65-XX) 11 Computer science (68-XX) 6 Combinatorics (05-XX) 2 Operations research, mathematical programming (90-XX) 2 Information and communication theory, circuits (94-XX) 1 General and overarching topics; collections (00-XX) 1 Ordinary differential equations (34-XX) 1 Systems theory; control (93-XX) Publications by Year all cited Publications top 5 cited Publications Citations contained in zbMATH Open 272 Publications have been cited 1,374 times in 1,086 Documents Cited by ▼ Year ▼ Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Zbl 1038.62110 Smyth, Gordon K. 95 2004 Super learner. Zbl 1166.62387 Van der Laan, Mark J.; Polley, Eric C.; Hubbard, Alan E. 73 2007 Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Zbl 1166.62379 Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S. 46 2004 A general framework for weighted gene co-expression network analysis. Zbl 1077.92042 Zhang, Bin; Horvath, Steve 42 2005 Error distribution for gene expression data. Zbl 1083.62114 Purdom, Elizabeth; Holmes, Susan P. 35 2005 Approximately sufficient statistics and Bayesian computation. Zbl 1276.62077 Joyce, Paul; Marjoram, Paul 34 2008 Sparse canonical correlation analysis with application to genomic data integration. Zbl 1276.92071 Parkhomenko, Elena; Tritchler, David; Beyene, Joseph 31 2009 Permutation \(p\)-values should never be zero: calculating exact \(p\)-values when permutations are randomly drawn. Zbl 1304.92098 Phipson, Belinda; Smyth, Gordon K. 25 2010 Multiple testing. I: Single-step procedures for control of general type I error rates. Zbl 1166.62338 Dudoit, Sandrine; Van der Laan, Mark J.; Pollard, Katherine S. 25 2004 Extensions of sparse canonical correlation analysis with applications to genomic data. Zbl 1276.62099 Witten, Daniela M.; Tibshirani, Robert J. 23 2009 Univariate shrinkage in the Cox model for high dimensional data. Zbl 1276.62096 Tibshirani, Robert J. 22 2009 On optimal selection of summary statistics for approximate Bayesian computation. Zbl 1304.92047 Nunes, Matthew A.; Balding, David J. 20 2010 A sparse PLS for variable selection when integrating omics data. Zbl 1276.62061 Cao, Kim-Anh Lê; Rossouw, Debra; Robert-Granié, Christèle; Besse, Philippe 19 2008 Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis. Zbl 1276.92077 Waaijenborg, Sandra; Verselewel de Witt Hamer, Philip C.; Zwinderman, Aeilko H. 18 2008 Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Zbl 1166.62361 Opgen-Rhein, Rainer; Strimmer, Korbinian 18 2007 FADO: a statistical method to detect favored or avoided distances between occurrences of motifs using the Hawkes’ model. Zbl 1095.62126 Gusto, Gaelle; Schbath, Sophie 17 2005 A generalized Sidak-Holm procedure and control of generalized error rates under independence. Zbl 1166.62316 Guo, Wenge; Romano, Joseph 17 2007 Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge. Zbl 1166.62373 Werhli, Adriano V.; Husmeier, Dirk 16 2007 Low-order conditional independence graphs for inferring genetic networks. Zbl 1166.62374 Wille, Anja; Bühlmann, Peter 15 2006 Combining results of microarray experiments: A rank aggregation approach. Zbl 1166.92306 Deconde, Robert P.; Hawley, Sarah; Falcon, Seth; Clegg, Nigel; Knudsen, Beatrice; Etzioni, Ruth 15 2006 Asymptotic optimality of likelihood-based cross-validation. Zbl 1038.62040 Van der Laan, Mark J.; Dudoit, Sandrine; Keles, Sunduz 14 2004 A method to increase the power of multiple testing procedures through sample splitting. Zbl 1166.62318 Rubin, Daniel; Dudoit, Sandrine; Van der Laan, Mark 14 2006 How to analyze many contingency tables simultaneously in genetic association studies. Zbl 1296.92027 Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi 13 2012 Classifying gene expression profiles from pairwise m{RNA} comparisons. Zbl 1072.62107 Geman, Donald; d’Avignon, Christian; Naiman, Daniel Q.; Winslow, Raimond L. 13 2004 Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380 Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon 13 2016 Adapting prediction error estimates for biased complexity selection in high-dimensional bootstrap samples. Zbl 1276.62060 Binder, Harald; Schumacher, Martin 13 2008 Importance sampling for the infinite sites model. Zbl 1276.62074 Hobolth, Asger; Uyenoyama, Marcy K.; Wiuf, Carsten 12 2008 Deletion/substitution/addition algorithm in learning with applications in genomics. Zbl 1166.62368 Sinisi, Sandra E.; Van der Laan, Mark J. 11 2004 Graph selection with GGMselect. Zbl 1296.92110 Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas 10 2012 Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089 Golightly, Andrew; Wilkinson, Darren J. 10 2015 Dimension reduction for classification with gene expression microarray data. Zbl 1166.62337 Dai, Jian J.; Lieu, Linh; Rocke, David 10 2006 Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065 Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P. 9 2014 A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Zbl 1296.92039 Grzegorczyk, Marco; Husmeier, Dirk 9 2012 Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions. Zbl 1311.62109 Bickel, David R. 9 2013 Space oriented rank-based data integration. Zbl 1304.92094 Lin, Shili 9 2010 Multiple testing. II: Step-down procedures for control of the family-wise error rate. Zbl 1166.62378 Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S. 9 2004 P{LS} dimension reduction for classification with microarray data. Zbl 1086.62119 Boulesteix, Anne-Laure 9 2004 Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Zbl 1296.92032 Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes 8 2014 Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045 Lee, Woojoo; Lee, Donghwan; Lee, Youngjo; Pawitan, Yudi 8 2011 Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018 Bickel, David R. 8 2012 Statistical inference in evolutionary models of DNA sequences via the EM algorithm. Zbl 1081.62094 Hobolth, Asger; Jensen, Jens Ledet 8 2005 Score statistics for mapping quantitative trait loci. Zbl 1276.62062 Chang, Myron N.; Wu, Rongling; Wu, Samuel S.; Casella, George 8 2009 TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008 Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili 7 2015 Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011 Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco 7 2014 Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079 Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S. 7 2015 Optimal tests shrinking both means and variances applicable to microarray data analysis. Zbl 1304.92044 Hwang, J. T. Gene; Liu, Peng 7 2010 Empirical Bayes estimation of a sparse vector of gene expression changes. Zbl 1081.62093 Erickson, Stephen; Sabatti, Chiara 7 2005 Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives. Zbl 1108.62303 Van der Laan, Mark J.; Birkner, Merrill D.; Hubbard, Alan E. 7 2005 Transformations for cDNA microarray data. Zbl 1038.92015 Cui, Xiangqin; Kathleen, M.; Kerr, Churchill; Gary, A. 7 2003 Survival analysis with high-dimensional covariates: an application in microarray studies. Zbl 1276.62067 Engler, David; Li, Yi 7 2009 Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063 Padilla, Marta; Bickel, David R. 6 2012 Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Zbl 1296.92187 Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.; Smyth, Gordon K. 6 2012 High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082 Zuber, Verena; Strimmer, Korbinian 6 2011 Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034 Francois, Olivier; Laval, Guillaume 6 2011 Sparse partial least squares classification for high dimensional data. Zbl 1304.92041 Chung, Dongjun; Keles, Sunduz 6 2010 BayesMendel: an R environment for Mendelian risk prediction. Zbl 1077.92029 Chen, Sining; Wang, Wenyi; Broman, Karl W.; Katki, Hormuzd A.; Parmigiani, Giovanni 6 2004 Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods. Zbl 1276.92033 Zucknick, Manuela; Richardson, Sylvia; Stronach, Euan A. 6 2008 Hypothesis tests for point-mass mixture data with application to ’omics data with many zero values. Zbl 1276.92074 Taylor, Sandra; Pollard, Katherine 6 2009 Numerical solutions for patterns statistics on Markov chains. Zbl 1166.62324 Nuel, Gregory 6 2006 Sparse logistic regression with \(L_p\) penalty for biomarker identification. Zbl 1166.62314 Liu, Zhenqiu; Jiang, Feng; Tian, Guoliang; Wang, Suna; Sato, Fumiaki; Meltzer, Stephen J.; Tan, Ming 6 2007 Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085 Charmpi, Konstantina; Ycart, Bernard 5 2015 Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043 Jung, Hsuan; Marjoram, Paul 5 2011 The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Zbl 1296.92026 Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; Chang, Jeff H. 5 2011 Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression. Zbl 1304.92046 Montazeri, Zahra; Yanofsky, Corey M.; Bickel, David R. 5 2010 HMM-DM: identifying differentially methylated regions using a hidden Markov model. Zbl 1343.92180 Yu, Xiaoqing; Sun, Shuying 5 2016 Structure learning in nested effects models. Zbl 1276.92075 Tresch, Achim; Markowetz, Florian 5 2008 Adaptive choice of the number of bootstrap samples in large scale multiple testing. Zbl 1276.62072 Guo, Wenge; Peddada, Shyamal 5 2008 Modeling DNA methylation in a population of cancer cells. Zbl 1276.92092 Siegmund, Kimberly D.; Marjoram, Paul; Shibata, Darryl 5 2008 Detecting outlier samples in microarray data. Zbl 1276.62092 Shieh, Albert D.; Hung, Yeung Sam 5 2009 Super learning: an application to the prediction of HIV-1 drug resistance. Zbl 1166.92315 Sinisi, Sandra E.; Polley, Eric C.; Petersen, Maya L.; Rhee, Soo-Yon; Van der Laan, Mark J. 5 2007 Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207 Koskela, Jere 4 2018 Weighted lasso with data integration. Zbl 1296.92017 Bergersen, Linn Cecilie; Glad, Ingrid K.; Lyng, Heidi 4 2011 A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139 Auer, Paul L.; Doerge, Rebecca W. 4 2011 Analyzing time-course microarray data using functional data analysis – a review. Zbl 1296.92025 Coffey, Norma; Hinde, John 4 2011 Stopping-time resampling and population genetic inference under coalescent models. Zbl 1296.92158 Jenkins, Paul A. 4 2012 The beta-binomial SGoF method for multiple dependent tests. Zbl 1296.92084 de Uña-Alvarez, Jacobo 4 2012 Weighted-LASSO for structured network inference from time course data. Zbl 1304.92085 Charbonnier, Camille; Chiquet, Julien; Ambroise, Christophe 4 2010 A random coefficients model for regional co-expression associated with DNA copy number. Zbl 1304.92064 van Wieringen, Wessel N.; Berkhof, Johannes; van de Wiel, Mark A. 4 2010 Buckley-James boosting for survival analysis with high-dimensional biomarker data. Zbl 1304.92101 Wang, Zhu; Wang, C. Y. 4 2010 Statistical significance threshold criteria for analysis of microarray gene expression data. Zbl 1166.62335 Cheng, Cheng; Pounds, Stanley B.; Boyett, James M.; Pei, Deqing; Kuo, Mei-Ling; Roussel, Martine F. 4 2004 Reproducible research: a bioinformatics case study. Zbl 1138.92300 Gentleman, Robert 4 2005 Drifting Markov models with polynomial drift and applications to DNA sequences. Zbl 1276.92095 Vergne, Nicolas 4 2008 A Bayesian analysis strategy for cross-study translation of gene expression biomarkers. Zbl 1276.92066 Lucas, Joseph; Carvalho, Carlos; West, Mike 4 2009 Weighted multiple hypothesis testing procedures. Zbl 1276.62078 Kang, Guolian; Ye, Keying; Liu, Nianjun; Allison, David B.; Gao, Guimin 4 2009 Estimation of selection intensity under overdominance by Bayesian methods. Zbl 1276.92050 Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid 4 2009 A new type of stochastic dependence revealed in gene expression data. Zbl 1166.92309 Klebanov, Lev; Jordan, Craig; Yakovlev, Andrei 4 2006 Detecting local high-scoring segments: a first-stage approach for genome-wide association studies. Zbl 1166.62341 Guedj, Mickael; Robelin, David; Hoebeke, Mark; Lamarine, Marc; Wojcik, Jérôme; Nuel, Gregory 4 2006 A Bayesian approach to estimation and testing in time-course microarray experiments. Zbl 1166.62327 Angelini, Claudia; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna 4 2007 A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007 Meijer, Rosa J.; Krebs, Thijmen J. P.; Goeman, Jelle J. 3 2015 Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017 Ji, Tieming; Chen, Jie 3 2015 A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type. Zbl 1396.92060 Lakhal-Chaieb, Lajmi; Greenwood, Celia M. T.; Ouhourane, Mohamed; Zhao, Kaiqiong; Abdous, Belkacem; Oualkacha, Karim 3 2017 Additive varying-coefficient model for nonlinear gene-environment interactions. Zbl 1398.92163 Wu, Cen; Zhong, Ping-Shou; Cui, Yuehua 3 2018 A penalized regression approach for DNA copy number study using the sequencing data. Zbl 1420.92085 Lee, Jaeeun; Chen, Jie 3 2019 Unsupervised classification for tiling arrays: chip-chip and transcriptome. Zbl 1296.92105 Bérard, Caroline; Martin-Magniette, Marie-Laure; Brunaud, Véronique; Aubourg, Sébastien; Robin, Stéphane 3 2011 On the statistical properties of SGoF multitesting method. Zbl 1296.92083 de Uña-Alvarez, Jacobo 3 2011 Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Zbl 1296.92053 Mayer, Claus-Dieter; Lorent, Julie; Horgan, Graham W. 3 2011 Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Zbl 1296.92072 Silver, Matt; Montana, Giovanni; Alzheimer’s Disease Neuroimaging Initiative 3 2012 Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044 Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris 3 2012 An integrated hierarchical Bayesian model for multivariate eQTL mapping. Zbl 1296.92071 Scott-Boyer, Marie Pier; Imholte, Gregory C.; Tayeb, Arafat; Labbe, Aurelie; Deschepper, Christian F.; Gottardo, Raphael 3 2012 A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in microarray time course data. Zbl 1296.92029 Farcomeni, Alessio; Arima, Serena 3 2012 Collocation based training of neural ordinary differential equations. Zbl 07413881 Roesch, Elisabeth; Rackauckas, Christopher; Stumpf, Michael P. H. 2 2021 Batch effect reduction of microarray data with dependent samples using an empirical Bayes approach (BRIDGE). Zbl 1496.92022 Xia, Qing; Thompson, Jeffrey A.; Koestler, Devin C. 2 2021 A penalized regression approach for DNA copy number study using the sequencing data. Zbl 1420.92085 Lee, Jaeeun; Chen, Jie 3 2019 Meta-analytic framework for modeling genetic coexpression dynamics. Zbl 1420.92027 Kinzy, Tyler G.; Starr, Timothy K.; Tseng, George C.; Ho, Yen-Yi 1 2019 Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model. Zbl 1420.92087 Li, Xiaohong; Wu, Dongfeng; Cooper, Nigel G. F.; Rai, Shesh N. 1 2019 A multivariate linear model for investigating the association between gene-module co-expression and a continuous covariate. Zbl 1420.92031 Padayachee, Trishanta; Khamiakova, Tatsiana; Shkedy, Ziv; Salo, Perttu; Perola, Markus; Burzykowski, Tomasz 1 2019 Stability selection for Lasso, ridge and elastic net implemented with AFT models. Zbl 1445.92142 Khan, Md Hasinur Rahaman; Bhadra, Anamika; Howlader, Tamanna 1 2019 Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics. Zbl 1445.92105 Crook, Oliver M.; Gatto, Laurent; Kirk, Paul D. W. 1 2019 Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207 Koskela, Jere 4 2018 Additive varying-coefficient model for nonlinear gene-environment interactions. Zbl 1398.92163 Wu, Cen; Zhong, Ping-Shou; Cui, Yuehua 3 2018 Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting. Zbl 1398.92010 Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter 1 2018 A statistical method for measuring activation of gene regulatory networks. Zbl 1398.92088 Esteves, Gustavo H.; Reis, Luiz F. L. 1 2018 Non-parametric estimation of population size changes from the site frequency spectrum. Zbl 1398.92191 Waltoft, Berit Lindum; Hobolth, Asger 1 2018 Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization. Zbl 1398.92011 Huang, Hsin-Hsiung; Hao, Shuai; Alarcon, Saul; Yang, Jie 1 2018 A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type. Zbl 1396.92060 Lakhal-Chaieb, Lajmi; Greenwood, Celia M. T.; Ouhourane, Mohamed; Zhao, Kaiqiong; Abdous, Belkacem; Oualkacha, Karim 3 2017 Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study. Zbl 1371.92014 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 2 2017 Binary Markov random fields and interpretable mass spectra discrimination. Zbl 1360.92065 Kong, Ao; Azencott, Robert 2 2017 Missing value imputation for gene expression data by tailored nearest neighbors. Zbl 1371.92048 Faisal, Shahla; Tutz, Gerhard 1 2017 Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset. Zbl 1360.92014 Su, Pei-Fang; Mau, Yu-Lin; Guo, Yan; Li, Chung-I; Liu, Qi; Boice, John D.; Shyr, Yu 1 2017 Polyunphased: an extension to polytomous outcomes of the unphased package for family-based genetic association analysis. Zbl 1360.92005 Bureau, Alexandre; Croteau, Jordie 1 2017 Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380 Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon 13 2016 HMM-DM: identifying differentially methylated regions using a hidden Markov model. Zbl 1343.92180 Yu, Xiaoqing; Sun, Shuying 5 2016 HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test. Zbl 1343.92173 Sun, Shuying; Yu, Xiaoqing 3 2016 Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Zbl 1343.92028 Yu, Xiaoqing; Sun, Shuying 3 2016 Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks. Zbl 1343.92024 Vinciotti, Veronica; Augugliaro, Luigi; Abbruzzo, Antonino; Wit, Ernst C. 2 2016 What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment. Zbl 1343.92009 Cui, Shiqi; Ji, Tieming; Li, Jilong; Cheng, Jianlin; Qiu, Jing 2 2016 Bayesian state space models for dynamic genetic network construction across multiple tissues. Zbl 1344.92012 Liang, Yulan; Kelemen, Arpad 1 2016 A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments. Zbl 1359.92034 Kruppa, Jochen; Kramer, Frank; Beißbarth, Tim; Jung, Klaus 1 2016 Accounting for isotopic clustering in Fourier transform mass spectrometry data analysis for clinical diagnostic studies. Zbl 1359.92004 Kakourou, Alexia; Vach, Werner; Nicolardi, Simone; van der Burgt, Yuri; Mertens, Bart 1 2016 Differential methylation tests of regulatory regions. Zbl 1343.92019 Ryu, Duchwan; Xu, Hongyan; George, Varghese; Su, Shaoyong; Wang, Xiaoling; Shi, Huidong; Podolsky, Robert H. 1 2016 Identification of consistent functional genetic modules. Zbl 1343.92017 Miecznikowski, Jeffrey C.; Gaile, Daniel P.; Chen, Xiwei; Tritchler, David L. 1 2016 Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089 Golightly, Andrew; Wilkinson, Darren J. 10 2015 TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008 Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili 7 2015 Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079 Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S. 7 2015 Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085 Charmpi, Konstantina; Ycart, Bernard 5 2015 A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007 Meijer, Rosa J.; Krebs, Thijmen J. P.; Goeman, Jelle J. 3 2015 Modeling the next generation sequencing read count data for DNA copy number variant study. Zbl 1329.92017 Ji, Tieming; Chen, Jie 3 2015 Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Zbl 1329.60246 Muchmore, Patrick; Marjoram, Paul 2 2015 Sample size reassessment for a two-stage design controlling the false discovery rate. Zbl 1330.92014 Zehetmayer, Sonja; Graf, Alexandra C.; Posch, Martin 2 2015 On an extended interpretation of linkage disequilibrium in genetic case-control association studies. Zbl 1330.92078 Dickhaus, Thorsten; Stange, Jens; Demirhan, Haydar 2 2015 A Bayesian mixture model for chromatin interaction data. Zbl 1306.92018 Niu, Liang; Lin, Shili 1 2015 A mutual information estimator with exponentially decaying bias. Zbl 1329.62107 Zhang, Zhiyi; Zheng, Lukun 1 2015 Application of the fractional-stable distributions for approximation of the gene expression profiles. Zbl 1329.92090 Saenko, Viacheslav; Saenko, Yury 1 2015 Simultaneous Bayesian analysis of contingency tables in genetic association studies. Zbl 1329.92015 Dickhaus, Thorsten 1 2015 A robust distribution-free test for genetic association studies of quantitative traits. Zbl 1330.92011 Kozlitina, Julia; Schucany, William R. 1 2015 Using informative multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling. Zbl 1330.92048 Samb, Rawane; Khadraoui, Khader; Belleau, Pascal; Deschênes, Astrid; Lakhal-Chaieb, Lajmi; Droit, Arnaud 1 2015 On the validity of within-nuclear-family genetic association analysis in samples of extended families. Zbl 1330.92076 Bureau, Alexandre; Duchesne, Thierry 1 2015 An empirical Bayes risk prediction model using multiple traits for sequencing data. Zbl 1330.92097 Li, Gengxin; Cui, Yuehua; Zhao, Hongyu 1 2015 Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles. Zbl 1311.92082 Grzegorczyk, Marco; Aderhold, Andrej; Husmeier, Dirk 1 2015 Corrigendum to: “Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions”. Zbl 1311.62110 Bickel, David R. 1 2015 Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065 Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P. 9 2014 Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Zbl 1296.92032 Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes 8 2014 Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011 Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco 7 2014 Quantifying the multi-scale performance of network inference algorithms. Zbl 1298.92043 Oates, Chris J.; Amos, Richard; Spencer, Simon E. F. 3 2014 Combining dependent \(F\)-tests for robust association of quantitative traits under genetic model uncertainty. Zbl 1296.92067 Qu, Long 2 2014 Penalized differential pathway analysis of integrative oncogenomics studies. Zbl 1296.92194 van Wieringen, Wessel N.; van de Wiel, Mark A. 2 2014 Scan statistics analysis for detection of introns in time-course tiling array data. Zbl 1296.92068 Reiner-Benaim, Anat; Davis, Ronald W.; Juneau, Kara 2 2014 Efficient parametric inference for stochastic biological systems with measured variability. Zbl 1296.92042 Johnston, Iain G. 2 2014 Bayesian modelling of compositional heterogeneity in molecular phylogenetics. Zbl 1298.92071 Heaps, Sarah E.; Nye, Tom M. W.; Boys, Richard J.; Williams, Tom A.; Embley, T. Martin 2 2014 Improved variational Bayes inference for transcript expression estimation. Zbl 1296.92064 Papastamoulis, Panagiotis; Hensman, James; Glaus, Peter; Rattray, Magnus 1 2014 A novel characterization of the generalized family wise error rate using empirical null distributions. Zbl 1296.92054 Miecznikowski, Jeffrey C.; Gaile, Daniel P. 1 2014 Multiple comparisons in genetic association studies: a hierarchical modeling approach. Zbl 1296.92178 Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel 1 2014 Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model. Zbl 1296.92157 Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka 1 2014 A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments. Zbl 1296.92038 Gómez-Villegas, Miguel A.; Salazar, Isabel; Sanz, Luis 1 2014 Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data. Zbl 1298.92041 Jow, Howsun; Boys, Richard J.; Wilkinson, Darren J. 1 2014 Gene set analysis for GWAS: assessing the use of modified Kolmogorov-Smirnov statistics. Zbl 1298.92063 Debrabant, Birgit; Soerensen, Mette 1 2014 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. Zbl 1302.92074 Langaas, Mette; Bakke, Øyvind 1 2014 Markovianness and conditional independence in annotated bacterial DNA. Zbl 1302.92069 Hart, Andrew; Martínez, Servet 1 2014 Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions. Zbl 1311.62109 Bickel, David R. 9 2013 Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure. Zbl 1311.92077 Zhang, Runchu; Mukerjee, Rahul 3 2013 Improving the efficiency of genomic selection. Zbl 1311.92126 Scutari, Marco; Mackay, Ian; Balding, David 2 2013 The mid \(p\)-value in exact tests for Hardy-Weinberg equilibrium. Zbl 1311.92014 Graffelman, Jan; Moreno, Victor 1 2013 General power and sample size calculations for high-dimensional genomic data. Zbl 1311.92015 van Iterson, Maarten; van de Wiel, Mark A.; Boer, Judith M.; de Menezes, Renée X. 1 2013 How to analyze many contingency tables simultaneously in genetic association studies. Zbl 1296.92027 Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi 13 2012 Graph selection with GGMselect. Zbl 1296.92110 Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas 10 2012 A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Zbl 1296.92039 Grzegorczyk, Marco; Husmeier, Dirk 9 2012 Empirical Bayes interval estimates that are conditionally equal to unadjusted confidence intervals or to default prior credibility intervals. Zbl 1296.92018 Bickel, David R. 8 2012 Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063 Padilla, Marta; Bickel, David R. 6 2012 Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Zbl 1296.92187 Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.; Smyth, Gordon K. 6 2012 Stopping-time resampling and population genetic inference under coalescent models. Zbl 1296.92158 Jenkins, Paul A. 4 2012 The beta-binomial SGoF method for multiple dependent tests. Zbl 1296.92084 de Uña-Alvarez, Jacobo 4 2012 Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Zbl 1296.92072 Silver, Matt; Montana, Giovanni; Alzheimer’s Disease Neuroimaging Initiative 3 2012 Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044 Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris 3 2012 An integrated hierarchical Bayesian model for multivariate eQTL mapping. Zbl 1296.92071 Scott-Boyer, Marie Pier; Imholte, Gregory C.; Tayeb, Arafat; Labbe, Aurelie; Deschepper, Christian F.; Gottardo, Raphael 3 2012 A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in microarray time course data. Zbl 1296.92029 Farcomeni, Alessio; Arima, Serena 3 2012 Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Zbl 1296.92035 Ghosh, Debashis 3 2012 Analyzing genetic association studies with an extended propensity score approach. Zbl 1296.92179 Zhao, Huaqing; Rebbeck, Timothy R.; Mitra, Nandita 2 2012 Fast wavelet based functional models for transcriptome analysis with tiling arrays. Zbl 1296.92024 Clement, Lieven; De Beuf, Kristof; Thas, Olivier; Vuylsteke, Marnik; Irizarry, Rafael A.; Crainiceanu, Ciprian M. 2 2012 Detection of differentially expressed gene sets in a partially paired microarray data set. Zbl 1296.92047 Lim, Johan; Kim, Jayoun; Kim, Sang-cheol; Yu, Donghyeon; Kim, Kyunga; Kim, Byung Soo 2 2012 Genotype copy number variations using Gaussian mixture models: theory and algorithms. Zbl 1296.92048 Lin, Chang-Yun; Lo, Yungtai; Ye, Kenny Q. 1 2012 A context dependent pair hidden Markov model for statistical alignment. Zbl 1296.92014 Arribas-Gil, Ana; Matias, Catherine 1 2012 A mixture-model approach for parallel testing for unequal variances. Zbl 1296.92015 Bar, Haim Y.; Booth, James G.; Wells, Martin T. 1 2012 A model-based analysis to infer the functional content of a gene list. Zbl 1296.92059 Newton, Michael A.; He, Qiuling; Kendziorski, Christina 1 2012 Adjusting for spurious gene-by-environment interaction using case-parent triads. Zbl 1296.92167 Shin, Ji-Hyung; Infante-Rivard, Claire; Graham, Jinko; McNeney, Brad 1 2012 Computing posterior probabilities for score-based alignments using ppALIGN. Zbl 1296.92192 Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory 1 2012 Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications. Zbl 1296.92159 Kenney, Toby; Gu, Hong 1 2012 Performance of MAX test and degree of dominance index in predicting the mode of inheritance. Zbl 1296.92180 Zintzaras, Elias; Santos, Mauro 1 2012 Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045 Lee, Woojoo; Lee, Donghwan; Lee, Youngjo; Pawitan, Yudi 8 2011 High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082 Zuber, Verena; Strimmer, Korbinian 6 2011 Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034 Francois, Olivier; Laval, Guillaume 6 2011 ...and 172 more Documents all cited Publications top 5 cited Publications all top 5 Cited by 2,337 Authors 22 Van der Laan, Mark Johannes 16 Bickel, David R. 10 Goeman, Jelle J. 9 Farcomeni, Alessio 9 Nettleton, Dan 8 Boulesteix, Anne-Laure Isabeau 8 Dickhaus, Thorsten 8 Grzegorczyk, Marco A. 8 Roquain, Étienne 8 Sarkar, Sanat Kumar 7 Drovandi, Christopher C. 7 Guillot, Dominique 7 Husmeier, Dirk 7 Liu, Yanyan 7 Rabier, Charles-Elie 7 Zhang, Jing 6 Carone, Marco 6 Golightly, Andrew 6 Jenkins, Paul A. 6 Robin, Stéphane 6 Romano, Joseph P. 6 Stumpf, Michael P. H. 6 Tibshirani, Robert John 5 Binder, Harald 5 Bubenik, Peter 5 Díaz, Iván M. 5 Guo, Wenge 5 Habiger, Joshua D. 5 Hahn, Georg 5 Hobolth, Asger 5 Khare, Apoorva 5 Liu, Jun S. 5 Liu, Peng 5 Miecznikowski, Jeffrey C. 5 Nuel, Gregory 5 Parmigiani, Giovanni 5 Rajaratnam, Bala 5 Verzelen, Nicolas 5 Zhou, Wen-Xin 4 Aderhold, Andrej 4 Arslan, Olcay 4 Braun, Danielle 4 Buzbas, Erkan Ozge 4 Cui, Yuehua 4 De Wiel, Mark A. van 4 Gandy, Axel 4 Gilbert, Peter B. 4 Hemerik, Jesse 4 Hossain, Ahmed 4 Koskela, Jere 4 Lee, Youngjo 4 Li, Hongzhe 4 Lim, Johan 4 Luedtke, Alex 4 Mercier, Sabine 4 Neuvial, Pierre 4 Nott, David John 4 Peña, Edsel A. 4 Pettitt, Anthony N. 4 Prangle, Dennis 4 Reynaud-Bouret, Patricia 4 Robert, Christian P. 4 Rosenberg, Noah A. 4 Schifano, Elizabeth D. 4 Tong, Tiejun 4 van Wieringen, Wessel N. 4 Witten, Daniela M. 4 Zhao, Sihai Dave 3 Alquier, Pierre 3 Ambroise, Christophe 3 Balakrishnan, Narayanaswamy 3 Bar, Haim Y. 3 Benner, Axel 3 Beyene, Joseph 3 Biau, Gérard 3 Blath, Jochen 3 Bogdan, Małgorzata 3 Burzykowski, Tomasz 3 Cabras, Stefano 3 Caffo, Brian S. 3 Chakraborty, Sounak 3 Chen, Jie 3 Chiquet, Julien 3 Corander, Jukka 3 de Menezes, Renée X. 3 Dudoit, Sandrine 3 Efron, Bradley 3 Everitt, Richard Geoffrey 3 Fan, Jianqing 3 Frazier, David T. 3 Frigessi, Arnoldo 3 Galimberti, Giuliano 3 Ghosh, Debashis 3 Gillespie, Colin S. 3 Gordon, Alexander Ya. 3 Hall, Peter Gavin 3 Hamid, Jemila Seid 3 Hastie, Trevor John 3 Huang, Haiyan 3 Jaffrézic, Florence ...and 2,237 more Authors all top 5 Cited in 179 Journals 84 Computational Statistics and Data Analysis 73 Statistical Applications in Genetics and Molecular Biology 71 The Annals of Applied Statistics 58 Biometrics 48 The Annals of Statistics 37 Journal of Applied Statistics 32 Journal of the American Statistical Association 30 Electronic Journal of Statistics 29 Statistics and Computing 24 Journal of Statistical Planning and Inference 23 Biometrical Journal 23 Journal of Multivariate Analysis 23 Computational Statistics 20 Statistics & Probability Letters 18 Theoretical Population Biology 18 Statistical Science 18 Journal of Theoretical Biology 17 Journal of Statistical Computation and Simulation 14 Scandinavian Journal of Statistics 14 Communications in Statistics. 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Series A 1 Journal of Computational and Applied Mathematics ...and 79 more Journals all top 5 Cited in 46 Fields 931 Statistics (62-XX) 317 Biology and other natural sciences (92-XX) 139 Numerical analysis (65-XX) 104 Probability theory and stochastic processes (60-XX) 77 Computer science (68-XX) 24 Combinatorics (05-XX) 23 Operations research, mathematical programming (90-XX) 20 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 15 Linear and multilinear algebra; matrix theory (15-XX) 14 Algebraic topology (55-XX) 9 Information and communication theory, circuits (94-XX) 8 Systems theory; control (93-XX) 4 Special functions (33-XX) 4 Partial differential equations (35-XX) 4 Harmonic analysis on Euclidean spaces (42-XX) 4 Functional analysis (46-XX) 4 Operator theory (47-XX) 4 Quantum theory (81-XX) 3 Algebraic geometry (14-XX) 3 Integral equations (45-XX) 3 Statistical mechanics, structure of matter (82-XX) 2 Number theory (11-XX) 2 Associative rings and algebras (16-XX) 2 Topological groups, Lie groups (22-XX) 2 Dynamical systems and ergodic theory (37-XX) 2 Calculus of variations and optimal control; optimization (49-XX) 2 Convex and discrete geometry (52-XX) 2 Manifolds and cell complexes (57-XX) 2 Global analysis, analysis on manifolds (58-XX) 1 General and overarching topics; collections (00-XX) 1 Mathematical logic and foundations (03-XX) 1 Commutative algebra (13-XX) 1 Nonassociative rings and algebras (17-XX) 1 Group theory and generalizations (20-XX) 1 Real functions (26-XX) 1 Measure and integration (28-XX) 1 Functions of a complex variable (30-XX) 1 Approximations and expansions (41-XX) 1 Integral transforms, operational calculus (44-XX) 1 Geometry (51-XX) 1 Differential geometry (53-XX) 1 General topology (54-XX) 1 Fluid mechanics (76-XX) 1 Relativity and gravitational theory (83-XX) 1 Astronomy and astrophysics (85-XX) 1 Mathematics education (97-XX) Citations by Year