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: 565 Publications (since 2002) References Indexed: 212 Publications with 7,582 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 Mertens, Bart J. A. 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 Hössjer, Ola G. 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 Mitra, Nandita 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 Wiuf, Carsten 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 ...and 1,282 more Authors all top 5 Fields 518 Biology and other natural sciences (92-XX) 365 Statistics (62-XX) 32 Probability theory and stochastic processes (60-XX) 17 Numerical analysis (65-XX) 10 Computer science (68-XX) 6 Combinatorics (05-XX) 2 Ordinary differential equations (34-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 Systems theory; control (93-XX) Publications by Year all cited Publications top 5 cited Publications Citations contained in zbMATH Open 269 Publications have been cited 1,309 times in 1,028 Documents Cited by ▼ Year ▼ Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Zbl 1038.62110Smyth, Gordon K. 91 2004 Super learner. Zbl 1166.62387Van der Laan, Mark J.; Polley, Eric C.; Hubbard, Alan E. 62 2007 Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Zbl 1166.62379Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S. 46 2004 A general framework for weighted gene co-expression network analysis. Zbl 1077.92042Zhang, Bin; Horvath, Steve 40 2005 Error distribution for gene expression data. Zbl 1083.62114Purdom, Elizabeth; Holmes, Susan P. 32 2005 Approximately sufficient statistics and Bayesian computation. Zbl 1276.62077Joyce, Paul; Marjoram, Paul 32 2008 Sparse canonical correlation analysis with application to genomic data integration. Zbl 1276.92071Parkhomenko, Elena; Tritchler, David; Beyene, Joseph 31 2009 Multiple testing. I: Single-step procedures for control of general type I error rates. Zbl 1166.62338Dudoit, Sandrine; Van der Laan, Mark J.; Pollard, Katherine S. 25 2004 Permutation \(p\)-values should never be zero: calculating exact \(p\)-values when permutations are randomly drawn. Zbl 1304.92098Phipson, Belinda; Smyth, Gordon K. 22 2010 On optimal selection of summary statistics for approximate Bayesian computation. Zbl 1304.92047Nunes, Matthew A.; Balding, David J. 20 2010 Extensions of sparse canonical correlation analysis with applications to genomic data. Zbl 1276.62099Witten, Daniela M.; Tibshirani, Robert J. 19 2009 A sparse PLS for variable selection when integrating omics data. Zbl 1276.62061Cao, Kim-Anh Lê; Rossouw, Debra; Robert-Granié, Christèle; Besse, Philippe 18 2008 Univariate shrinkage in the Cox model for high dimensional data. Zbl 1276.62096Tibshirani, Robert J. 18 2009 A generalized Sidak-Holm procedure and control of generalized error rates under independence. Zbl 1166.62316Guo, Wenge; Romano, Joseph 17 2007 Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach. Zbl 1166.62361Opgen-Rhein, Rainer; Strimmer, Korbinian 17 2007 FADO: a statistical method to detect favored or avoided distances between occurrences of motifs using the Hawkes’ model. Zbl 1095.62126Gusto, Gaelle; Schbath, Sophie 17 2005 Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis. Zbl 1276.92077Waaijenborg, Sandra; Verselewel de Witt Hamer, Philip C.; Zwinderman, Aeilko H. 17 2008 Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge. Zbl 1166.62373Werhli, Adriano V.; Husmeier, Dirk 16 2007 Low-order conditional independence graphs for inferring genetic networks. Zbl 1166.62374Wille, Anja; Bühlmann, Peter 15 2006 Combining results of microarray experiments: A rank aggregation approach. Zbl 1166.92306Deconde, Robert P.; Hawley, Sarah; Falcon, Seth; Clegg, Nigel; Knudsen, Beatrice; Etzioni, Ruth 15 2006 Asymptotic optimality of likelihood-based cross-validation. Zbl 1038.62040Van der Laan, Mark J.; Dudoit, Sandrine; Keles, Sunduz 14 2004 A method to increase the power of multiple testing procedures through sample splitting. Zbl 1166.62318Rubin, Daniel; Dudoit, Sandrine; Van der Laan, Mark 13 2006 Classifying gene expression profiles from pairwise m{RNA} comparisons. Zbl 1072.62107Geman, Donald; d’Avignon, Christian; Naiman, Daniel Q.; Winslow, Raimond L. 13 2004 Adapting prediction error estimates for biased complexity selection in high-dimensional bootstrap samples. Zbl 1276.62060Binder, Harald; Schumacher, Martin 13 2008 How to analyze many contingency tables simultaneously in genetic association studies. Zbl 1296.92027Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi 12 2012 Importance sampling for the infinite sites model. Zbl 1276.62074Hobolth, Asger; Uyenoyama, Marcy K.; Wiuf, Carsten 12 2008 Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon 12 2016 Deletion/substitution/addition algorithm in learning with applications in genomics. Zbl 1166.62368Sinisi, Sandra E.; Van der Laan, Mark J. 11 2004 Graph selection with GGMselect. Zbl 1296.92110Giraud, Christophe; Huet, Sylvie; Verzelen, Nicolas 10 2012 Dimension reduction for classification with gene expression microarray data. Zbl 1166.62337Dai, Jian J.; Lieu, Linh; Rocke, David 10 2006 Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065Prangle, Dennis; Fearnhead, Paul; Cox, Murray P.; Biggs, Patrick J.; French, Nigel P. 9 2014 Space oriented rank-based data integration. Zbl 1304.92094Lin, Shili 9 2010 Simple estimators of false discovery rates given as few as one or two \(p\)-values without strong parametric assumptions. Zbl 1311.62109Bickel, David R. 9 2013 Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089Golightly, Andrew; Wilkinson, Darren J. 9 2015 Multiple testing. II: Step-down procedures for control of the family-wise error rate. Zbl 1166.62378Van der Laan, Mark J.; Dudoit, Sandrine; Pollard, Katherine S. 9 2004 P{LS} dimension reduction for classification with microarray data. Zbl 1086.62119Boulesteix, Anne-Laure 9 2004 Modeling angles in proteins and circular genomes using multivariate angular distributions based on multiple nonnegative trigonometric sums. Zbl 1296.92032Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes 8 2014 A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology. Zbl 1296.92039Grzegorczyk, Marco; Husmeier, Dirk 8 2012 Sparse canonical covariance analysis for high-throughput data. Zbl 1296.92045Lee, 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 1296.92018Bickel, David R. 8 2012 Statistical inference in evolutionary models of DNA sequences via the EM algorithm. Zbl 1081.62094Hobolth, Asger; Jensen, Jens Ledet 8 2005 Score statistics for mapping quantitative trait loci. Zbl 1276.62062Chang, Myron N.; Wu, Rongling; Wu, Samuel S.; Casella, George 8 2009 Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco 7 2014 Optimal tests shrinking both means and variances applicable to microarray data analysis. Zbl 1304.92044Hwang, J. T. Gene; Liu, Peng 7 2010 Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S. 7 2015 Transformations for cDNA microarray data. Zbl 1038.92015Cui, Xiangqin; Kathleen, M.; Kerr, Churchill; Gary, A. 7 2003 Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives. Zbl 1108.62303Van der Laan, Mark J.; Birkner, Merrill D.; Hubbard, Alan E. 7 2005 Estimators of the local false discovery rate designed for small numbers of tests. Zbl 1296.92063Padilla, Marta; Bickel, David R. 6 2012 Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates. Zbl 1296.92187Lund, Steven P.; Nettleton, Dan; McCarthy, Davis J.; Smyth, Gordon K. 6 2012 High-dimensional regression and variable selection using CAR scores. Zbl 1296.92082Zuber, Verena; Strimmer, Korbinian 6 2011 Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034Francois, Olivier; Laval, Guillaume 6 2011 Numerical solutions for patterns statistics on Markov chains. Zbl 1166.62324Nuel, Gregory 6 2006 Sparse logistic regression with \(L_p\) penalty for biomarker identification. Zbl 1166.62314Liu, Zhenqiu; Jiang, Feng; Tian, Guoliang; Wang, Suna; Sato, Fumiaki; Meltzer, Stephen J.; Tan, Ming 6 2007 Empirical Bayes estimation of a sparse vector of gene expression changes. Zbl 1081.62093Erickson, Stephen; Sabatti, Chiara 6 2005 TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili 6 2015 Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods. Zbl 1276.92033Zucknick, 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 1276.92074Taylor, Sandra; Pollard, Katherine 6 2009 Survival analysis with high-dimensional covariates: an application in microarray studies. Zbl 1276.62067Engler, David; Li, Yi 6 2009 Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043Jung, Hsuan; Marjoram, Paul 5 2011 The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Zbl 1296.92026Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; Chang, Jeff H. 5 2011 Sparse partial least squares classification for high dimensional data. Zbl 1304.92041Chung, Dongjun; Keles, Sunduz 5 2010 Shrinkage estimation of effect sizes as an alternative to hypothesis testing followed by estimation in high-dimensional biology: applications to differential gene expression. Zbl 1304.92046Montazeri, Zahra; Yanofsky, Corey M.; Bickel, David R. 5 2010 Super learning: an application to the prediction of HIV-1 drug resistance. Zbl 1166.92315Sinisi, Sandra E.; Polley, Eric C.; Petersen, Maya L.; Rhee, Soo-Yon; Van der Laan, Mark J. 5 2007 BayesMendel: an R environment for Mendelian risk prediction. Zbl 1077.92029Chen, Sining; Wang, Wenyi; Broman, Karl W.; Katki, Hormuzd A.; Parmigiani, Giovanni 5 2004 Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085Charmpi, Konstantina; Ycart, Bernard 5 2015 Structure learning in nested effects models. Zbl 1276.92075Tresch, Achim; Markowetz, Florian 5 2008 Adaptive choice of the number of bootstrap samples in large scale multiple testing. Zbl 1276.62072Guo, Wenge; Peddada, Shyamal 5 2008 Modeling DNA methylation in a population of cancer cells. Zbl 1276.92092Siegmund, Kimberly D.; Marjoram, Paul; Shibata, Darryl 5 2008 A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139Auer, Paul L.; Doerge, Rebecca W. 4 2011 Analyzing time-course microarray data using functional data analysis – a review. Zbl 1296.92025Coffey, Norma; Hinde, John 4 2011 Stopping-time resampling and population genetic inference under coalescent models. Zbl 1296.92158Jenkins, Paul A. 4 2012 The beta-binomial SGoF method for multiple dependent tests. Zbl 1296.92084de Uña-Alvarez, Jacobo 4 2012 Weighted-LASSO for structured network inference from time course data. Zbl 1304.92085Charbonnier, Camille; Chiquet, Julien; Ambroise, Christophe 4 2010 A random coefficients model for regional co-expression associated with DNA copy number. Zbl 1304.92064van Wieringen, Wessel N.; Berkhof, Johannes; van de Wiel, Mark A. 4 2010 A new type of stochastic dependence revealed in gene expression data. Zbl 1166.92309Klebanov, Lev; Jordan, Craig; Yakovlev, Andrei 4 2006 Detecting local high-scoring segments: a first-stage approach for genome-wide association studies. Zbl 1166.62341Guedj, 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 1166.62327Angelini, Claudia; De Canditiis, Daniela; Mutarelli, Margherita; Pensky, Marianna 4 2007 Statistical significance threshold criteria for analysis of microarray gene expression data. Zbl 1166.62335Cheng, Cheng; Pounds, Stanley B.; Boyett, James M.; Pei, Deqing; Kuo, Mei-Ling; Roussel, Martine F. 4 2004 Reproducible research: a bioinformatics case study. Zbl 1138.92300Gentleman, Robert 4 2005 Drifting Markov models with polynomial drift and applications to DNA sequences. Zbl 1276.92095Vergne, Nicolas 4 2008 A Bayesian analysis strategy for cross-study translation of gene expression biomarkers. Zbl 1276.92066Lucas, Joseph; Carvalho, Carlos; West, Mike 4 2009 Detecting outlier samples in microarray data. Zbl 1276.62092Shieh, Albert D.; Hung, Yeung Sam 4 2009 Weighted multiple hypothesis testing procedures. Zbl 1276.62078Kang, Guolian; Ye, Keying; Liu, Nianjun; Allison, David B.; Gao, Guimin 4 2009 Estimation of selection intensity under overdominance by Bayesian methods. Zbl 1276.92050Buzbas, Erkan Ozge; Joyce, Paul; Abdo, Zaid 4 2009 HMM-DM: identifying differentially methylated regions using a hidden Markov model. Zbl 1343.92180Yu, Xiaoqing; Sun, Shuying 4 2016 An integrated hierarchical Bayesian model for multivariate eQTL mapping. Zbl 1296.92071Scott-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 1296.92029Farcomeni, Alessio; Arima, Serena 3 2012 Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Zbl 1296.92035Ghosh, Debashis 3 2012 Unsupervised classification for tiling arrays: chip-chip and transcriptome. Zbl 1296.92105Bérard, Caroline; Martin-Magniette, Marie-Laure; Brunaud, Véronique; Aubourg, Sébastien; Robin, Stéphane 3 2011 Weighted lasso with data integration. Zbl 1296.92017Bergersen, Linn Cecilie; Glad, Ingrid K.; Lyng, Heidi 3 2011 On the statistical properties of SGoF multitesting method. Zbl 1296.92083de Uña-Alvarez, Jacobo 3 2011 Exploratory analysis of multiple omics datasets using the adjusted RV coefficient. Zbl 1296.92053Mayer, Claus-Dieter; Lorent, Julie; Horgan, Graham W. 3 2011 Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris 3 2012 Quantifying the multi-scale performance of network inference algorithms. Zbl 1298.92043Oates, Chris J.; Amos, Richard; Spencer, Simon E. F. 3 2014 Network enrichment analysis in complex experiments. Zbl 1304.92067Shojaie, Ali; Michailidis, George 3 2010 An empirical Bayesian method for estimating biological networks from temporal microarray data. Zbl 1304.92066Rau, Andrea; Jaffrézic, Florence; Foulley, Jean-Louis; Doerge, Rebecca W. 3 2010 Buckley-James boosting for survival analysis with high-dimensional biomarker data. Zbl 1304.92101Wang, Zhu; Wang, C. Y. 3 2010 A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007Meijer, Rosa J.; Krebs, Thijmen J. P.; Goeman, Jelle J. 3 2015 Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure. Zbl 1311.92077Zhang, Runchu; Mukerjee, Rahul 3 2013 Pre-validation and inference in microarrays. Zbl 1037.62116Tibshirani, Robert J.; Efron, Brad 3 2002 Collocation based training of neural ordinary differential equations. Zbl 07413881Roesch, 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 1496.92022Xia, Qing; Thompson, Jeffrey A.; Koestler, Devin C. 2 2021 A penalized regression approach for DNA copy number study using the sequencing data. Zbl 1420.92085Lee, Jaeeun; Chen, Jie 2 2019 Stability selection for Lasso, ridge and elastic net implemented with AFT models. Zbl 1445.92142Khan, 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 1445.92105Crook, Oliver M.; Gatto, Laurent; Kirk, Paul D. W. 1 2019 Sample size calculations for the differential expression analysis of RNA-seq data using a negative binomial regression model. Zbl 1420.92087Li, 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 1420.92031Padayachee, Trishanta; Khamiakova, Tatsiana; Shkedy, Ziv; Salo, Perttu; Perola, Markus; Burzykowski, Tomasz 1 2019 Multi-locus data distinguishes between population growth and multiple merger coalescents. Zbl 1398.92207Koskela, Jere 3 2018 Ensemble survival tree models to reveal pairwise interactions of variables with time-to-events outcomes in low-dimensional setting. Zbl 1398.92010Dazard, Jean-Eudes; Ishwaran, Hemant; Mehlotra, Rajeev; Weinberg, Aaron; Zimmerman, Peter 1 2018 Additive varying-coefficient model for nonlinear gene-environment interactions. Zbl 1398.92163Wu, Cen; Zhong, Ping-Shou; Cui, Yuehua 1 2018 A statistical method for measuring activation of gene regulatory networks. Zbl 1398.92088Esteves, Gustavo H.; Reis, Luiz F. L. 1 2018 Non-parametric estimation of population size changes from the site frequency spectrum. Zbl 1398.92191Waltoft, Berit Lindum; Hobolth, Asger 1 2018 Comparisons of classification methods for viral genomes and protein families using alignment-free vectorization. Zbl 1398.92011Huang, Hsin-Hsiung; Hao, Shuai; Alarcon, Saul; Yang, Jie 1 2018 Binary Markov random fields and interpretable mass spectra discrimination. Zbl 1360.92065Kong, Ao; Azencott, Robert 2 2017 Regularized estimation in sparse high-dimensional multivariate regression, with application to a DNA methylation study. Zbl 1371.92014Zhang, 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 A smoothed EM-algorithm for DNA methylation profiles from sequencing-based methods in cell lines or for a single cell type. Zbl 1396.92060Lakhal-Chaieb, Lajmi; Greenwood, Celia M. T.; Ouhourane, Mohamed; Zhao, Kaiqiong; Abdous, Belkacem; Oualkacha, Karim 2 2017 Bivariate Poisson models with varying offsets: an application to the paired mitochondrial DNA dataset. Zbl 1360.92014Su, 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 1360.92005Bureau, Alexandre; Croteau, Jordie 1 2017 Missing value imputation for gene expression data by tailored nearest neighbors. Zbl 1371.92048Faisal, Shahla; Tutz, Gerhard 1 2017 Using persistent homology and dynamical distances to analyze protein binding. Zbl 1343.92380Kovacev-Nikolic, Violeta; Bubenik, Peter; Nikolić, Dragan; Heo, Giseon 12 2016 HMM-DM: identifying differentially methylated regions using a hidden Markov model. Zbl 1343.92180Yu, Xiaoqing; Sun, Shuying 4 2016 HMM-Fisher: identifying differential methylation using a hidden Markov model and Fisher’s exact test. Zbl 1343.92173Sun, Shuying; Yu, Xiaoqing 2 2016 What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment. Zbl 1343.92009Cui, Shiqi; Ji, Tieming; Li, Jilong; Cheng, Jianlin; Qiu, Jing 2 2016 Comparing five statistical methods of differential methylation identification using bisulfite sequencing data. Zbl 1343.92028Yu, Xiaoqing; Sun, Shuying 2 2016 A simulation framework for correlated count data of features subsets in high-throughput sequencing or proteomics experiments. Zbl 1359.92034Kruppa, 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 1359.92004Kakourou, Alexia; Vach, Werner; Nicolardi, Simone; van der Burgt, Yuri; Mertens, Bart 1 2016 Differential methylation tests of regulatory regions. Zbl 1343.92019Ryu, Duchwan; Xu, Hongyan; George, Varghese; Su, Shaoyong; Wang, Xiaoling; Shi, Huidong; Podolsky, Robert H. 1 2016 Identification of consistent functional genetic modules. Zbl 1343.92017Miecznikowski, Jeffrey C.; Gaile, Daniel P.; Chen, Xiwei; Tritchler, David L. 1 2016 Bayesian state space models for dynamic genetic network construction across multiple tissues. Zbl 1344.92012Liang, Yulan; Kelemen, Arpad 1 2016 Bayesian inference for Markov jump processes with informative observations. Zbl 1311.92089Golightly, Andrew; Wilkinson, Darren J. 9 2015 Likelihood free inference for Markov processes: a comparison. Zbl 1311.60079Owen, Jamie; Wilkinson, Darren J.; Gillespie, Colin S. 7 2015 TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. Zbl 1329.92008Schimek, Michael G.; Budinská, Eva; Kugler, Karl G.; Švendová, Vendula; Ding, Jie; Lin, Shili 6 2015 Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis. Zbl 1329.92085Charmpi, Konstantina; Ycart, Bernard 5 2015 A region-based multiple testing method for hypotheses ordered in space or time. Zbl 1306.92007Meijer, 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 1329.92017Ji, Tieming; Chen, Jie 3 2015 Exact likelihood-free Markov chain Monte Carlo for elliptically contoured distributions. Zbl 1329.60246Muchmore, Patrick; Marjoram, Paul 2 2015 Sample size reassessment for a two-stage design controlling the false discovery rate. Zbl 1330.92014Zehetmayer, Sonja; Graf, Alexandra C.; Posch, Martin 2 2015 A Bayesian mixture model for chromatin interaction data. Zbl 1306.92018Niu, Liang; Lin, Shili 1 2015 Inferring bi-directional interactions between circadian clock genes and metabolism with model ensembles. Zbl 1311.92082Grzegorczyk, 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 1311.62110Bickel, David R. 1 2015 A mutual information estimator with exponentially decaying bias. Zbl 1329.62107Zhang, Zhiyi; Zheng, Lukun 1 2015 Application of the fractional-stable distributions for approximation of the gene expression profiles. Zbl 1329.92090Saenko, Viacheslav; Saenko, Yury 1 2015 A robust distribution-free test for genetic association studies of quantitative traits. Zbl 1330.92011Kozlitina, Julia; Schucany, William R. 1 2015 On an extended interpretation of linkage disequilibrium in genetic case-control association studies. Zbl 1330.92078Dickhaus, Thorsten; Stange, Jens; Demirhan, Haydar 1 2015 Using informative multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling. Zbl 1330.92048Samb, 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 1330.92076Bureau, Alexandre; Duchesne, Thierry 1 2015 An empirical Bayes risk prediction model using multiple traits for sequencing data. Zbl 1330.92097Li, Gengxin; Cui, Yuehua; Zhao, Hongyu 1 2015 Semi-automatic selection of summary statistics for ABC model choice. Zbl 1296.92065Prangle, 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 1296.92032Fernández-Durán, Juan José; Gregorio-Domínguez, María Mercedes 8 2014 Statistical inference of regulatory networks for circadian regulation. Zbl 1296.92011Aderhold, Andrej; Husmeier, Dirk; Grzegorczyk, Marco 7 2014 Quantifying the multi-scale performance of network inference algorithms. Zbl 1298.92043Oates, Chris J.; Amos, Richard; Spencer, Simon E. 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Zbl 1296.92064Papastamoulis, Panagiotis; Hensman, James; Glaus, Peter; Rattray, Magnus 1 2014 A novel characterization of the generalized family wise error rate using empirical null distributions. Zbl 1296.92054Miecznikowski, Jeffrey C.; Gaile, Daniel P. 1 2014 Multiple comparisons in genetic association studies: a hierarchical modeling approach. Zbl 1296.92178Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel 1 2014 Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model. Zbl 1296.92157Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka 1 2014 A Bayesian decision procedure for testing multiple hypotheses in DNA microarray experiments. Zbl 1296.92038Gómez-Villegas, Miguel A.; Salazar, Isabel; Sanz, Luis 1 2014 Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data. 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Zbl 1296.92071Scott-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 1296.92029Farcomeni, Alessio; Arima, Serena 3 2012 Incorporating the empirical null hypothesis into the Benjamini-Hochberg procedure. Zbl 1296.92035Ghosh, Debashis 3 2012 Bayesian sparsity-path-analysis of genetic association signal using generalized \(t\) priors. Zbl 1296.92044Lee, Anthony; Caron, Francois; Doucet, Arnaud; Holmes, Chris 3 2012 Analyzing genetic association studies with an extended propensity score approach. Zbl 1296.92179Zhao, Huaqing; Rebbeck, Timothy R.; Mitra, Nandita 2 2012 Fast identification of biological pathways associated with a quantitative trait using group lasso with overlaps. Zbl 1296.92072Silver, Matt; Montana, Giovanni; Alzheimer’s Disease Neuroimaging Initiative 2 2012 Fast wavelet based functional models for transcriptome analysis with tiling arrays. Zbl 1296.92024Clement, 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 1296.92047Lim, Johan; Kim, Jayoun; Kim, Sang-cheol; Yu, Donghyeon; Kim, Kyunga; Kim, Byung Soo 2 2012 Computing posterior probabilities for score-based alignments using ppALIGN. Zbl 1296.92192Wolfsheimer, Stefan; Hartmann, Alexander; Rabus, Ralf; Nuel, Gregory 1 2012 Hessian calculation for phylogenetic likelihood based on the pruning algorithm and its applications. Zbl 1296.92159Kenney, Toby; Gu, Hong 1 2012 Performance of MAX test and degree of dominance index in predicting the mode of inheritance. 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Zbl 1296.92082Zuber, Verena; Strimmer, Korbinian 6 2011 Deviance information criteria for model selection in approximate Bayesian computation. Zbl 1296.92034Francois, Olivier; Laval, Guillaume 6 2011 Choice of summary statistic weights in approximate Bayesian computation. Zbl 1296.92043Jung, Hsuan; Marjoram, Paul 5 2011 The NBP negative binomial model for assessing differential gene expression from RNA-Seq. Zbl 1296.92026Di, Yanming; Schafer, Daniel W.; Cumbie, Jason S.; Chang, Jeff H. 5 2011 A two-stage Poisson model for testing RNA-Seq data. Zbl 1296.92139Auer, Paul L.; Doerge, Rebecca W. 4 2011 ...and 169 more Documents all cited Publications top 5 cited Publications all top 5 Cited by 2,207 Authors 21 Van der Laan, Mark Johannes 16 Bickel, David R. 9 Farcomeni, Alessio 9 Goeman, Jelle J. 9 Nettleton, Dan 8 Boulesteix, Anne-Laure Isabeau 8 Roquain, Étienne 8 Sarkar, Sanat Kumar 7 Dickhaus, Thorsten 7 Grzegorczyk, Marco A. 7 Guillot, Dominique 7 Husmeier, Dirk 7 Rabier, Charles-Elie 6 Jenkins, Paul A. 6 Robin, Stéphane 6 Romano, Joseph P. 6 Stumpf, Michael P. H. 5 Binder, Harald 5 Bubenik, Peter 5 Díaz, Iván M. 5 Drovandi, Christopher C. 5 Golightly, Andrew 5 Guo, Wenge 5 Habiger, Joshua D. 5 Hahn, Georg 5 Hobolth, Asger 5 Khare, Apoorva 5 Liu, Peng 5 Liu, Yanyan 5 Miecznikowski, Jeffrey C. 5 Nuel, Gregory 5 Parmigiani, Giovanni 5 Rajaratnam, Bala 5 Tibshirani, Robert John 5 Verzelen, Nicolas 5 Zhang, Jing 4 Aderhold, Andrej 4 Arslan, Olcay 4 Buzbas, Erkan Ozge 4 Carone, Marco 4 Gandy, Axel 4 Hossain, Ahmed 4 Koskela, Jere 4 Lee, Youngjo 4 Li, Hongzhe 4 Liu, Jun S. 4 Neuvial, Pierre 4 Peña, Edsel A. 4 Pettitt, Anthony N. 4 Reynaud-Bouret, Patricia 4 Robert, Christian P. 4 Rosenberg, Noah A. 4 Schifano, Elizabeth D. 4 van Wieringen, Wessel N. 4 Zhou, Wen-Xin 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 Braun, Danielle 3 Burzykowski, Tomasz 3 Cabras, Stefano 3 Caffo, Brian S. 3 Chakraborty, Sounak 3 Chen, Jie 3 Cheng, Cheng 3 Chiquet, Julien 3 Cui, Yuehua 3 de Menezes, Renée X. 3 Dudoit, Sandrine 3 Efron, Bradley 3 Fan, Jianqing 3 Galimberti, Giuliano 3 Gillespie, Colin S. 3 Gordon, Alexander Ya. 3 Hall, Peter Gavin 3 Hamid, Jemila Seid 3 Hemerik, Jesse 3 Huang, Haiyan 3 Jaffrézic, Florence 3 Jana, Sayantee 3 Jose, Kanichukattu Korakutty 3 Kim, Sungsu 3 Liang, Kun 3 Lim, Johan 3 Liquet, Benoit 3 Liu, Yufeng 3 Luedtke, Alex 3 Marron, James Stephen 3 Mercier, Sabine 3 Mertens, Bart J. A. 3 Nott, David John 3 Novikov, Aleksandr Aleksandrovich 3 Porzelius, Christine 3 Prangle, Dennis ...and 2,107 more Authors all top 5 Cited in 169 Journals 84 Computational Statistics and Data Analysis 73 Statistical Applications in Genetics and Molecular Biology 68 The Annals of Applied Statistics 47 The Annals of Statistics 47 Biometrics 35 Journal of Applied Statistics 29 Statistics and Computing 28 Journal of the American Statistical Association 28 Electronic Journal of Statistics 24 Journal of Statistical Planning and Inference 23 Journal of Multivariate Analysis 23 Computational Statistics 20 Biometrical Journal 20 Statistics & Probability Letters 18 Theoretical Population Biology 18 Statistical Science 18 Journal of Theoretical Biology 17 Journal of Statistical Computation and Simulation 14 Communications in Statistics. Simulation and Computation 12 Scandinavian Journal of Statistics 11 Test 10 Communications in Statistics. 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Probabilités et Statistiques 3 Australian & New Zealand Journal of Statistics 3 Statistical Methods in Medical Research 3 Mathematical Biosciences and Engineering 3 Journal of the Korean Statistical Society 3 Sankhyā. Series A 3 Sankhyā. Series B 2 Advances in Applied Probability 2 Journal of Statistical Physics 2 Applied Mathematics and Computation 2 Information Sciences 2 Transactions of the American Mathematical Society 2 Neural Networks 2 Neural Computation 2 European Journal of Operational Research 2 Stochastic Processes and their Applications 2 Applied Mathematics. Series B (English Edition) 2 Applied and Computational Harmonic Analysis 2 Journal of Nonparametric Statistics 2 Comptes Rendus. Mathématique. Académie des Sciences, Paris 2 Optimization Letters 2 Science China. Mathematics 2 Revista de la Real Academia de Ciencias Exactas, Físicas y Naturales. Serie A: Matemáticas. RACSAM 2 Journal of Applied and Computational Topology 1 Computers & Mathematics with Applications 1 Computer Methods in Applied Mechanics and Engineering 1 Discrete Applied Mathematics 1 Inverse Problems 1 Information Processing Letters 1 Journal of Computational Physics 1 Journal of the Franklin Institute 1 Journal of Mathematical Analysis and Applications 1 Metrika 1 Psychometrika 1 Advances in Mathematics 1 Demonstratio Mathematica 1 Journal of Combinatorial Theory. Series A 1 Journal of Computational and Applied Mathematics 1 Journal of Computer and System Sciences 1 Journal of Econometrics 1 Metron 1 Statistica 1 Statistica Neerlandica ...and 69 more Journals all top 5 Cited in 44 Fields 878 Statistics (62-XX) 314 Biology and other natural sciences (92-XX) 136 Numerical analysis (65-XX) 102 Probability theory and stochastic processes (60-XX) 75 Computer science (68-XX) 22 Combinatorics (05-XX) 20 Operations research, mathematical programming (90-XX) 20 Game theory, economics, finance, and other social and behavioral sciences (91-XX) 12 Linear and multilinear algebra; matrix theory (15-XX) 12 Algebraic topology (55-XX) 8 Systems theory; control (93-XX) 8 Information and communication theory, circuits (94-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 Integral equations (45-XX) 3 Statistical mechanics, structure of matter (82-XX) 2 Number theory (11-XX) 2 Algebraic geometry (14-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 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 Nonassociative rings and algebras (17-XX) 1 Real functions (26-XX) 1 Measure and integration (28-XX) 1 Functions of a complex variable (30-XX) 1 Ordinary differential equations (34-XX) 1 Approximations and expansions (41-XX) 1 Integral transforms, operational calculus (44-XX) 1 Geometry (51-XX) 1 Convex and discrete geometry (52-XX) 1 Differential geometry (53-XX) 1 General topology (54-XX) 1 Relativity and gravitational theory (83-XX) 1 Astronomy and astrophysics (85-XX) 1 Mathematics education (97-XX) Citations by Year